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Comparison of backbone dynamics of the type III antifreeze protein and antifreeze-like domain of human sialic acid synthase

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Abstract

Antifreeze proteins (AFPs) are found in a variety of cold-adapted (psychrophilic) organisms to promote survival at subzero temperatures by binding to ice crystals and decreasing the freezing temperature of body fluids. The type III AFPs are small globular proteins that consist of one α-helix, three 310-helices, and two β-strands. Sialic acids play important roles in a variety of biological functions, such as development, recognition, and cell adhesion and are synthesized by conserved enzymatic pathways that include sialic acid synthase (SAS). SAS consists of an N-terminal catalytic domain and a C-terminal antifreeze-like (AFL) domain, which is similar to the type III AFPs. Despite having very similar structures, AFL and the type III AFPs exhibit very different temperature-dependent stability and activity. In this study, we have performed backbone dynamics analyses of a type III AFP (HPLC12 isoform) and the AFL domain of human SAS (hAFL) at various temperatures. We also characterized the structural/dynamic properties of the ice-binding surfaces by analyzing the temperature gradient of the amide proton chemical shift and its correlation with chemical shift deviation from random coil. The dynamic properties of the two proteins were very different from each other. While HPLC12 was mostly rigid with a few residues exhibiting slow motions, hAFL showed fast internal motions at low temperature. Our results provide insight into the molecular basis of thermostability and structural flexibility in homologous psychrophilic HPLC12 and mesophilic hAFL proteins.

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Abbreviations

AFP:

Antifreeze protein

QAE:

Quaternary-amino-ethyl

SP:

Sulfopropyl

TH:

Thermal hysteresis

IBS:

Ice-binding surface

AFL:

Domain antifreeze-like domain

Sialic acid:

N-acetylneuraminic acid

SAS:

Sialic acid synthase

PEP:

Phosphoenolpyruvate

ManNAc:

N-acetylmannosamine

NeuNAc:

N-acetylneuraminic acid

ManNAc-6P:

ManNAc 6-phosphate

NeuNAc-9P:

NeuNAc 9-phosphate

3D:

Three-dimensional

CSD:

Chemical shift deviation

H-bond:

Hydrogen-bond

NOE:

Nuclear Overhauser effect

References

  • Andersen NH, Neidigh JW, Harris SM et al (1997) Extracting information from the temperature gradients of polypeptide NH chemical shifts. 1. the importance of conformational averaging. J Am Chem Soc 119:8547–8561

    Article  Google Scholar 

  • Antson AA, Smith DJ, Roper DI et al (2001) Understanding the mechanism of ice binding by type III antifreeze proteins. J Mol Biol 305:875–889

    Article  Google Scholar 

  • Baardsnes J, Davies PL (2002) Contribution of hydrophobic residues to ice binding by fish type III antifreeze protein. Biochim Biophys Acta 1601:49–54

    Article  Google Scholar 

  • Bracken C, Carr PA, Cavanagh J, Palmer AG (1999) Temperature dependence of intramolecular dynamics of the basic leucine zipper of GCN4: implications for the entropy of association with DNA. J Mol Biol 285:2133–2146

    Article  Google Scholar 

  • Brandsdal BO, Heimstad ES, Sylte I, Smalås AO (1999) Comparative molecular dynamics of mesophilic and psychrophilic protein homologues studied by 1.2 ns simulations. J Biomol Struct Dyn 17:493–506

    Article  Google Scholar 

  • Chao H, Sönnichsen FD, DeLuca CI et al (1994) Structure-function relationship in the globular type III antifreeze protein: identification of a cluster of surface residues required for binding to ice. Protein Sci 3:1760–1769

    Article  Google Scholar 

  • Chen G, Jia Z (1999) Ice-binding surface of fish type III antifreeze. Biophys J 77:1602–1608

    Article  Google Scholar 

  • Cierpicki T, Otlewski J (2001) Amide proton temperature coefficients as hydrogen bond indicators in proteins. J Biomol NMR 21:249–261

    Article  Google Scholar 

  • Cierpicki T, Zhukov I, Byrd RA, Otlewski J (2002) Hydrogen bonds in human ubiquitin reflected in temperature coefficients of amide protons. J Magn Reson 157:178–180

    Article  ADS  Google Scholar 

  • Daley ME, Sykes BD (2003) The role of side chain conformational flexibility in surface recognition by Tenebrio molitor antifreeze protein. Protein Sci 12:1323–1331

    Article  Google Scholar 

  • Daley ME, Spyracopoulos L, Jia Z et al (2002) Structure and dynamics of a β-helical antifreeze protein. Biochemistry 41:5515–5525

    Article  Google Scholar 

  • Daley ME, Graether SP, Sykes BD (2004) Hydrogen bonding on the ice-binding face of a β-helical antifreeze protein indicated by amide proton NMR chemical shifts. Biochemistry 43:13012–13017

    Article  Google Scholar 

  • Davies PL, Baardsnes J, Kuiper MJ, Walker VK (2002) Structure and function of antifreeze proteins. Philos Trans R Soc Lond B 357:927–935

    Article  Google Scholar 

  • Delaglio F, Grzesiek S, Vuister GW et al (1995) NMRPipe: a multidimensional spectral processing system based on UNIX pipes. J Biomol NMR 6:277–293

    Article  Google Scholar 

  • DeLuca CI, Davies PL, Ye Q, Jia Z (1998) The effects of steric mutations on the structure of type III antifreeze protein and its interaction with ice. J Mol Biol 275:515–525

    Article  Google Scholar 

  • Ewart KV, Lin Q, Hew CL (1999) Structure, function and evolution of antifreeze proteins. Cell Mol Life Sci 55:271–283

    Article  Google Scholar 

  • Fletcher GL, Hew CL, Davies PL (2001) Antifreeze proteins of teleost fishes. Annu Rev Physiol 63:359–390

    Article  Google Scholar 

  • Garnham CP, Campbell RL, Davies PL (2011) Anchored clathrate waters bind antifreeze proteins to ice. Proc Natl Acad Sci USA 108:7363–7367

    Article  ADS  Google Scholar 

  • Garnham CP, Nishimiya Y, Tsuda S et al (2012) Engineering a naturally inactive isoform of type III antifreeze protein into one that can stop the growth of ice. FEBS Lett 586:3876–3881

    Article  Google Scholar 

  • Gauthier SY, Scotter AJ, Lin FH et al (2008) A re-evaluation of the role of type IV antifreeze protein. Cryobiology 57:292–296

    Article  Google Scholar 

  • Goddard TD, Kneller DG (2003) SPARKY 3. University of California, San Francisco

    Google Scholar 

  • Graether SP, Sykes BD (2004) Cold survival in freeze-tolerant insects: structure and function of beta-helica proteins. Eur J Biochem 271:3285–3296

    Article  Google Scholar 

  • Graether SP, DeLuca CI, Baardsnes J et al (1999) Quantitative and qualitative analysis of type III antifreeze protein structure and function. J Biol Chem 274:11842–11847

    Article  Google Scholar 

  • Graether SP, Gagné SM, Spyracopoulos L et al (2003) Spruce budworm antifreeze protein: changes in structure and dynamics at low temperature. J Mol Biol 327:1155–1168

    Article  Google Scholar 

  • Gunawan J, Simard D, Gilbert M et al (2005) Structural and mechanistic analysis of sialic acid synthase NeuB from Neisseria meningitidis in complex with Mn2+, phosphoenolpyruvate, and N-acetylmannosaminitol. J Biol Chem 280:3555–3563

    Article  Google Scholar 

  • Hamada T, Ito Y, Abe T et al (2006) Solution structure of the antifreeze-like domain of human sialic acid synthase. Protein Sci 15:1010–1016

    Article  Google Scholar 

  • Harding MM, Ward LG, Haymet AD (1999) Type I ‘antifreeze’ proteins. Structure-activity studies and mechanisms of ice growth inhibition. Eur J Biochem 264:653–665

    Article  Google Scholar 

  • Hew CL, Wang NC, Joshi S et al (1988) Multiple genes provide the basis for antifreeze protein diversity and dosage in the ocean pout, Macrozoarces americanus. J Biol Chem 263:12049–12055

    Google Scholar 

  • Hong J, Hu Y, Li C et al (2010) NMR characterizations of the ice binding surface of an antifreeze protein. PLoS One 5:e15682

    Article  ADS  Google Scholar 

  • Jia Z, Davies PL (2002) Antifreeze proteins: an unusual receptor-ligand interaction. Trends Biochem Sci 27:101–106

    Article  Google Scholar 

  • Jia Z, DeLuca CI, Chao H, Davies PL (1996) Structural basis for the binding of a globular antifreeze protein to ice. Nature 384:285–288

    Article  ADS  Google Scholar 

  • Kumeta H, Ogura K, Nishimiya Y et al (2013) NMR structure note: a defective isoform and its activity-improved variant of a type III antifreeze protein from Zoarces elongates Kner. J Biomol NMR 55:225–230

    Article  Google Scholar 

  • Kundu S, Roy D (2009) Comparative structural studies of psychrophilic and mesophilic protein homologues by molecular dynamics simulation. J Mol Graph Model 27:871–880

    Article  Google Scholar 

  • Lawrence SM, Huddleston KA, Pitts LR et al (2000) Cloning and expression of the human N-acetylneuraminic acid phosphate synthase gene with 2-keto-3-deoxy-d-glycero-d-galacto-nononic acid biosynthetic ability. J Biol Chem 275:17869–17877

    Article  Google Scholar 

  • Lefevre JF, Dayie KT, Peng JW, Wagner G (1996) Internal mobility in the partially folded DNA binding and dimerization domains of GAL4: NMR analysis of the N-H spectral density functions. Biochemistry 35:2674–2686

    Article  Google Scholar 

  • Liu Y, Li Z, Lin Q et al (2007) Structure and evolutionary origin of Ca2+-dependent herring type II antifreeze protein. PLoS One 2:e548

    Article  ADS  Google Scholar 

  • Masson L, Holbein BE (1983) Physiology of sialic acid capsular polysaccharide synthesis in serogroup B Neisseria meningitidis. J Bacteriol 154:728–736

    Google Scholar 

  • Miura K, Ohgiya S, Hoshino T et al (2001) NMR analysis of type III antifreeze protein intramolecular dimer. Structural basis for enhanced activity. J Biol Chem 276:1304–1310

    Article  Google Scholar 

  • Nishimiya Y, Sato R, Takamichi M et al (2005) Co-operative effect of the isoforms of type III antifreeze protein expressed in Notched-fin eelpout, Zoarces elongatus Kner. FEBS J 272:482–492

    Article  Google Scholar 

  • Ohnishi M, Urry DW (1969) Temperature dependence of amide proton chemical shifts: the secondary structures of gramicidin S and valinomycin. Biochem Biophys Res Commun 36:194–202

    Article  Google Scholar 

  • Olufsen M, Brandsdal BO, Smalås AO (2007) Comparative unfolding studies of psychrophilic and mesophilic uracil DNA glycosylase: MD simulations show reduced thermal stability of the cold-adapted enzyme. J Mol Graph Model 26:124–134

    Article  Google Scholar 

  • Papaleo E, Riccardi L, Villa C et al (2006) Flexibility and enzymatic cold-adaptation: a comparative molecular dynamics investigation of the elastase family. Biochim Biophys Acta 1764:1397–1406

    Article  Google Scholar 

  • Papaleo E, Olufsen M, De Gioia L, Brandsdal BO (2007) Optimization of electrostatics as a strategy for cold-adaptation: a case study of cold- and warm-active elastases. J Mol Graph Model 26:93–103

    Article  Google Scholar 

  • Papaleo E, Pasi M, Riccardi L et al (2008) Protein flexibility in psychrophilic and mesophilic trypsins. Evidence of evolutionary conservation of protein dynamics in trypsin-like serine-proteases. FEBS Lett 582:1008–1018

    Article  Google Scholar 

  • Schauer R (2004) Sialic acids: fascinating sugars in higher animals and man. Zoology 107:49–64

    Article  Google Scholar 

  • Sönnichsen FD, DeLuca CI, Davies PL, Sykes BD (1996) Refined solution structure of type III antifreeze protein: hydrophobic groups may be involved in the energetics of the protein–ice interaction. Structure 4:1325–1337

    Article  Google Scholar 

  • Suryanti V, Nelson A, Berry A (2003) Cloning, over-expression, purification, and characterisation of N-acetylneuraminate synthase from Streptococcus agalactiae. Protein Expr Purif 27:346–356

    Article  Google Scholar 

  • Tjandra N, Feller SE, Pastor RW, Bax A (1995) Rotational diffusion anisotropy of human ubiquitin from 15N NMR relaxation. J Am Chem Soc 117:12562–12566

    Article  Google Scholar 

  • Yang DSC, Hon WC, Bubanko S et al (1998) Identification of the ice-binding surface on a type III antifreeze protein with a “flatness function” algorithm. Biophys J 74:2142–2151

    Article  Google Scholar 

  • Yeh Y, Feeney RE (1996) Antifreeze proteins: structures and mechanisms of function. Chem Rev 96:601–618

    Article  Google Scholar 

Download references

Acknowledgments

This work was supported by several National Research Foundation of Korea (NRF) Grants funded by the Korean Government (MSIP) [2010-0020480, 2013R1A2A2A05003837, 2012R1A4A1027750 (BRL)]. This work was also supported by a Grant from the Next-Generation BioGreen 21 Program (SSAC, No. PJ009041), Rural Development Administration, Korea. We thank the GNU Central Instrument Facility for performing the NMR experiments and Dr. Melissa Stauffer and Miss Laura Mizoue, of Scientific Editing Solutions, for editing the manuscript.

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    Authors and Affiliations

    1. Department of Chemistry and Research Institute of Natural Science, Gyeongsang National University, Jinju, Gyeongnam, 660-701, Republic of Korea

      Yong-Geun Choi, Hee-Eun Kim, Yeo-Jin Seo, Ae-Ree Lee, Seo-Ree Choi, Shim Sung Lee & Joon-Hwa Lee

    2. Division of Liberal Arts and Sciences and Department of Chemistry, Gwangju Institute of Science and Technology, Gwangju, 500-712, Republic of Korea

      Chin-Ju Park

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    1. Yong-Geun Choi
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    Yong-Geun Choi and Chin-Ju Park have contributed equally to this work.

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    Choi, YG., Park, CJ., Kim, HE. et al. Comparison of backbone dynamics of the type III antifreeze protein and antifreeze-like domain of human sialic acid synthase. J Biomol NMR 61, 137–150 (2015). https://doi.org/10.1007/s10858-014-9895-2

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