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Experimental Methods for Determination of Protein–Protein Interactions

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Protein-Protein Interactions

Abstract

Study of protein–protein interactions in the cell provides better insights into the molecular network of the cell. It is therefore essential to establish the existing interactions by experimental techniques. Such techniques not only help to discover new interactions, but also validate interactions that have been hypothesized. The techniques can be broadly classified as biophysical, biochemical, and genetic. This chapter discusses the techniques under each classification and also outlines their respective working principles, advantages, drawbacks, and recent developments. The future prospects have been delineated based on their current status of applications.

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References

  • Ackers GK (1970) Analytical gel chromatography of proteins. In: Advances in protein chemistry, vol 24. Elsevier, London, pp 343-446

    Google Scholar 

  • Aebersold R, Mann M. (2003). Mass spectrometry-based proteomics. Nature, 422, 198-207.

    Article  CAS  PubMed  Google Scholar 

  • Agarwal N, Nair MS, Mazumder A, Poluri KM (2018) Characterization of nanomaterials using nuclear magnetic resonance spectroscopy. In: Characterization of nanomaterials. Elsevier, London, pp 61-102

    Chapter  Google Scholar 

  • Amberg DC, Basart E, Botstein D. (1995). Defining protein interactions with yeast actin in vivo. Nat Struct Biol, 2, 28-35.

    Article  CAS  PubMed  Google Scholar 

  • Arbel N, Ben-Hail D, Shoshan-Barmatz V. (2012). Mediation of the antiapoptotic activity of Bcl-xL protein upon interaction with VDAC1 protein. J Biol Chem, 287, 23152-23161.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Arkin MR, Glicksman MA, Fu H, Havel JJ, Du Y. (2012). Inhibition of protein-protein interactions: non-cellular assay formats. Assay guidance manual. Bethesda: Eli Lilly

    Google Scholar 

  • Attri AK, Minton AP. (2005). Composition gradient static light scattering: a new technique for rapid detection and quantitative characterization of reversible macromolecular hetero-associations in solution. Anal Biochem, 346, 132-138.

    Article  CAS  PubMed  Google Scholar 

  • Attri AK, Fernandez C, Minton AP. (2010). Self-association of Zn-insulin at neutral pH: investigation by concentration gradient-static and dynamic light scattering. Biophys Chem, 148, 23-27.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Bacart J, Corbel C, Jockers R, Bach S, Couturier C. (2008). The BRET technology and its application to screening assays. Biotechnol J, 3, 311-324.

    Article  CAS  PubMed  Google Scholar 

  • Bai Y (2015) Detecting protein-protein interactions by gel filtration chromatography. In: Protein-protein interactions. Springer, New York, pp 223-232

    Chapter  Google Scholar 

  • Baker BM, Murphy KP. (1997). Dissecting the energetics of a protein-protein interaction: the binding of ovomucoid third domain to elastase. J Mol Biol, 268, 557-569.

    Article  CAS  PubMed  Google Scholar 

  • Balbo A, Schuck P. (2005). Analytical ultracentrifugation in the study of protein self-association and heterogeneous protein-protein interactions. Protein-Protein Interact 14, 253-277.

    Google Scholar 

  • Balhara V, Deshmukh SS, Kalman L, Kornblatt JA. (2014). The interaction of streptococcal enolase with canine plasminogen: the role of surfaces in complex formation. PLoS One, 9, e88395.

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  • Barrios-Rodiles M, Ellis JD, Blencowe BJ, Wrana JL (2017) LUMIER: a discovery tool for mammalian protein interaction networks. In: Proteomics. Springer, New York, pp 137-148

    Chapter  Google Scholar 

  • Barron LD. (2015). The development of biomolecular Raman optical activity spectroscopy. Biomed Spectrosc Imaging, 4, 223-253.

    Article  CAS  Google Scholar 

  • Belanger KD. (2009). Using affinity chromatography to investigate novel protein-protein interactions in an undergraduate cell and molecular biology lab course. CBE Life Sci Educ, 8, 214-225.

    Article  PubMed  PubMed Central  Google Scholar 

  • Bender A, Pringle JR. (1991). Use of a screen for synthetic lethal and multicopy suppressee mutants to identify two new genes involved in morphogenesis in Saccharomyces cerevisiae. Mol Cell Biol, 11, 1295-1305.

    CAS  PubMed  PubMed Central  Google Scholar 

  • Bhagwat S, Kumar A. (2018). Biolayer interferometry and its applications. J Mol Biol Technol, 2, 106.

    Google Scholar 

  • Biehle SJ, Carrozzella J, Shukla R, Popplewell J, Swann M, Freeman N, Clark JF. (2004). Apolipoprotein E isoprotein-specific interactions with tissue plasminogen activator. Biochim Biophys Acta, 1689, 244-251.

    Article  CAS  PubMed  Google Scholar 

  • Bleil JD, Wassarman PM. (1990). Identification of a ZP3-binding protein on acrosome-intact mouse sperm by photoaffinity crosslinking. Proc Natl Acad Sci U S A, 87, 5563-5567.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Bolte S, Cordelieres FP. (2006). A guided tour into subcellular colocalization analysis in light microscopy. J Microsc, 224, 213-232.

    Article  CAS  PubMed  Google Scholar 

  • Bothner B, Lewis WS, DiGiammarino EL, Weber JD, Bothner SJ, Kriwacki RW. (2001). Defining the molecular basis of Arf and Hdm2 interactions. J Mol Biol, 314, 263-277.

    Article  CAS  PubMed  Google Scholar 

  • Boudjemline A, Saridakis E, Swann MJ, Govada L, Mavridis IM, Chayen NE. (2011). Use of dual polarization interferometry as a diagnostic tool for protein crystallization. Anal Chem, 83, 7881-7887.

    Article  CAS  PubMed  Google Scholar 

  • Buntru A, Trepte P, Klockmeier K, Schnoegl S, Wanker EE. (2016). Current approaches toward quantitative mapping of the interactome. Front Genet, 7, 74.

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  • Burger VM, Arenas DJ, Stultz CM. (2016). A structure-free method for quantifying conformational flexibility in proteins. Sci Rep, 6, 29040.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Caberoy NB, Zhou YX, Li W. (2010). Tubby and tubby-like protein 1 are new MerTK ligands for phagocytosis. EMBO J, 29, 3898-3910.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Cafarelli TM, Desbuleux A, Wang Y, Choi SG, De Ridder D, Vidal M. (2017). Mapping, modeling, and characterization of protein-protein interactions on a proteomic scale. Curr Opin Struct Biol, 44, 201-210.

    Article  CAS  PubMed  Google Scholar 

  • Calakos N, Bennett MK, Peterson KE, Scheller RH. (1994). Protein-protein interactions contributing to the specificity of intracellular vesicular trafficking. Science, 263, 1146-1149.

    Article  CAS  PubMed  Google Scholar 

  • Chan CS, Howell JM, Workentine ML, Turner RJ. (2006). Twin-arginine translocase may have a role in the chaperone function of NarJ from Escherichia coli. Biochem Biophy Res, 343, 244-251.

    Article  CAS  Google Scholar 

  • Chan CS, Winstone TM, Turner RJ (2008) Investigating protein–protein interactions by far-Westerns. In: Protein–protein interaction. Springer, New York, pp 195-214

    Chapter  Google Scholar 

  • Chapman JR (2000) Mass spectrometry of proteins and peptides, vol 146. Springer Science & Business Media, Cham

    Book  Google Scholar 

  • Chen PC, Hennig J. (2018). The role of small-angle scattering in structure-based screening applications. Biophys Rev, 10, 1295-1310.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Chen K, Tjandra N (2011) The use of residual dipolar coupling in studying proteins by NMR. In: NMR of proteins and small biomolecules. Springer, New York, pp 47-67

    Chapter  Google Scholar 

  • Chen Y, Ebright YW, Ebright RH. (1994). Identification of the target of a transcription activator protein by protein-protein photocrosslinking. Science, 265, 90-92.

    Article  CAS  PubMed  Google Scholar 

  • Chen Y et al. (2013). Bcl2-associated athanogene 3 interactome analysis reveals a new role in modulating proteasome activity. MCP, 12, 2804-2819.

    CAS  PubMed  PubMed Central  Google Scholar 

  • Chen J et al. (2014). Single-molecule dynamics of enhanceosome assembly in embryonic stem cells. Cell, 156, 1274-1285.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Chevray PM, Nathans D. (1992). Protein-interaction cloning in yeast - identification of mammalian proteins that react with the leucine zipper of jun. Proc Natl Acad Sci U S A, 89, 5789-5793.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Clore GM, Tang C, Iwahara J. (2007). Elucidating transient macromolecular interactions using paramagnetic relaxation enhancement. Curr Opin Struct Biol, 17, 603-616.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Cohen BD, Lowy DR, Schiller JT. (1993). The conserved C-terminal domain of the bovine papillomavirus E5 oncoprotein can associate with an alpha-adaptin-like molecule - a possible link between growth-factor receptors and viral transformation. Mol Cell Biol, 13, 6462-6468.

    CAS  PubMed  PubMed Central  Google Scholar 

  • Cole JL, Lary JW, Laue TM. (2008). Analytical ultracentrifugation: sedimentation velocity and sedimentation equilibrium. Methods Cell Biol, 84, 143-179.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Cordeiro TN et al. (2017). Disentangling polydispersity in the PCNA− p15PAF complex, a disordered, transient and multivalent macromolecular assembly. Nucleic Acids Res, 45, 1501-1515.

    Article  CAS  PubMed  Google Scholar 

  • Costa TR, Ignatiou A, Orlova EV (2017) Structural analysis of protein complexes by cryo electron microscopy. In: Bacterial protein secretion systems. Springer, New York, pp 377-413

    Chapter  Google Scholar 

  • Costes SV, Daelemans D, Cho EH, Dobbin Z, Pavlakis G, Lockett S. (2004). Automatic and quantitative measurement of protein-protein colocalization in live cells. Biophys J, 86, 3993-4003.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Cowieson NP, Miles AJ, Robin G, Forwood JK, Kobe B, Martin JL, Wallace BA. (2008). Evaluating protein : protein complex formation using synchrotron radiation circular dichroism spectroscopy. Proteins, 70, 1142-1146.

    Article  CAS  PubMed  Google Scholar 

  • Cui Y, Zhang X, Yu M, Zhu Y, Xing J, Lin J. (2019). Techniques for detecting protein-protein interactions in living cells: principles, limitations, and recent progress. Science China. Life Sci, 62, 619-632.

    Article  CAS  Google Scholar 

  • D’Silva L, Ozdowy P, Krajewski M, Rothweiler U, Singh M, Holak TA. (2005). Monitoring the effects of antagonists on protein− protein interactions with NMR spectroscopy. J Am Chem Soc, 127, 13220-13226.

    Article  PubMed  CAS  Google Scholar 

  • Demir F et al. (2013). Arabidopsis nanodomain-delimited ABA signaling pathway regulates the anion channel SLAH3. Proc Natl Acad Sci U S A, 110, 8296-8301.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Dhalluin C et al. (2000). Structural basis of SNT PTB domain interactions with distinct neurotrophic receptors. Mol Cell, 6, 921-929.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Drescher DG, Drescher MJ, Ramakrishnan NA (2009) Surface plasmon resonance (SPR) analysis of binding interactions of proteins in inner-ear sensory epithelia. In: Auditory and vestibular research. Springer, New York, pp 323-343

    Chapter  Google Scholar 

  • Du Y (2015) Fluorescence polarization assay to quantify protein-protein interactions in an HTS format. In: Protein-protein interactions. Springer, New York, pp 529-544

    Chapter  Google Scholar 

  • Dunnwald M, Varshavsky A, Johnsson N. (1999). Detection of transient in vivo interactions between substrate and transporter during protein translocation into the endoplasmic reticulum. Mol Biol Cell, 10, 329-344.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Durfee T et al. (1993). The retinoblastoma protein associates with the protein phosphatase type 1 catalytic subunit. Genes Dev, 7, 555-569.

    Article  CAS  PubMed  Google Scholar 

  • Escorihuela J, Gonzalez-Martinez MA, Lopez-Paz JL, Puchades R, Maquieira A, Gimenez-Romero D. (2015). Dual-polarization interferometry: a novel technique to light up the nanomolecular world. Chem Rev, 115, 265-294.

    Article  CAS  PubMed  Google Scholar 

  • Formosa T, Barry J, Alberts BM, Greenblatt J (1991) Using protein affinity chromatography to probe structure of protein machines. In: Methods in enzymology, vol 208. Elsevier, London, pp 24-45

    Google Scholar 

  • Frank R. (1992). Spot-synthesis - an easy technique for the positionally addressable, parallel chemical synthesis on a membrane support. Tetrahedron, 48, 9217-9232.

    Article  CAS  Google Scholar 

  • Frank R. (2002). High-density synthetic peptide microarrays: emerging tools for functional genomics and proteomics. Comb Chem, 5, 429-440.

    CAS  Google Scholar 

  • Fraser HB, Hirsh AE, Wall DP, Eisen MB. (2004). Coevolution of gene expression among interacting proteins. Proc Natl Acad Sci U S A, 101, 9033-9038.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Fredriksson S et al. (2002). Protein detection using proximity-dependent DNA ligation assays. Nat Biotechnol, 20, 473-477.

    Article  CAS  PubMed  Google Scholar 

  • Fronzes R, Schafer E, Wang L, Saibil HR, Orlova EV, Waksman G. (2009). Structure of a type IV secretion system core complex. Science, 323, 266-268.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Fujii Y, Yoshimura A, Kodama Y. (2018). A novel orange-colored bimolecular fluorescence complementation (BiFC) assay using monomeric Kusabira-Orange protein. Biotechniques, 64, 153-161.

    Article  CAS  PubMed  Google Scholar 

  • Fujikawa Y, Kato N. (2007). Technical advance: split luciferase complementation assay to study protein–protein interactions in Arabidopsis protoplasts. Plant J, 52, 185-195.

    Article  CAS  PubMed  Google Scholar 

  • Gadkari RA, Srinivasan N. (2010). Prediction of protein-protein interactions in dengue virus coat proteins guided by low resolution cryoEM structures. BMC Struct Biol, 10, 17.

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  • Gangele K, Gulati K, Joshi N, Kumar D, Poluri KM. (2020). Molecular insights into the differential structure-dynamics-stability features of interleukin-8 orthologs: Implications to functional specificity. Int J Biol Macromol, 164, 3221-3234.

    Article  CAS  PubMed  Google Scholar 

  • Gao G, Williams JG, Campbell SL (2004) Protein-protein interaction analysis by nuclear magnetic resonance spectroscopy. In: Protein-protein interactions. Springer, New York, pp 79-91

    Chapter  Google Scholar 

  • Garrett DS, Seok YJ, Peterkofsky A, Clore GM, Gronenborn AM. (1997). Identification by NMR of the binding surface for the histidine-containing phosphocarrier protein HPr on the N-terminal domain of enzyme I of the Escherichia coli phosphotransferase system. Biochemistry, 36, 4393-4398.

    Article  CAS  PubMed  Google Scholar 

  • Garrett DS, Seok YJ, Peterkofsky A, Gronenborn AM, Clore GM. (1999). Solution structure of the 40,000 M-r phosphoryl transfer complex between the N-terminal domain of enzyme I and HPr. Nat Struct Biol, 6, 166-173.

    Article  CAS  PubMed  Google Scholar 

  • Ge F, Li W-L, Bi L-J, Tao S-C, Zhang Z-P, Zhang X-E. (2010). Identification of novel 14-3-3ζ interacting proteins by quantitative immunoprecipitation combined with knockdown (QUICK). J Proteome Res, 9, 5848-5858.

    Article  CAS  PubMed  Google Scholar 

  • Gegner JA, Dahlquist FW. (1991). Signal transduction in bacteria: CheW forms a reversible complex with the protein kinase CheA. Proc Natl Acad Sci U S A, 88, 750-754.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Gill SC, Weitzel SE, von Hippel PH. (1991). Escherichia coli σ70 and NusA proteins: I. Binding interactions with core RNA polymerase in solution and within the transcription complex. J Mol Biol, 220, 307-324.

    Article  CAS  PubMed  Google Scholar 

  • Glatter O, Kratky O (1982) Small angle X-ray scattering. Academic, New York

    Google Scholar 

  • Gray PN, Busser KJ, Chappell TG. (2007). A novel approach for generating full-length, high coverage allele libraries for the analysis of protein interactions. Mol Cell Proteomics, 6, 514-526.

    Article  CAS  PubMed  Google Scholar 

  • Greene MK, Maskos K, Landry SJ. (1998). Role of the J-domain in the cooperation of Hsp40 with Hsp70. Proc Natl Acad Sci U S A, 95, 6108-6113.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Greenfield NJ. (2006). Using circular dichroism spectra to estimate protein secondary structure. Nat Protoc, 1, 2876-2890.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Greenfield NJ, Fowler VM. (2002). Tropomyosin requires an intact N-terminal coiled coil to interact with tropomodulin. Biophys J, 82, 2580-2591.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Grigoriev A. (2001). A relationship between gene expression and protein interactions on the proteome scale: analysis of the bacteriophage T7 and the yeast Saccharomyces cerevisiae. Nucleic Acids Res, 29, 3513-3519.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Groemping Y, Hellmann N. (2005). Spectroscopic methods for the determination of protein interactions. Curr Protoc Protein Sci 20: 28.

    Google Scholar 

  • Gulati K, Gangele K, Agarwal N, Jamsandekar M, Kumar D, Poluri KM. (2018). Molecular cloning and biophysical characterization of CXCL3 chemokine. Int J Biol Macromol, 107, 575-584.

    Article  CAS  PubMed  Google Scholar 

  • Gulati K, Gangele K, Kumar D, Poluri KM. (2019). An inter-switch between hydrophobic and charged amino acids generated druggable small molecule binding pocket in chemokine paralog CXCL3. Arch Biochem Biophys, 662, 121-128.

    Article  CAS  PubMed  Google Scholar 

  • Gunsalus KC, Piano F. (2005). RNAi as a tool to study cell biology: building the genome–phenome bridge. Curr Opin Cell Biol, 17, 3-8.

    Article  CAS  PubMed  Google Scholar 

  • Hall DA, Ptacek J, Snyder M. (2007). Protein microarray technology. Mech Ageing Dev, 128, 161-167.

    Article  CAS  PubMed  Google Scholar 

  • Hamdi A, Colas P. (2012). Yeast two-hybrid methods and their applications in drug discovery. Trends Pharmacol Sci, 33, 109-118.

    Article  CAS  PubMed  Google Scholar 

  • Hanlon AD, Larkin MI, Reddick RM. (2010). Free-solution, label-free protein-protein interactions characterized by dynamic light scattering. Biophys J, 98, 297-304.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Hansma PK, Elings VB, Marti O, Bracker CE. (1988). Scanning tunneling microscopy and atomic force microscopy: application to biology and technology. Science, 242, 209-216.

    Article  CAS  PubMed  Google Scholar 

  • Harding SE, Rowe AJ (2010) Insight into protein–protein interactions from analytical ultracentrifugation. Portland Press Ltd., London

    Book  Google Scholar 

  • Helmuth JA, Paul G, Sbalzarini IF. (2010). Beyond co-localization: inferring spatial interactions between sub-cellular structures from microscopy images. BMC Bioinf, 11, 372.

    Article  Google Scholar 

  • Herberg FW, Taylor SS. (1993). Physiological inhibitors of the catalytic subunit of cAMP-dependent protein kinase: effect of magnesium-ATP on protein-protein interactions. Biochemistry, 32, 14015-14022.

    Article  CAS  PubMed  Google Scholar 

  • Hertveldt K, Beliën T, Volckaert G (2009) General M13 phage display: M13 phage display in identification and characterization of protein–protein interactions. In: Bacteriophages. Springer, New York, pp 321-339

    Chapter  Google Scholar 

  • Hoffmüller U et al. (1999). Interaction of a PDZ protein domain with a synthetic library of all human protein C termini. Angew Chem Int Ed, 38, 2000-2004.

    Article  Google Scholar 

  • Homola J. (2003). Present and future of surface plasmon resonance biosensors. Anal Bioanal Chem, 377, 528-539.

    Article  CAS  PubMed  Google Scholar 

  • Honda S, Kobayashi N, Munekata E, Uedaira H. (1999). Fragment reconstitution of a small protein: folding energetics of the reconstituted immunoglobulin binding domain B1 of streptococcal protein G. Biochemistry, 38, 1203-1213.

    Article  CAS  PubMed  Google Scholar 

  • Huang J, Schreiber SL. (1997). A yeast genetic system for selecting small molecule inhibitors of protein-protein interactions in nanodroplets. Proc Natl Acad Sci U S A, 94, 13396-13401.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Huffaker TC, Hoyt MA, Botstein D. (1987). Genetic analysis of the yeast cytoskeleton. Annu Rev Genet, 21, 259-284.

    Article  CAS  PubMed  Google Scholar 

  • Hummel JP, Dreyer WJ. (1962). Measurement of protein-binding phenomena by gel filtration. Biochim Biophys Acta, 63, 530-532.

    Article  CAS  PubMed  Google Scholar 

  • Ivanov YD, Frantsuzov PA, Zollner A, Medvedeva NV, Archakov AI, Reinle W, Bernhardt R. (2011). Atomic force microscopy study of protein-protein interactions in the cytochrome CYP11A1 (P450scc)-containing steroid hydroxylase system. Nanoscale Res Lett, 6, 54.

    CAS  PubMed  Google Scholar 

  • Jaiswal N, Raikwal N, Pandey H, Agarwal N, Arora A, Poluri KM, Kumar D. (2018). NMR elucidation of monomer–dimer transition and conformational heterogeneity in histone-like DNA binding protein of Helicobacter pylori. Magn Reson Chem, 56, 285-299.

    Article  CAS  PubMed  Google Scholar 

  • Jaiswal N et al. (2019). Molecular interaction between human SUMO-I and histone like DNA binding protein of Helicobacter pylori (Hup) investigated by NMR and other biophysical tools. Int J Biol Macromol, 123, 446-456.

    Article  CAS  PubMed  Google Scholar 

  • Jansen R, Greenbaum D, Gerstein M. (2002). Relating whole-genome expression data with protein-protein interactions. Genome Res, 12, 37-46.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Jensen H, Ostergaard J. (2010). Flow induced dispersion analysis quantifies noncovalent interactions in nanoliter samples. J Am Chem Soc, 132, 4070-4071.

    Article  CAS  PubMed  Google Scholar 

  • Jensen MR, Ortega-Roldan JL, Salmon L, van Nuland N, Blackledge M. (2011). Characterizing weak protein-protein complexes by NMR residual dipolar couplings. Eur Biophys J Biophy, 40, 1371-1381.

    Article  CAS  Google Scholar 

  • Jerabek-Willemsen M, Wienken CJ, Braun D, Baaske P, Duhr S. (2011). Molecular interaction studies using microscale thermophoresis. Assay Drug Dev Technol, 9, 342-353.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Jerabek-Willemsen M, Andre T, Wanner R, Roth HM, Duhr S, Baaske P, Breitsprecher D. (2014). MicroScale thermophoresis: interaction analysis and beyond. J Mol Struct, 1077, 101-113.

    Article  CAS  Google Scholar 

  • Jonsson U et al. (1991). Real-time biospecific interaction analysis using surface-plasmon resonance and a sensor chip technology. Biotechniques, 11, 620.

    CAS  PubMed  Google Scholar 

  • Joseph C et al. (2001). A structural characterization of the interactions between titin Z-repeats and the α-actinin C-terminal domain. Biochemistry, 40, 4957-4965.

    Article  CAS  PubMed  Google Scholar 

  • Joshi N, Kumar D, Poluri KM. (2020a). Elucidating the molecular interactions of chemokine CCL2 orthologs with flavonoid baicalin. ACS Omega, 5, 22637-22651.

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  • Joshi N, Nagar N, Gulati K, Gangele K, Mishra A, Kumar D, Poluri KM. (2020b). Dissecting the differential structural and dynamics features of CCL2 chemokine orthologs. Int J Biol Macromol, 156, 239-251.

    Article  CAS  PubMed  Google Scholar 

  • Kaelin Jr WG, Pallas DC, DeCaprio JA, Kaye FJ, Livingston DM. (1991). Identification of cellular proteins that can interact specifically with the T/ElA-binding region of the retinoblastoma gene product. Cell, 64, 521-532.

    Article  CAS  PubMed  Google Scholar 

  • Kapoor N, Gupta R, Menon ST, Folta-Stogniew E, Raleigh DP, Sakmar TP. (2010). Nucleobindin 1 is a calcium-regulated guanine nucleotide dissociation inhibitor of Gαi1. J Biol Chem, 285, 31647-31660.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Kärkkäinen S et al. (2006). Identification of preferred protein interactions by phage-display of the human Src homology-3 proteome. EMBO Rep, 7, 186-191.

    Article  PubMed  CAS  Google Scholar 

  • Karlsson R, Michaelsson A, Mattsson L. (1991). Kinetic analysis of monoclonal antibody-antigen interactions with a new biosensor based analytical system. J Immunol Methods, 145, 229-240.

    Article  CAS  PubMed  Google Scholar 

  • Keegan L, Gill G, Ptashne M. (1986). Separation of DNA binding from the transcription-activating function of a eukaryotic regulatory protein. Science, 231, 699-704.

    Article  CAS  PubMed  Google Scholar 

  • Kemmeren P, van Berkum NL, Vilo J, Bijma T, Donders R, Brazma A, Holstege FC. (2002). Protein interaction verification and functional annotation by integrated analysis of genome-scale data. Mol Cell, 9, 1133-1143.

    Article  CAS  PubMed  Google Scholar 

  • Kengne-Momo R, Daniel P, Lagarde F, Jeyachandran Y, Pilard J, Durand-Thouand M, Thouand G. (2012). Protein interactions investigated by the Raman spectroscopy for biosensor applications. Int J Spectrosc, 2012, 1702-1713.

    Article  CAS  Google Scholar 

  • Kim YT, Tabor S, Churchich JE, Richardson CC. (1992). Interactions of gene 2.5 protein and DNA polymerase of bacteriophage T7. J Biol Chem, 267, 15032-15040.

    Article  CAS  PubMed  Google Scholar 

  • Kim SK et al. (2001). A gene expression map for Caenorhabditis elegans. Science, 293, 2087-2092.

    Article  CAS  PubMed  Google Scholar 

  • Knapp S et al. (2001). Thermodynamics of the high-affinity interaction of TCF4 with β-catenin. J Mol Biol, 306, 1179-1189.

    Article  CAS  PubMed  Google Scholar 

  • Kobe B et al. (2008). Crystallography and protein-protein interactions: biological interfaces and crystal contacts. Biochem Soc Trans, 36, 1438-1441.

    Article  CAS  PubMed  Google Scholar 

  • Kodama Y, Hu CD. (2012). Bimolecular fluorescence complementation (BiFC): a 5-year update and future perspectives. Biotechniques, 53, 285-298.

    Article  CAS  PubMed  Google Scholar 

  • Krachler AM, Sharma A, Cauldwell A, Papadakos G, Kleanthous C. (2010). TolA modulates the oligomeric status of YbgF in the bacterial periplasm. J Mol Biol, 403, 270-285.

    Article  CAS  PubMed  Google Scholar 

  • Krogan NJ et al. (2006). Global landscape of protein complexes in the yeast Saccharomyces cerevisiae. Nature, 440, 637-643.

    Article  CAS  PubMed  Google Scholar 

  • Lagache T et al. (2018). Mapping molecular assemblies with fluorescence microscopy and object-based spatial statistics. Nat Commun, 9, 698.

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  • Lam YA, Lawson TG, Velayutham M, Zweier JL, Pickart CM. (2002). A proteasomal ATPase subunit recognizes the polyubiquitin degradation signal. Nature, 416, 763-767.

    Article  CAS  PubMed  Google Scholar 

  • Laue T. (2004). Analytical ultracentrifugation: a powerful ‘new’technology in drug discovery. Drug Discov Today, 1, 309-315.

    Article  CAS  Google Scholar 

  • Lea WA, Simeonov A. (2011). Fluorescence polarization assays in small molecule screening. Expert Opin Drug Discovery, 6, 17-32.

    Article  CAS  Google Scholar 

  • Leavitt S, Freire E. (2001). Direct measurement of protein binding energetics by isothermal titration calorimetry. Curr Opin Struct Biol, 11, 560-566.

    Article  CAS  PubMed  Google Scholar 

  • Lebowitz J, Lewis MS, Schuck P. (2002). Modern analytical ultracentrifugation in protein science: a tutorial review. Protein Sci, 11, 2067-2079.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Leuchowius KJ, Weibrecht I, Landegren U, Gedda L, Soderberg O. (2009). Flow cytometric in situ proximity ligation analyses of protein interactions and post-translational modification of the epidermal growth factor receptor family. Cytom Part A, 75A, 833-839.

    Article  CAS  Google Scholar 

  • Li TS, Talvenheimo J, Zeni L, Rosenfeld R, Stearns G, Arakawa T. (2002). Changes in protein conformation and dynamics upon complex formation of brain-derived neurotrophic factor and its receptor: Investigation by isotope-edited Fourier transform IR spectroscopy. Biopolymers, 67, 10-19.

    Article  CAS  PubMed  Google Scholar 

  • Li S et al. (2004). A map of the interactome network of the metazoan C. elegans. Science, 303, 540-543.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Lin CW, Tu PF, Hsiao NW, Chang CY, Wan L, Lin YT, Chang HW. (2007). Identification of a novel septin 4 protein binding to human herpesvirus 8 kaposin A protein using a phage display cDNA library. J Virol Methods, 143, 65-72.

    Article  CAS  PubMed  Google Scholar 

  • Lin CC et al. (2012). Inhibition of basal FGF receptor signaling by dimeric Grb2. Cell, 149, 1514-1524.

    Article  CAS  PubMed  Google Scholar 

  • Lin JS, Ma LS, Lai EM. (2013). Systematic dissection of the agrobacterium type VI secretion system reveals machinery and secreted components for subcomplex formation. PLoS One, 8, e67647.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Liu Z et al. (2004). Crystal structure of spinach major light-harvesting complex at 2.72 Å resolution. Nat Commun, 428, 287-292.

    Article  CAS  Google Scholar 

  • Liu B, Archer CT, Burdine L, Gillette TG, Kodadek T. (2007). Label transfer chemistry for the characterization of protein-protein interactions. J Am Chem Soc, 129, 12348.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Liu Z, Gong Z, Dong X, Tang C. (2016). Transient protein-protein interactions visualized by solution NMR. BBA Proteins Proteom, 1864, 115-122.

    Article  CAS  Google Scholar 

  • Mahajan NP, Linder K, Berry G, Gordon GW, Heim R, Herman B. (1998). Bcl-2 and Bax interactions in mitochondria probed with green fluorescent protein and fluorescence resonance energy transfer. Nat Biotechnol, 16, 547-552.

    Article  CAS  PubMed  Google Scholar 

  • Maldonado AY, Burz DS, Shekhtman A. (2011). In-cell NMR spectroscopy. Prog Nucl Magn Reson Spectrosc, 59, 197-212.

    Article  CAS  PubMed  Google Scholar 

  • Martos A, Alfonso C, Lopez-Navajas P, Ahijado-Guzman R, Mingorance J, Minton AP, Rivas G. (2010). Characterization of self-association and heteroassociation of bacterial cell division proteins FtsZ and ZipA in solution by composition gradient-static light scattering. Biochemistry, 49, 10780-10787.

    Article  CAS  PubMed  Google Scholar 

  • McGaughey KM, Wheeler LJ, Moore JT, Maley GF, Maley F, Mathews CK. (1996). Protein-protein interactions involving T4 phage-coded deoxycytidylate deaminase and thymidylate synthase. J Biol Chem, 271, 23037-23042.

    Article  CAS  PubMed  Google Scholar 

  • McPhie P. (2000). Principles of fluorescence spectroscopy, Anal Biochem, 2, 353-354.

    Article  CAS  Google Scholar 

  • Miao YM, Cross TA. (2013). Solid state NMR and protein-protein interactions in membranes. Curr Opin Struct Biol, 23, 919-928.

    Article  CAS  PubMed  Google Scholar 

  • Michnick SW, Ear PH, Landry C, Malleshaiah MK, Messier V (2011) Protein-fragment complementation assays for large-scale analysis, functional dissection and dynamic studies of protein–protein interactions in living cells. In: Signal transduction protocols. Springer, New York, pp 395-425

    Chapter  Google Scholar 

  • Mills JS, Walsh MP, Nemcek K, Johnson JD. (1988). Biologically-active fluorescent derivatives of spinach calmodulin that report calmodulin target protein-binding. Biochemistry, 27, 991-996.

    Article  CAS  PubMed  Google Scholar 

  • Miura K. (2018). An overview of current methods to confirm protein-protein interactions. Protein Pept Lett, 25, 728-733.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Miura K, Miki H, Shimazaki K, Kawai N, Takenawa T. (1996). Interaction of Ash/Grb-2 via its SH3 domains with neuron-specific p150 and p65. Biochem J, 316 (Pt 2), 639-645.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Moore JM. (1999). NMR techniques for characterization of ligand binding: utility for lead generation and optimization in drug discovery. Biopolymers, 51, 221-243.

    Article  CAS  PubMed  Google Scholar 

  • Morris VJ, Kirby AR, Gunning AP (1999) Atomic force microscopy for biologists. World Scientific, Singapore

    Book  Google Scholar 

  • Moscetti I, Cannistraro S, Bizzarri AR. (2017). Surface plasmon resonance sensing of biorecognition interactions within the tumor suppressor p53 network. Sensors, 17, 2680.

    Article  PubMed Central  Google Scholar 

  • Mukhija S, Germeroth L, Schneider-Mergener J, Erni B. (1998). Identification of peptides inhibiting enzyme I of the bacterial phosphotransferase system using combinatorial cellulose-bound peptide libraries. Eur J Biochem, 254, 433-438.

    Article  CAS  PubMed  Google Scholar 

  • Murphy RM. (1997). Static and dynamic light scattering of biological macromolecules: what can we learn? Curr Opin Biotechnol, 8, 25-30.

    Article  CAS  PubMed  Google Scholar 

  • Nealon JO, Philomina LS, McGuffin LJ. (2017). Predictive and experimental approaches for elucidating protein-protein interactions and quaternary structures. Int J Mol Sci, 18, 2623.

    Article  PubMed Central  CAS  Google Scholar 

  • Nguyen HH, Park J, Kang S, Kim M. (2015). Surface plasmon resonance: a versatile technique for biosensor applications. Sensors, 15, 10481-10510.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • O’Connell MR, Gamsjaeger R, Mackay JP. (2009). The structural analysis of protein-protein interactions by NMR spectroscopy. Proteomics, 9, 5224-5232.

    Article  PubMed  CAS  Google Scholar 

  • Oeffinger M. (2012). Two steps forward—one step back: advances in affinity purification mass spectrometry of macromolecular complexes. J Proteome, 12, 1591-1608.

    Article  CAS  Google Scholar 

  • Oesterreicher S, Blum WF, Schmidt B, Braulke T, Kubler B. (2005). Interaction of insulin-like growth factor II (IGF-II) with multiple plasma proteins: high affinity binding of plasminogen to IGF-II and IGF-binding protein-3. J Biol Chem, 280, 9994-10000.

    Article  CAS  PubMed  Google Scholar 

  • Oggero M, Frank R, Etcheverrigaray M, Kratje R. (2004). Defining the antigenic structure of human GM-CSF and its implications for receptor interaction and therapeutic treatments. Mol Divers, 8, 257-269.

    Article  CAS  PubMed  Google Scholar 

  • Ong SE, Blagoev B, Kratchmarova I, Kristensen DB, Steen H, Pandey A, Mann M. (2002). Stable isotope labeling by amino acids in cell culture, SILAC, as a simple and accurate approach to expression proteomics. Mol Cell Proteomics, 1, 376-386.

    Article  CAS  PubMed  Google Scholar 

  • Ooi SL et al. (2006). Global synthetic-lethality analysis and yeast functional profiling. Tigerpaper, 22, 56-63.

    CAS  Google Scholar 

  • Otto-Bruc A, Antonny B, Minh Vuong T, Chardin P, Chabre M. (1993). Interaction between the retinal cyclic GMP phosphodiesterase inhibitor and transducin. Kinetics and affinity studies. J Biochem, 32, 8636-8645.

    Article  CAS  Google Scholar 

  • Owicki JC. (2000). Fluorescence polarization and anisotropy in high throughput screening: perspectives and primer. J Biomol Screen, 5, 297-306.

    Article  CAS  PubMed  Google Scholar 

  • Pande J, Szewczyk MM, Grover AK. (2010). Phage display: concept, innovations, applications and future. Biotechnol Adv, 28, 849-858.

    Article  CAS  PubMed  Google Scholar 

  • Patel SS, Rexach MF. (2008). Discovering novel interactions at the nuclear pore complex using bead halo: a rapid method for detecting molecular interactions of high and low affinity at equilibrium. Mol Cell Proteom, 7, 121-131.

    Article  CAS  Google Scholar 

  • Pedersen ME, Østergaard J, Jensen H (2019) Flow-induced dispersion analysis (FIDA) for protein quantification and characterization. In: Clinical applications of capillary electrophoresis. Springer, New York, pp 109-123

    Chapter  Google Scholar 

  • Pelicci G et al. (1992). A novel transforming protein (Shc) with an Sh2 domain is implicated in mitogenic signal transduction. Cell, 70, 93-104.

    Article  CAS  PubMed  Google Scholar 

  • Pelletier J, Sidhu S. (2001). Mapping protein-protein interactions with combinatorial biology methods. Curr Opin Biotechnol, 12, 340-347.

    Article  CAS  PubMed  Google Scholar 

  • Periasamy A. (2001). Fluorescence resonance energy transfer microscopy: a mini review. J Biomed Opt, 6, 287-291.

    Article  CAS  PubMed  Google Scholar 

  • Pfleger KD, Seeber RM, Eidne KA. (2006). Bioluminescence resonance energy transfer (BRET) for the real-time detection of protein-protein interactions. Nat Protoc, 1, 337-345.

    Article  CAS  PubMed  Google Scholar 

  • Philo JS, Wen J, Wypych J, Schwartz MG, Mendiaz EA, Langley KE. (1996). Human stem cell factor dimer forms a complex with two molecules of the extracellular domain of its receptor, Kit. J Biol Chem, 271, 6895-6902.

    Article  CAS  PubMed  Google Scholar 

  • Phizicky EM, Fields S. (1995). Protein-protein interactions: methods for detection and analysis. Microbiol Rev, 59, 94-123.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Pierce MM, Raman CS, Nall BT. (1999). Isothermal titration calorimetry of protein-protein interactions. Methods, 19, 213-221.

    Article  CAS  PubMed  Google Scholar 

  • Poluri KM, Joseph PRB, Sawant KV, Rajarathnam K. (2013). Molecular basis of glycosaminoglycan heparin binding to the chemokine CXCL1 dimer. J Biol Chem, 288, 25143-25153.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Popescu SC et al. (2007). Differential binding of calmodulin-related proteins to their targets revealed through high-density Arabidopsis protein microarrays. Proc Natl Acad Sci U S A, 104, 4730-4735.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Poulard C, Rambaud J, Le Romancer M, Corbo L (2014) Proximity ligation assay to detect and localize the interactions of ERα with PI3-K and Src in breast cancer cells and tumor samples. In: Steroid receptors. Springer, New York, pp 135-143

    Chapter  Google Scholar 

  • Poulsen NN, Andersen NZ, Ostergaard J, Zhuang G, Petersen NJ, Jensen H. (2015). Flow induced dispersion analysis rapidly quantifies proteins in human plasma samples. Analyst, 140, 4365-4369.

    Article  CAS  PubMed  Google Scholar 

  • Raj R, Agarwal N, Raghavan S, Chakraborti T, Poluri KM, Kumar D. (2020). Exquisite binding interaction of 18β-Glycyrrhetinic acid with histone like DNA binding protein of Helicobacter pylori: a computational and experimental study. Int J Biol Macromol, 161, 231-246.

    Article  CAS  PubMed  Google Scholar 

  • Ranjbar B, Gill P. (2009). Circular dichroism techniques: biomolecular and nanostructural analyses- a review. Chem Biol Drug Des, 74, 101-120.

    Article  CAS  PubMed  Google Scholar 

  • Rao VS, Srinivas K, Sujini GN, Kumar GN. (2014). Protein-protein interaction detection: methods and analysis. Int J Proteom, 2014, 147648.

    Article  CAS  Google Scholar 

  • Ratcliff GC, Erie DA. (2001). A novel single-molecule study to determine protein-protein association constants. J Am Chem Soc, 123, 5632-5635.

    Article  CAS  PubMed  Google Scholar 

  • Rich RL, Myszka DG. (2000). Advances in surface plasmon resonance biosensor analysis. Curr Opin Biotechnol, 11, 54-61.

    Article  CAS  PubMed  Google Scholar 

  • Rich RL, Myszka DG. (2007). Higher-throughput, label-free, real-time molecular interaction analysis. Anal Biochem, 361, 1-6.

    Article  CAS  PubMed  Google Scholar 

  • Rigaut G, Shevchenko A, Rutz B, Wilm M, Mann M, Seraphin B. (1999). A generic protein purification method for protein complex characterization and proteome exploration. Nat Biotechnol, 17, 1030-1032.

    Article  CAS  PubMed  Google Scholar 

  • Rivas G, Minton A (2003) Tracer sedimentation equilibrium: a powerful tool for the quantitative characterization of macromolecular self-and hetero-associations in solution. Portland Press Ltd., London

    Google Scholar 

  • Roberts GCK (1993) NMR of macromolecules. Oxford: Oxford University Press,

    Google Scholar 

  • Robinson RC, Turbedsky K, Kaiser DA, Marchand JB, Higgs HN, Choe S, Pollard TD. (2001). Crystal structure of Arp2/3 complex. Science, 294, 1679-1684.

    Article  CAS  PubMed  Google Scholar 

  • Rohila JS et al. (2009). Protein-protein interactions of tandem affinity purified protein kinases from rice. PLoS One, 4, e6685.

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  • Rüdiger S, Schneider-Mergener J, Bukau BJ. (2001). Its substrate specificity characterizes the DnaJ co-chaperone as a scanning factor for the DnaK chaperone. EMBO J, 20, 1042-1050.

    Article  PubMed  PubMed Central  Google Scholar 

  • Ruffner H, Bauer A, Bouwmeester T. (2007). Human protein-protein interaction networks and the value for drug discovery. Drug Discov Today, 12, 709-716.

    Article  CAS  PubMed  Google Scholar 

  • Russell RB et al. (2004). A structural perspective on protein-protein interactions. Curr Opin Struct Biol, 14, 313-324.

    Article  CAS  PubMed  Google Scholar 

  • Ryu W-S (2016) Molecular virology of human pathogenic viruses. Academic, New York

    Google Scholar 

  • Salminen A, Novick PJ. (1987). A ras-like protein is required for a post-golgi event in yeast secretion. Cell, 49, 527-538.

    Article  CAS  PubMed  Google Scholar 

  • Sanders SL, Whitfield KM, Vogel JP, Rose MD, Schekman RW. (1992). Sec61p and bip directly facilitate polypeptide translocation into the Er. Cell, 69, 353-365.

    Article  CAS  PubMed  Google Scholar 

  • Schulte R, Talamas J, Doucet C, Hetzer MW. (2008). Single bead affinity detection (SINBAD) for the analysis of protein-protein interactions. PLoS One, 3, e2061.

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  • Schuster SC, Swanson RV, Alex LA, Bourret RB, Simon MI. (1993). Assembly and function of a quaternary signal transduction complex monitored by surface plasmon resonance. Nature, 365, 343-347.

    Article  CAS  PubMed  Google Scholar 

  • Selbach M, Mann M. (2006). Protein interaction screening by quantitative immunoprecipitation combined with knockdown (QUICK). Nat Methods, 3, 981-983.

    Article  CAS  PubMed  Google Scholar 

  • Shah NB, Duncan TM. (2014). Bio-layer interferometry for measuring kinetics of protein-protein interactions and allosteric ligand effects. JoVE, 2014 e51383.

    Google Scholar 

  • Shoemaker BA, Panchenko AR. (2007). Deciphering protein–protein interactions. Part I. Experimental techniques and databases PLoS Comput Biol, 3, e42.

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  • Silkowski H, Davis SJ, Barclay AN, Rowe AJ, Harding SE, Byron O. (1997). Characterisation of the low affinity interaction between rat cell adhesion molecules CD2 and CD48 by analytical ultracentrifugation. Eur Biophys J Biophy, 25, 455-462.

    Article  CAS  Google Scholar 

  • Slonimskiy YB et al. (2018). Functional interaction of low-homology FRPs from different cyanobacteria with Synechocystis OCP. Bioenergetics, 1859, 382-393.

    Article  CAS  PubMed  Google Scholar 

  • Snider J, Kotlyar M, Saraon P, Yao Z, Jurisica I, Stagljar I. (2015). Fundamentals of protein interaction network mapping. Mol Syst Biol, 11, 848.

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  • Söderberg O et al. (2006). Direct observation of individual endogenous protein complexes in situ by proximity ligation. Nat Methods, 3, 995-1000.

    Article  PubMed  CAS  Google Scholar 

  • Söderberg O, Leuchowius K-J, Gullberg M, Jarvius M, Weibrecht I, Larsson L-G, Landegren U. (2008). Characterizing proteins and their interactions in cells and tissues using the in situ proximity ligation assay. Methods, 45, 227-232.

    Article  PubMed  CAS  Google Scholar 

  • Some D. (2013). Light-scattering-based analysis of biomolecular interactions. Biophys Rev, 5, 147-158.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Song Y, Liao JY. (2012). An in vitro forster resonance energy transfer-based high-throughput screening assay for inhibitors of protein-protein interactions in SUMOylation pathway. Assay Drug Dev Technol, 10, 336-343.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Song Y, Madahar V, Liao JY. (2011). Development of FRET assay into quantitative and high-throughput screening technology platforms for protein-protein interactions. Ann Biomed Eng, 39, 1224-1234.

    Article  PubMed  Google Scholar 

  • Sopta M, Carthew RW, Greenblatt J. (1985). Isolation of three proteins that bind to mammalian RNA polymerase II. J Biol Chem, 260, 10353-10360.

    Article  CAS  PubMed  Google Scholar 

  • Sreerama N, Woody RW (2004) Computation and analysis of protein circular dichroism spectra. In: Methods in enzymology, 383. Elsevier, London, pp 318-351

    Google Scholar 

  • Stynen B, Tournu H, Tavernier J, Van Dijck P. (2012). Diversity in genetic in vivo methods for protein-protein interaction studies: from the yeast two-hybrid system to the mammalian split-luciferase system. MMBR, 76, 331-382.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Tang C, Iwahara J, Clore GM. (2006). Visualization of transient encounter complexes in protein-protein association. Nature, 444, 383-386.

    Article  CAS  PubMed  Google Scholar 

  • Taylor KA, Glaeser RM. (2008). Retrospective on the early development of cryoelectron microscopy of macromolecules and a prospective on opportunities for the future. J Struct Biol, 163, 214-223.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Thompson PM, Beck MR, Campbell SL (2015) Protein-protein interaction analysis by nuclear magnetic resonance spectroscopy. In: Protein-protein interactions. Springer, New York, pp 267-279

    Chapter  Google Scholar 

  • Tong AH et al. (2002). A combined experimental and computational strategy to define protein interaction networks for peptide recognition modules. Science, 295, 321-324.

    Article  CAS  PubMed  Google Scholar 

  • Troyanskaya OG, Garber ME, Brown PO, Botstein D, Altman RB. (2002). Nonparametric methods for identifying differentially expressed genes in microarray data. Bioinformatics, 18, 1454-1461.

    Article  CAS  PubMed  Google Scholar 

  • Truant R, Xiao H, Ingles CJ, Greenblatt J. (1993). Direct interaction between the transcriptional activation domain of human P53 and the tata box-binding protein. J Biol Chem, 268, 2284-2287.

    Article  CAS  PubMed  Google Scholar 

  • Ullman EF et al. (1996). Luminescent oxygen channeling assay (LOCI): sensitive, broadly applicable homogeneous immunoassay method. Clin Chem, 42, 1518-1526.

    Article  CAS  PubMed  Google Scholar 

  • Uzarska MA, Dutkiewicz R, Freibert SA, Lill R, Muhlenhoff U. (2013). The mitochondrial Hsp70 chaperone Ssq1 facilitates Fe/S cluster transfer from Isu1 to Grx5 by complex formation. Mol Biol Cell, 24, 1830-1841.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Vasilescu J, Guo XC, Kast J. (2004). Identification of protein-protein interactions using in vivo cross-linking and mass spectrometry. Proteomics, 4, 3845-3854.

    Article  CAS  PubMed  Google Scholar 

  • Velazquez-Campoy A, Leavitt SA, Freire E (2004) Characterization of protein-protein interactions by isothermal titration calorimetry. In: Protein-protein interactions. Springer, New York, pp 35-54

    Chapter  Google Scholar 

  • Vernon-Wilson EF, Kee WJ, Willis AC, Barclay AN, Simmons DL, Brown MH. (2000). CD47 is a ligand for rat macrophage membrane signal regulatory protein SIRP (OX41) and human SIRPα 1. Eur J Immunol, 30, 2130-2137.

    CAS  PubMed  Google Scholar 

  • Vidal M, Brachmann RK, Fattaey A, Harlow E, Boeke JD. (1996). Reverse two-hybrid and one-hybrid systems to detect dissociation of protein-protein and DNA-protein interactions. Proc Natl Acad Sci U S A, 93, 10315-10320.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Vidal M, Cusick ME, Barabasi AL. (2011). Interactome networks and human disease. Cell, 144, 986-998.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Wallace BA, Janes RW. (2010). Synchrotron radiation circular dichroism (SRCD) spectroscopy: an enhanced method for examining protein conformations and protein interactions. Biochem Soc Trans, 38, 861-873.

    Article  CAS  PubMed  Google Scholar 

  • Wang L et al. (2010). Cultivation of green algae Chlorella sp. in different wastewaters from municipal wastewater treatment plant. Appl Biochem Biotechnol, 162, 1174-1186.

    Article  CAS  PubMed  Google Scholar 

  • Wang L et al. (2015). Spatiotemporal dynamics of the BRI1 receptor and its regulation by membrane microdomains in living arabidopsis cells. Mol Plant, 8, 1334-1349.

    Article  CAS  PubMed  Google Scholar 

  • Wang L, Xue Y, Xing J, Song K, Lin J. (2018). Exploring the spatiotemporal organization of membrane proteins in living plant cells. Annu Rev Plant Biol, 69, 525-551.

    Article  CAS  PubMed  Google Scholar 

  • Wang Y, Tadayon R, Shaw GS (2019) Monitoring interactions between S100B and the dopamine D2 receptor using NMR spectroscopy. In: Calcium-binding proteins of the EF-hand superfamily. Springer, New York, pp 311-324

    Chapter  Google Scholar 

  • Watson VG, Drake KM, Peng Y, Napper AD. (2013). Development of a high-throughput screening-compatible assay for the discovery of inhibitors of the AF4-AF9 interaction using alphascreen technology. Assay Drug Dev Technol, 11, 253-268.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Weber PJ, Beck-Sickinger AG. (1997). Comparison of the photochemical behavior of four different photoactivatable probes. J Pept Res, 49, 375-383.

    Article  CAS  PubMed  Google Scholar 

  • Wei Z-H, Chen H, Zhang C, Ye B-C. (2014). FRET-based system for probing protein-protein interactions between σ R and RsrA from streptomyces coelicolor in response to the redox environment. PLoS One, 9, e92330.

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  • Weibrecht I et al. (2010). Proximity ligation assays: a recent addition to the proteomics toolbox. Expert Rev Proteomics, 7, 401-409.

    Article  CAS  PubMed  Google Scholar 

  • Weiel J, Hershey JW. (1981). Fluorescence polarization studies of the interaction of Escherichia coli protein synthesis initiation factor 3 with 30S ribosomal subunits. Biochemistry, 20, 5859-5865.

    Article  CAS  PubMed  Google Scholar 

  • Wellhausen A, Lehming N. (1999). Analysis of the in vivo interaction between a basic repressor and an acidic activator. FEBS Lett, 453, 299-304.

    Article  CAS  PubMed  Google Scholar 

  • Werther M, Seitz H (2008) Protein-protein interaction. Springer, New York

    Book  Google Scholar 

  • Wienken CJ, Baaske P, Rothbauer U, Braun D, Duhr S. (2010). Protein-binding assays in biological liquids using microscale thermophoresis. Nat Commun, 1, 100.

    Article  PubMed  CAS  Google Scholar 

  • Williams JG, Drugan JK, Yi GS, Clark GJ, Der CJ, Campbell SL. (2000). Elucidation of binding determinants and functional consequences of Ras/Raf-cysteine-rich domain interactions. J Biol Chem, 275, 22172-22179.

    Article  CAS  PubMed  Google Scholar 

  • Wilson JL, Scott IM, McMurry JL. (2010). Optical biosensing: kinetics of protein A-IGG binding using biolayer interferometry. Biochem Mol Biol Educ, 38, 400-407.

    Article  CAS  PubMed  Google Scholar 

  • Winstone TL, Workentine ML, Sarfo KJ, Binding AJ, Haslam BD, Turner RJ. (2006). Physical nature of signal peptide binding to DmsD. Arch Biochem Biophys, 455, 89-97.

    Article  CAS  PubMed  Google Scholar 

  • Wu Y, Eghbali M, Ou J, Lu R, Toro L, Stefani E. (2010). Quantitative determination of spatial protein-protein correlations in fluorescence confocal microscopy. Biophys J, 98, 493-504.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Xia Z, Zhou Q, Lin J, Liu Y. (2001). Stable SNARE complex prior to evoked synaptic vesicle fusion revealed by fluorescence resonance energy transfer. J Biol Chem, 276, 1766-1771.

    Article  CAS  PubMed  Google Scholar 

  • Xue Y et al. (2018). Arabidopsis blue light receptor phototropin 1 undergoes blue light-induced activation in membrane microdomains. Mol Plant, 11, 846-859.

    Article  CAS  PubMed  Google Scholar 

  • Yang Y, Wang H, Erie DA. (2003). Quantitative characterization of biomolecular assemblies and interactions using atomic force microscopy. Methods, 29, 175-187.

    Article  CAS  PubMed  Google Scholar 

  • Yasgar A, Jadhav A, Simeonov A, Coussens NP (2016) AlphaScreen-based assays: ultra-high-throughput screening for small-molecule inhibitors of challenging enzymes and protein-protein interactions. In: High throughput screening. Springer, New York, pp 77-98

    Chapter  Google Scholar 

  • Yegorova S, Chavaroche AE, Rodriguez MC, Minond D, Cudic M. (2013). Development of an AlphaScreen assay for discovery of inhibitors of low-affinity glycan-lectin interactions. Anal Biochem, 439, 123-131.

    Article  CAS  PubMed  Google Scholar 

  • Yurlova L et al. (2014). The fluorescent two-hybrid assay to screen for protein–protein interaction inhibitors in live cells: targeting the interaction of p53 with Mdm2 and Mdm4. J Biomol Screen, 19, 516-525.

    Article  CAS  PubMed  Google Scholar 

  • Zhang M, Wisniewski JA, Ji H. (2015). AlphaScreen selectivity assay for β-catenin/B-cell lymphoma 9 inhibitors. Anal Biochem, 469, 43-53.

    Article  CAS  PubMed  Google Scholar 

  • Zhao Y, Chen SS, Yoshioka C, Baconguis I, Gouaux E. (2016). Architecture of fully occupied GluA2 AMPA receptor-TARP complex elucidated by cryo-EM. Nature, 536, 108.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Zhou M, Felder S, Rubinstein M, Hurwitz DR, Ullrich A, Lax I, Schlessinger J. (1993). Real-time measurements of kinetics of EGF binding to soluble EGF receptor monomers and dimers support the dimerization model for receptor activation. Biochemistry, 32, 8193-8198.

    Article  CAS  PubMed  Google Scholar 

  • Zhou M, Li Q, Wang RX. (2016). Current experimental methods for characterizing protein-protein interactions. ChemMedChem, 11, 738-756.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Zlatanova J, Lindsay SM, Leuba SH. (2000). Single molecule force spectroscopy in biology using the atomic force microscope. Prog Biophys Mol Biol, 74, 37-61.

    Article  CAS  PubMed  Google Scholar 

  • Zolghadr K et al. (2008). A fluorescent two-hybrid assay for direct visualization of protein interactions in living cells. MCP, 7, 2279-2287.

    CAS  PubMed  Google Scholar 

  • Zuiderweg ERP. (2002). Mapping protein-protein interactions in solution by NMR spectroscopy. Biochemistry, 41, 1-7.

    Article  CAS  PubMed  Google Scholar 

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Poluri, K.M., Gulati, K., Sarkar, S. (2021). Experimental Methods for Determination of Protein–Protein Interactions. In: Protein-Protein Interactions. Springer, Singapore. https://doi.org/10.1007/978-981-16-1594-8_5

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