Dynamic proteins

Keynote lecture. T G Spiro, e-mail address spiro .princeton.edu (RRS and TRRRS). Review of protein dynamics followed by TRRRS selective to specific structural and prosthetic elements. 

Deak J, Richard L, Pereira M, Chui H-L and Miller R J D 1994 Picosecond phase grating spectroscopy applications to bioenergetics and protein dynamics Meth. Enzymol. 232 322-60... 

Rector K D, Rella C W, Hill J R, Kwok A S, Sligar S G, Chien E Y T, DIott D D and Fayer M D 1997 Mutant and wild-type myoglobin-CO protein dynamics vibrational echo experiments J. Phys. Chem. 

Loncharich, R.J., Brooks, B.R. The effects of truncating long-range forces on protein dynamics. Proteins 6 (1989) 32 5. 

Guenot, J., Kollman, P.A. Conformational and energetic effects of truncating nonbonded interactions in an aqueous protein dynamics simulation. J. Comput. Chem. 14 (1993) 295-311. 

Niedermeier, C, Tavan, P. A structure-adapted multipole method for electrostatic interactions in protein dynamics. J. chem. Phys. 101 (1994) 734-748. 

Protein dynamics occurs on very different time scales ([McCammon and Harvey 1987, Jardetzky 1996]). Here, we are most interested in long time scale motions such as relative motion between secondary structure elements, and inter-domain motion. 

The study of slow protein dynamics is a fascinating field with still many unknowns. We have presented a number of computational techniques that are currently being used to tackle those questions. Most promising for our case seems the development of methods that combine an implicit solvent description with techniques to induce conformational transitions. 

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... 

M. Levitt and R. Sharon. Accurate simulation of protein dynamics in solution. Proc. Natl. Acad. Sci. USA, 85 7557-7561, 1988. 

C. Niedermeier and P. Tavan. Fast version of the structure adapted multipole method — efficient calculation of electrostatic forces in protein dynamics. Mol. Sim., 17 57-66, 1996. 

D. A. Case. Normal mode analysis of protein dynamics. Curr. Opin. Struc. Biol., 4 385-290, 1994. 

M. A. Balsera, W. Wriggers, Y. Oono, and K. Schulten. Principal component analysis and long time protein dynamics. J. Phys. Chem., 100 2567-2572, 1996. 

For 25 years, molecular dynamics simulations of proteins have provided detailed insights into the role of dynamics in biological activity and function [1-3]. The earliest simulations of proteins probed fast vibrational dynamics on a picosecond time scale. Fifteen years later, it proved possible to simulate protein dynamics on a nanosecond time scale. At present it is possible to simulate the dynamics of a solvated protein on the microsecond time scale [4]. These gains have been made through a combination of improved computer processing (Moore s law) and clever computational algorithms [5]. 

The secondary and tertiary structures of myoglobin and ribonuclease A illustrate the importance of packing in tertiary structures. Secondary structures pack closely to one another and also intercalate with (insert between) extended polypeptide chains. If the sum of the van der Waals volumes of a protein s constituent amino acids is divided by the volume occupied by the protein, packing densities of 0.72 to 0.77 are typically obtained. This means that, even with close packing, approximately 25% of the total volume of a protein is not occupied by protein atoms. Nearly all of this space is in the form of very small cavities. Cavities the size of water molecules or larger do occasionally occur, but they make up only a small fraction of the total protein volume. It is likely that such cavities provide flexibility for proteins and facilitate conformation changes and a wide range of protein dynamics (discussed later). 

Protein dynamics—the action of enzymes and molecular motors—provides the key to understanding the biochemistry of this cheetah and the grasses through which it runs. (Frank Lane/Parfitt/Tony Stone Images)... 

More detailed aspects of protein function can be obtained also by force-field based approaches. Whereas protein function requires protein dynamics, no experimental technique can observe it directly on an atomic scale, and motions have to be simulated by molecular dynamics (MD) simulations. Also free energy differences (e.g. between binding energies of different protein ligands) can be characterised by MD simulations. Molecular mechanics or molecular dynamics based approaches are also necessary for homology modelling and for structure refinement in X-ray crystallography and NMR structure determination. 

Real-time spectroscopic methods can be used to measure the binding, dissociation, and internalization of fluorescent ligands with cell-surface receptors on cells and membranes. The time resolution available in these methods is sufficient to permit a detailed analysis of complex processes involved in cell activation, particularly receptor-G protein dynamics. A description of the kinetics and thermodynamics of these processes will contribute to our understanding of the basis of stimulus potency and efficacy. 

The Effects of Long Range Cutoffs on Protein Dynamics... 

Liu HY, Elstner M, Kaxiras E, Frauenheim T, Hermans J, Yang WT. Quantum mechanics simulation of protein dynamics on long timescale. Proteins 2001 44 484-9. 

The only (to the best of our knowledge) theoretical treatment of hydrogen transfer by tunnelling to explicitly recognise the role of protein dynamics, and relate this in turn to the observed kinetic isotope effect, was described by Bruno and Bialek. This approach has been termed vibration-ally enhanced ground state tunnelling theory. A key feature of this theory... 

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