European Biophysics Journal

, Volume 42, Issue 4, pp 291–300 | Cite as

Low-temperature molecular dynamics simulations of horse heart cytochrome c and comparison with inelastic neutron scattering data

  • Wojciech Pulawski
  • Slawomir Filipek
  • Anna Zwolinska
  • Aleksander Debinski
  • Krystiana Krzysko
  • Ramón Garduño-Juárez
  • Sowmya Viswanathan
  • Venkatesan RenugopalakrishnanEmail author
Original Paper


Molecular dynamics (MD) simulation combined with inelastic neutron scattering can provide information about the thermal dynamics of proteins, especially the low-frequency vibrational modes responsible for large movement of some parts of protein molecules. We performed several 30-ns MD simulations of cytochrome c (Cyt c) in a water box for temperatures ranging from 110 to 300 K and compared the results with those from experimental inelastic neutron scattering. The low-frequency vibrational modes were obtained via dynamic structure factors, S(Q, ω), obtained both from inelastic neutron scattering experiments and calculated from MD simulations for Cyt c in the same range of temperatures. The well known thermal transition in structural movements of Cyt c is clearly seen in MD simulations; it is, however, confined to unstructured fragments of loops Ω1 and Ω2; movement of structured loop Ω3 and both helical ends of the protein is resistant to thermal disturbance. Calculated and experimental S(Qω) plots are in qualitative agreement for low temperatures whereas above 200 K a boson peak vanishes from the calculated plots. This may be a result of loss of crystal structure by the protein–water system compared with the protein crystal.


Cytochrome c Molecular dynamics Inelastic neutron scattering Dynamic structure factor 



V.R. and S.V. acknowledge the Rothschild Foundation, NIH, NSF, USAFOSR, and the Wallace H. Coulter Foundation for support. The authors also wish to acknowledge Pittsburgh Supercomputing Center for generous allocation of Supercomputer time on TeraGrid through Project Serial Number: TG-CH090102. V.R. acknowledges neutron beam time at Argonne National Laboratory, Argonne, IL, USA.


  1. Abel S, Waks M, Marchi M (2010) Molecular dynamics simulations of cytochrome c unfolding in AOT reverse micelles: the first steps. Eur Phys E Soft Matter 32:399–409CrossRefGoogle Scholar
  2. Autenrieth F, Tajkhorshid E, Baudry J, Luthey-Schulten Z (2004) Classical force field parameters for the heme prosthetic group of cytochrome c. J Comput Chem 25:1613–1622PubMedCrossRefGoogle Scholar
  3. Banci L, Gori-Savellini G, Turano P (1997) A molecular dynamics study in explicit water of the reduced and oxidized forms of yeast iso-1-cytochrome c. Eur J Biochem 249:716–723PubMedCrossRefGoogle Scholar
  4. Battistuzzi G, Borsari M, Sola M (2001) Redox properties of cytochrome c. Antioxid. Redox Signal 3:279–291CrossRefGoogle Scholar
  5. Beissenhirtz MK, Scheller FW, Lisdat F (2004) A superoxide sensor based on a multilayer cytochrome c electrode. Anal Chem 76:4665–4671PubMedCrossRefGoogle Scholar
  6. Bellissent-Funel MC (2004) Internal motions in proteins: a combined neutron scattering and molecular modelling approach. Pramana 63:91–97CrossRefGoogle Scholar
  7. Bertini I, Rosato A, Turano P (2004) Cytochrome c folding/unfolding: a unifying picture. J Porphyrins Phthalocyanines 8:238–245CrossRefGoogle Scholar
  8. Brooks BR, Bruccoleri RE, Olafson BD, States DJ, Swaminathan S, Karplus M (1983) CHARMM: a program for macromolecular energy, minimization, and dynamics calculations. J Comput Chem 4:187–217CrossRefGoogle Scholar
  9. Brown KG, Erfurth SC, Small EW, Peticolas WL (1972) Conformationally dependent low-frequency motions of proteins by laser Raman spectroscopy. Proc Natl Acad Sci USA 69:1467–1469PubMedCrossRefGoogle Scholar
  10. Bu L, Straub JE (2003a) Vibrational frequency shifts and relaxation rates for a selected vibrational mode in cytochrome c. Biophys J 85:1429–1439PubMedCrossRefGoogle Scholar
  11. Bu L, Straub JE (2003b) Simulating vibrational energy flow in proteins: relaxation rate and mechanism for heme cooling in cytochrome c. J Phys Chem B 107:12339–12345CrossRefGoogle Scholar
  12. Bushnell GW, Louie GV, Brayer GD (1990) High-resolution three-dimensional structure of horse heart cytochrome c. J Mol Biol 214:585–595PubMedCrossRefGoogle Scholar
  13. Connatser RW Jr, Belch H, Jirik L, Leach DJ, Trouw FR, Zanotti JM, Ren Y, Crawford RK, Carpenter JM, Price DL, Loong CK, Hodges JP, Herwig KW (2003) The QuasiElastic Neutron Spectrometer (QENS): recent upgrade and performance. In: Mank G, Conrad H (eds) Proceedings of the 16th meeting of the international collaboration on advanced neutron sources, Forschungszentrum Julich GmbH: Julich, pp 279–288Google Scholar
  14. Cukier RI (2004) Quantum molecular dynamics simulation of proton transfer in cytochrome c oxidase. Biochim Biophys Acta 1656:189–202PubMedCrossRefGoogle Scholar
  15. Cukier RI (2005) A molecular dynamics study of water chain formation in the proton-conducting K channel of cytochrome c oxidase. Biochim Biophys Acta 1706:134–146PubMedCrossRefGoogle Scholar
  16. Cusack S, Smith J, Finney J, Karplus M, Trewhella J (1986) Low frequency dynamics of proteins studied by neutron time-of-flight spectroscopy. Physica B+C 136:256–259Google Scholar
  17. Cusack S, Smith J, Finney J, Tidor B, Karplus M (1988) Inelastic neutron scattering analysis of picosecond internal protein dynamics: comparison of harmonic theory with experiment. J Mol Biol 202:903–908PubMedCrossRefGoogle Scholar
  18. Daidone I, Amadei A, Roccatano D, No AD (2003) Molecular dynamics simulation of protein folding by essential dynamics sampling: folding landscape of horse heart cytochrome c. Biophys J 85:2865–2871PubMedCrossRefGoogle Scholar
  19. de Biase PM, Paggi DA, Doctorovich F, Hildebrandt P, Estrin DA, Murgida DH, Marti MA (2009) Molecular basis for the electric field modulation of cytochrome c structure and function. J Am Chem Soc 131:16248–16256PubMedCrossRefGoogle Scholar
  20. Essmann U, Perera L, Berkowitz ML, Darden T, Lee H, Pedersen LG (1995) A smooth particle mesh Ewald method. J Chem Phys 103:8577–8593CrossRefGoogle Scholar
  21. Gabel F, Bicout D, Lehnert U, Tehei M, Weik M, Zaccai G (2002) Protein dynamics studied by neutron scattering. Q Rev Biophys 35:327–367PubMedCrossRefGoogle Scholar
  22. Garcia AE, Hummer G (1999) Conformational dynamics of cytochrome c: correlation to hydrogen exchange. Proteins Struct Funct Genet 36:175–191PubMedCrossRefGoogle Scholar
  23. Genzel L, Keilmann F, Martin TP, Winterling G, Yacoby Y, Frohlich H, Makinen MW (1976) Low frequency Raman spectra of lysozyme. Biopolymers 15:219–225PubMedCrossRefGoogle Scholar
  24. Goupil-Lamy AV, Smith JC, Yunoki J, Parker SF, Kataoka M (1997) High-resolution vibrational inelastic neutron scattering: a new spectroscopic tool for globular proteins. J Am Chem Soc 119:9268–9273CrossRefGoogle Scholar
  25. Jorgensen WL, Chandrasekhar J, Madura JD, Impey RW, Klein MLJ (1983) Comparison of simple potential functions for simulating liquid water. J Chem Phys 79:926–935CrossRefGoogle Scholar
  26. Joti Y, Kitao A, Go N (2004) Molecular simulation study to examine the possibility of detecting collective motion in protein by inelastic neutron scattering. Phys B 350:e627–e630CrossRefGoogle Scholar
  27. Karino K, Matubayasi N (2011) Communication: free-energy analysis of hydration effect on protein with explicit solvent: equilibrium fluctuation of cytochrome c. J Chem Phys 134:041105PubMedCrossRefGoogle Scholar
  28. Karplus M, Gao YQ, Ma JP, van der Vaart A, Yang W (2005) Protein structural transitions and their functional role. Philos Trans R Soc Lond Ser A 363:331–355CrossRefGoogle Scholar
  29. Kataoka M, Kamikubo H, Nakagawa H, Parker SF, Smith J (2003) Neutron inelastic scattering as a high-resolution vibrational spectroscopy: new tool for the study of protein dynamics. Spectroscopy 17:529–535CrossRefGoogle Scholar
  30. Kiel JL (1995) Type-b cytochromes: sensors and switches. CRC Press, Boca RatonGoogle Scholar
  31. Kumar A, Mishra PC, Verma CS, Renugopalakrishnan V (2005) Density functional study of the heme moiety of cytochrome c. Int J Quantum Chem 102:1002–1009CrossRefGoogle Scholar
  32. Loong CK, Ikeda S, Carpenter J (1987) The resolution function of a pulsed-source neutron chopper spectrometer. Nucl Instrum Methods Phys Res Sect A 260:381–402CrossRefGoogle Scholar
  33. MacKerell AD Jr, Banavali N, Foloppe N (2000) Development and current status of the CHARMM force field for nucleic acids. Biopolymers 56:257–265PubMedCrossRefGoogle Scholar
  34. Mao Y, Ratner MA, Jarrold MF (2001) Molecular dynamics simulations of the rehydration of folded and unfolded cytochrome C ions in the vapor phase. J Am Chem Soc 123:6503–6507PubMedCrossRefGoogle Scholar
  35. McCammon JA, Gelin BR, Karplus M, Wolynes PG (1976) The hinge-bending mode in lysozyme. Nature 262:325–326PubMedCrossRefGoogle Scholar
  36. McCammon JA, Gelin BR, Karplus M (1977) Dynamics of folded proteins. Nature 267:585–590PubMedCrossRefGoogle Scholar
  37. Miyamoto S, Kollman PA (1992) SETTLE: an analytical version of the SHAKE and RATTLE algorithms for rigid water models. J Comput Chem 13:952–962CrossRefGoogle Scholar
  38. Norberg J, Nilsson L (2003) Advances in biomolecular simulations: methodology and recent applications. Q Rev Biophys 36:257–306PubMedCrossRefGoogle Scholar
  39. Nordgren CE, Tobias DJ, Klein ML, Blasie JK (2002) Molecular dynamics simulations of a hydrated protein vectorially oriented on polar and nonpolar soft surfaces. Biophys J 83:2906–2917PubMedCrossRefGoogle Scholar
  40. Olkhova E, Hutter MC, Lill MA, Helms V, Michel H (2004) Dynamic water networks in cytochrome c oxidase from Paracoccus denitrificans investigated by molecular dynamics simulations. Biophys J 86:1873–1889PubMedCrossRefGoogle Scholar
  41. Parrish JC, Guillemette JG, Wallace CJ (2001) A tale of two charges: distinct roles for an acidic and a basic amino acid in the structure and function of cytochrome c. Biochem Cell Biol 79:83–91PubMedGoogle Scholar
  42. Phillips JC, Braun R, Wang W, Gumbart J, Tajkhorshid E, Villa E, Chipot C, Skeel RD, Kale L, Schulten K (2005) Scalable molecular dynamics with NAMD. J Comput Chem 26:1781–1802PubMedCrossRefGoogle Scholar
  43. Prabhakaran M, Gursahani SH, Verma CS, Garduno-Juarez R, Renugopalakrishnan V (2004) Cytochrome c: the effect of temperature and pressure from molecular dynamics simulations. J Phys Chem Solids 65:1615–1622CrossRefGoogle Scholar
  44. Price DL, Sköld K (1986) Introduction to neutron scattering. In: Celotta R, Levine J (eds) Methods of experimental physics. Academic Press, London, pp 1–98Google Scholar
  45. Renugopalakrishnan V, Bhatnagar RS (1984) Fourier transform infrared photoacoustic spectroscopy: a novel conformational probe. Demonstration of α-helical conformation of poly (γ-benzyl glutamate). J Am Chem Soc 106:2217–2219CrossRefGoogle Scholar
  46. Renugopalakrishnan V, Collette TW, Carreira LA, Bhatnagar RS (1985) Low-frequency Raman spectra as a conformational probe for polypeptides and proteins. Macromolecules 18:1786–1788CrossRefGoogle Scholar
  47. Renugopalakrishnan V, Ortiz-Lombardia M, Verma CJ (2005) Electrostatics of cytochrome-c assemblies. J Mol Model 11:265–270PubMedCrossRefGoogle Scholar
  48. Ryckaert JP, Ciccotti G, Berendsen HJC (1977) Numerical integration of the Cartesian equations of motion of a system with constraints: molecular dynamics of n-alkanes. J Comput Phys 23:327–341CrossRefGoogle Scholar
  49. Simonson T (2002) Gaussian fluctuations and linear response in an electron transfer protein. Proc Natl Acad Sci USA 99:6544–6549PubMedCrossRefGoogle Scholar
  50. Singh SR, Prakash S, Vasu V, Karunakaran C (2009) Conformational flexibility decreased due to Y67F and F82H mutations in cytochrome c: molecular dynamics simulation studies. J Mol Graphics Model 28:270–277CrossRefGoogle Scholar
  51. Smith JC (2000) Inelastic and quasielastic neutron scattering: complementarity with biomolecular simulation. In: Fanchon E (ed) Structure and dynamics of biomolecules. Oxford University Press, Oxford, pp 161–180Google Scholar
  52. Tarek M, Tobias DJ (2000) The dynamics of protein hydration water: a quantitative comparison of molecular dynamics simulations and neutron-scattering experiments. Biophys J 79:3244–3257PubMedCrossRefGoogle Scholar
  53. Tarek M, Tobias DJ (2001) Effects of solvent damping on side chain and backbone contributions to the protein boson peak. J Chem Phys 115:1607–1612CrossRefGoogle Scholar
  54. Tarek M, Tobias DJ (2002) Role of protein-water hydrogen bond dynamics in the protein dynamical transition. Phys Rev Lett 88:138101PubMedCrossRefGoogle Scholar
  55. van Gunsteren WF, Berendsen HJC (1988) A leap-frog algorithm for stochastic dynamics. Mol Simul 1:173–185CrossRefGoogle Scholar
  56. Verma CS, Renugopalakrishnan V (2004) Computer experiments in the design of bionanodevices, modeling and simulating materials nanoworld. In: Vincenzini P, Zerbetto F (eds) Advances in science and technology. Techna Group Srl., Faenza, pp 321–328Google Scholar
  57. Zaccai G (2004) The effect of water on protein dynamics. Philos Trans R Soc London A 359:1269–1275CrossRefGoogle Scholar

Copyright information

© European Biophysical Societies' Association 2012

Authors and Affiliations

  • Wojciech Pulawski
    • 1
  • Slawomir Filipek
    • 1
  • Anna Zwolinska
    • 2
    • 3
  • Aleksander Debinski
    • 1
  • Krystiana Krzysko
    • 3
    • 4
  • Ramón Garduño-Juárez
    • 5
  • Sowmya Viswanathan
    • 6
  • Venkatesan Renugopalakrishnan
    • 7
    • 8
    • 9
    Email author
  1. 1.Faculty of ChemistryUniversity of WarsawWarsawPoland
  2. 2.Faculty of PharmacyMedical University of WarsawWarsawPoland
  3. 3.International Institute of Molecular and Cell BiologyWarsawPoland
  4. 4.Faculty of Physics, CoE BioExploratoriumUniversity of WarsawWarsawPoland
  5. 5.Instituto de Ciencias FísicasUniversidad Nacional Autónoma de MéxicoCuernavacaMexico
  6. 6.Wellesley Hospital/Partners Healthcare SystemNewtonUSA
  7. 7.Children’s HospitalHarvard Medical SchoolBostonUSA
  8. 8.Department of Chemistry and Chemical BiologyNortheastern UniversityBostonUSA
  9. 9.Children’s HospitalHarvard Medical SchoolBostonUSA

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