Vladimir Makarov - Academia.edu (original) (raw)

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Papers by Vladimir Makarov

Biophysical Journal, 2000

Hydration sites are high-density regions in the three-dimensional time-averaged solvent structure... more Hydration sites are high-density regions in the three-dimensional time-averaged solvent structure in molecular dynamics simulations and diffraction experiments. In a simulation of sperm whale myoglobin, we found 294 such high-density regions. Their positions appear to agree reasonably well with the distributions of waters of hydration found in 38 x-ray and 1 neutron high-resolution structures of this protein. The hydration sites are characterized by an average occupancy and a combination of residence time parameters designed to approximate a distribution of residence times. It appears that although the occupancy and residence times of the majority of sites are rather bulk-like, the residence time distribution is shifted toward the longer components, relative to bulk. The sites with particularly long residence times are located only in the cavities and clefts of the protein. This indicates that other factors, such as hydrogen bonds and hydrophobicity of underlying protein residues, play a lesser role in determining the residence times of the longest-lived sites.

Accounts of Chemical Research, 2002

Many theoretical, computational, and experimental techniques recently have been successfully used... more Many theoretical, computational, and experimental techniques recently have been successfully used for description of the solvent distribution around macromolecules. In this Account, we consider recent developments in the areas of protein and nucleic acid solvation and hydration as seen by experiment, theory, and simulations. We find that in most cases not only the general phenomena of solvation but even local hydration patterns are more accurately discussed in the context of water distributions rather than individual molecules of water. While a few localized or highresidency waters are often associated with macromolecules in solution (or crystals from aqueous liquors), these are readily and accurately included in this more general description. The goal of this Account is to review the theoretical models used for the description of the interfacial solvent structure on the border near DNA and protein molecules. In particular, we hope to highlight the progress in this field over the past five years with a focus on comparison of simulation and experimental results. Proteins Over the past decade there has been an extensive accumulation of evidence pointing to the critical role that solvation plays in the function and structural stability of proteins. 11,12 Simulation and theoretical studies of solva-Vladimir Makarov was a scientist at Paracel when this article was written and currently is with BionomiX.

Current opinion in structural biology, 1998

218 Protein hydration density: theory, simulations and crystallography B Montgomery Pettitt*t, Vl... more 218 Protein hydration density: theory, simulations and crystallography B Montgomery Pettitt*t, Vladimir A Makarov** and B Kim Andrews* Models of protein hydration are becoming increasingly more accurate in comparison with experimental data. The recent success of ...

Biopolymers, 1998

Abstract: Using molecular dynamics simulations of fully hydrated proteins and analysis of crystal... more Abstract: Using molecular dynamics simulations of fully hydrated proteins and analysis of crystal structures contained in the Protein Data Bank, we develop a transferable set of perpen-dicular radial distribution functions for water molecules around globular proteins. These universal ...

Biophysical journal, 1998

Effects of the macromolecular solute on the translational mobility of surrounding solvent water, ... more Effects of the macromolecular solute on the translational mobility of surrounding solvent water, and Na + and Cl − ions are investigated by molecular dynamics (MD) simulation. Using MD trajectories of myoglobin and d(C 5 T 5 ) · d(G 5 A 5 ) DNA decamer of high quality ...

Biophysical Journal, 2000

Hydration sites are high-density regions in the three-dimensional time-averaged solvent structure... more Hydration sites are high-density regions in the three-dimensional time-averaged solvent structure in molecular dynamics simulations and diffraction experiments. In a simulation of sperm whale myoglobin, we found 294 such high-density regions. Their positions appear to agree reasonably well with the distributions of waters of hydration found in 38 x-ray and 1 neutron high-resolution structures of this protein. The hydration sites are characterized by an average occupancy and a combination of residence time parameters designed to approximate a distribution of residence times. It appears that although the occupancy and residence times of the majority of sites are rather bulk-like, the residence time distribution is shifted toward the longer components, relative to bulk. The sites with particularly long residence times are located only in the cavities and clefts of the protein. This indicates that other factors, such as hydrogen bonds and hydrophobicity of underlying protein residues, play a lesser role in determining the residence times of the longest-lived sites.

Accounts of Chemical Research, 2002

Many theoretical, computational, and experimental techniques recently have been successfully used... more Many theoretical, computational, and experimental techniques recently have been successfully used for description of the solvent distribution around macromolecules. In this Account, we consider recent developments in the areas of protein and nucleic acid solvation and hydration as seen by experiment, theory, and simulations. We find that in most cases not only the general phenomena of solvation but even local hydration patterns are more accurately discussed in the context of water distributions rather than individual molecules of water. While a few localized or highresidency waters are often associated with macromolecules in solution (or crystals from aqueous liquors), these are readily and accurately included in this more general description. The goal of this Account is to review the theoretical models used for the description of the interfacial solvent structure on the border near DNA and protein molecules. In particular, we hope to highlight the progress in this field over the past five years with a focus on comparison of simulation and experimental results. Proteins Over the past decade there has been an extensive accumulation of evidence pointing to the critical role that solvation plays in the function and structural stability of proteins. 11,12 Simulation and theoretical studies of solva-Vladimir Makarov was a scientist at Paracel when this article was written and currently is with BionomiX.

Current opinion in structural biology, 1998

218 Protein hydration density: theory, simulations and crystallography B Montgomery Pettitt*t, Vl... more 218 Protein hydration density: theory, simulations and crystallography B Montgomery Pettitt*t, Vladimir A Makarov** and B Kim Andrews* Models of protein hydration are becoming increasingly more accurate in comparison with experimental data. The recent success of ...

Biopolymers, 1998

Abstract: Using molecular dynamics simulations of fully hydrated proteins and analysis of crystal... more Abstract: Using molecular dynamics simulations of fully hydrated proteins and analysis of crystal structures contained in the Protein Data Bank, we develop a transferable set of perpen-dicular radial distribution functions for water molecules around globular proteins. These universal ...

Biophysical journal, 1998

Effects of the macromolecular solute on the translational mobility of surrounding solvent water, ... more Effects of the macromolecular solute on the translational mobility of surrounding solvent water, and Na + and Cl − ions are investigated by molecular dynamics (MD) simulation. Using MD trajectories of myoglobin and d(C 5 T 5 ) · d(G 5 A 5 ) DNA decamer of high quality ...