Simulations biopolymers

D. Beglov and B. Roux. Dominant solvations effects from the primary shell of hydration Approximation for molecular dynamics simulations. Biopolymers, 35 171-178, 1994. 

The computational description of a large biomolecular complex such as the chromatin fiber requires techniques that are difierent from the widely applied molecular dynamics methods used to simulate biopolymers at atomic resolution. 

Langowski, J., Kapp, U., Klenin, K., and Vologodskii, A. (1994) Solution structure and dynamics of DNA topoisomers. Dynamic light scattering studies and Monte-Carlo simulations. Biopolymers 34, 639-646. 

Allison, S.A. and McCammon, J.A. (1984) Transport properties of rigid and fiexible macromolecules by Brownian dynamics simulation. Biopolymers 23, 167-187. 

Chirico, G. and Langowski, J. (1994) Kinetics of DNA supercoiling studied by Brownian dynamics simulation. Biopolymers 34, 415-433. 

Tsui V, Case DA (2001) Theory and applications of the generalized Born solvation model in macromolecular simulations, Biopolymers, 56 275-291... 

Tsui, V., Case, D. Theory and applications of fhe Generalized Bom solvation model in macromolec-ular simulations. Biopolymers 2001, 56,275-91. 

Huang, H.C., Jupiter, D., Qiu, M., Briggs, J.M., and VanBuren, V. (2008) Cluster analysis of hydration waters around the active sites of bacterial alanine racemase using a 2-ns MD simulation. Biopolymers, 89, 210-219. 

Lefevre, T., Arseneault, K. and Pezolet, M. (2004). Study of protein aggregation using two-dimensional correlation infrared spectroscopy and spectral simulations. Biopolymers 73 705-715. 

Shestopalova AV (2007) The binding of actinocin derivative with DNA fragments (Monte Carlo simulation). Biopolym Cell 23(l) 35-44... 

Kostjukov VV, Khomytova NM, Evstigneev MP(2010) Hydration change on eomplexation of aromatie ligands with DNA moleeular dynamies simulations. Biopolym Cell 26(1) 36-44... 

Using Computer Simulations To Probe the Structure and Dynamics of Biopolymers... 

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. 

Vibrational spectroscopy has played a very important role in the development of potential functions for molecular mechanics studies of proteins. Force constants which appear in the energy expressions are heavily parameterized from infrared and Raman studies of small model compounds. One approach to the interpretation of vibrational spectra for biopolymers has been a harmonic analysis whereby spectra are fit by geometry and/or force constant changes. There are a number of reasons for developing other approaches. The consistent force field (CFF) type potentials used in computer simulations are meant to model the motions of the atoms over a large ranee of conformations and, implicitly temperatures, without reparameterization. It is also desirable to develop a formalism for interpreting vibrational spectra which takes into account the variation in the conformations of the chromophore and surroundings which occur due to thermal motions. 

Though carried further here, these theoretical ideas were first explored by Pratt and Rempe (1999). They argued that shape fluctuations were the most important concerns for simulations of biopolymers. This is particularly true for unfolded proteins. It deserves emphasis, therefore, that in this approach shape fluctuations are directly conditioned by. V 0) (JZn). 

Stem, P. S., M. Chorev, M. Goodman, and A. T. Hagler. 1983. Computer Simulation of the Conformational Properties of Retro-Inverso Peptides. II Ab Initio Study, Spatial Electron Distribution, and Population Analysis of N-Formylglycine Methylamide, N-Formyl N -Acetyldiaminomethane, and N-Methylmalonamide. Biopolymers 22, 1901-1917. 

Mitsutake, A. Sugita, Y. Okamoto, Y., Generalized-ensemble algorithms for molecular simulations of biopolymers, Biopolymers 2001, 60, 96-123... 

Time scales for various motions within biopolymers (upper) and nonbiological polymers (lower). The year scale at the bottom shows estimates of when each such process might be accessible to brute force molecular simulation on supercomputers, assuming that parallel processing capability on supercomputers increases by about a factor of 1,000 every 10 years (i.e., one order of magnitude more than Moore s law) and neglecting new approaches or breakthroughs. Reprinted with permission from H.S. Chan and K. A. Dill. Physics Today, 46, 2, 24, (1993). 

W. Windig, P. G. Kistenmaker, and J. Haverkamp, Chemical interpretation of differences in pyrolysis—Mass spectra of simulated mixtures of biopolymers by factor analysis with graphical rotation, J. Anal. Appl. Pyrolysis 3(3), 199-212 (1981/1982)... 

Comparisons as in Fig. 6.31 serve as tool to improve and vahdate MD simulation results and methods and will help to develop more efficient simulation methods. The interplay between validating experiments and successively improved simulations is a very promising approach for arriving at a very detailed picture of the internal motion within biopolymers. 

For calculating the time-dependent properties of biopolymers, the equations of motion of the molecule in a viscous medium (i.e., water) under the influence of thermal motion must be solved. This can be done numerically by the method of Brownian dynamics (BD) [83]. Allison and co-workers [61,62,84] and later others [85-88] have employed BD calculations to simulate the dynamics of linear and superhelical DNA BD models for the chromatin chain will be discussed below. 

Cheatham, T.E., 3rd and Young, M.A. (2000) Molecular dynamics simulation of nucleic acids successes, limitations, and promise. Biopolymers 56, 232-256. 

The first reported molecular dynamics simulations of carbohydrates began to appear in 1986, with the publication of studies of the vacutim motions of a-D-glucopyranose (9), discussed below, and the dynamics of a hexa-NAG substrate bound to lysozyme (IQ), which are described in greater detail in the chapter by Post, et al. in this voltime. Since that time, simulations of the dynamics of many more carbohydrate molecules have been undertaken. A number of these studies are described in subsequent chapters of this voltime. The introduction of this well developed technique to problems of carbohydrate structure and function could contribute substantially to the understanding of this class of molecules, as has been the case for proteins and related biopolymers. 

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