Dynamics of proteins

J. McCammon and S. Harvey, Dynamics of proteins and nucleic acids, Cambridge University Press, Cambridge, U.K., 1987. 

McCammon and Harvey, 1987] McCammon, J. A., and Harvey, S. C. Dynamics of Proteins and Nucleic Acids. Cambridge University Press, Cambridge, 1987. 

Amadei et al. 1993] Amadei, A., Linssen, A.B.M., Berendsen, H.J.C. Essential Dynamics of Proteins. Proteins 17 (1993) 412-425 [Balsera et al. 1997] Balsera, M., Stepaniants, S., Izrailev, S., Oono, Y., Schiilten, K. Reconstructing Potential Energy Functions from Simulated Force-Induced Unbinding Processes. Biophys. J. 73 (1997) 1281-1287 [Case 1996] Case, D.A. Normal mode analysis of protein dynamics. Curr. Op. Struct. Biol. 4 (1994) 285-290... 

Walter Nadler, Axel T. Briinger, Klaus Schulten, and Martin Karplus. Molecular and stochastic dynamics of proteins. Proc. Natl. Acad. Sci. USA, 84 7933-7937, Nov. 1987. 

G.H. Peters, D.M.F van Aalten, O. Edholm, S. Toxvaerd, and R. Bywater. Dynamics of proteins in different solvent systems Analysis of essential motion in lipases. Biophys. J., 71 2245-2255, 1996. 

H. Grubmiiller, N. Ehrenhofer, and P. Tavan. Conformational dynamics of proteins Beyond the nanosecond time scale. In M. Peyard, editor. Proceedings of the Workshop Nonlinear Excitations in BiomoleculesMay 30-June 4, 1994, Houches (Prance), Seiten 231-240. Centre de Physique des Houches (France), Springer-Verlag, 1995. 

The new formalism is especially useful for parallel and distributed computers, since the communication intensity is exceptionally low and excellent load balancing is easy to achieve. In fact, we have used cluster of workstations (Silicon Graphics) and parallel computers - Terra 2000 and IBM SP/2 - to study dynamics of proteins. 

Brooks B and M Karplus 1983. Harmonic Dynamics of Proteins Normal Modes and Fluctuations in Bovine Pancreatic Trypsin Inhibitor. Proceedings of the National Academy of Sciences USA 80 6571-6575. 

J M 1992. Molecular Dynamics Simulation. Elementary Methods. New York, John Wiley Sons, ammon J A and S C Harvey 1987. Dynamics of Proteins and Nucleic Acids. Cambridge, Cambridge Jniversity Press. 

A Amadei, ABM Lmssen, FIJC Berendsen. Essential dynamics of proteins. Proteins 17 412-425, 1993. 

FIGURE 3.3 The enthalpy change, ATT, for a reaction can be determined from the slope of a plot of R In versus l/T. To illns-trate the method, the values of the data points on either side of the 327.5 K (54.5 C) data point have been nsed to calculate ATT at 54.5 C. Regression analysis would normally be preferable. (Adapted from Brandts, ]. F., 1964. Tim thermo-dynamics of protein denatnration. I. The denatnration of ehy-motrypsinogen. om Q.7A of the American Chemical Society m 429 -430L)... 

The use of computer simulations to study internal motions and thermodynamic properties is receiving increased attention. One important use of the method is to provide a more fundamental understanding of the molecular information contained in various kinds of experiments on these complex systems. In the first part of this paper we review recent work in our laboratory concerned with the use of computer simulations for the interpretation of experimental probes of molecular structure and dynamics of proteins and nucleic acids. The interplay between computer simulations and three experimental techniques is emphasized (1) nuclear magnetic resonance relaxation spectroscopy, (2) refinement of macro-molecular x-ray structures, and (3) vibrational spectroscopy. The treatment of solvent effects in biopolymer simulations is a difficult problem. It is not possible to study systematically the effect of solvent conditions, e.g. added salt concentration, on biopolymer properties by means of simulations alone. In the last part of the paper we review a more analytical approach we have developed to study polyelectrolyte properties of solvated biopolymers. The results are compared with computer simulations. 

TRIR methods have also found utility in the elucidation of reaction mechanisms involved in biological systems, most notably photosynthetic and respiratory proteins. In addition, TRIR spectroscopy has also been used to enhance our understanding of the dynamics of protein folding processes. ... 

A fascinating future area of study will be experimental and computational evaluation of the dynamics of protein networks. For example, how do protein complexes and interaction networks change in response to environmental signals or developmental states How do the networks of... 

Walczak M, Antosiewicz JM (2002) Langevin dynamics of proteins at constant pH. Phys Rev E 66 051911. 

Toptygin D, Gronenbom AM, Brand L (2006) Nanosecond relaxation dynamics of protein GB1 identified by the time-dependent red shift in the fluorescence of tryptophan and 5-fluorotryptophan. J Phys Chem B 110(51) 26292-26302... 

The discovery of Green Fluorescent Protein (GFP) and the development of technology that allows specific proteins to be tagged with GFP has fundamentally altered the types of question that can be asked using cell biological methods. It is now possible not only to study where a protein is within a cell, but also feasible to study the precise dynamics of protein movement within living cells. We have exploited these technical developments and applied them to the study of translation initiation factors in yeast, focusing particularly on the... 

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