Low-temperature molecular dynamics simulations of horse heart cytochrome c and comparison with inelastic neutron scattering data
- 430 Downloads
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(Q, ω) 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.
KeywordsCytochrome 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.
- 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
- 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
- Kiel JL (1995) Type-b cytochromes: sensors and switches. CRC Press, Boca RatonGoogle Scholar
- 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
- 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
- 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