Biomedical subjects

Alexey Onufriev

Publications and source records attributed to Alexey Onufriev.

11 recordsLinked to original sources

PubMed2006

A computational study of nucleosomal DNA flexibility.

Molecular dynamics simulations of the nucleosome core particle and its isolated DNA free in solution are reported. The simulations are based on the implicit solvent methodology and provide insights into the nature of large-scale structural fluctuations and flexibility of the nucleosomal DNA. In addition to the kinked regions previously identified in the x-ray structure of the nucleosome, the simulations support the existence of a biochemically identified distorted region of the DNA. Comparison of computed relative free energies shows that formation of the kinks is associated with little, if any, energy cost relative to a smooth, ideal conformation of the DNA superhelix. Isolated nucleosomal DNA is found to be considerably more flexible than expected for a 147 bp stretch of DNA based on its canonical persistence length of 500 A. Notably, the significant bending of the DNA observed in our simulations occurs without breaking of Watson-Crick bonds. The computed relative stability of bent conformations is sensitive to the ionic strength of the solution in the physiological range; the sensitivity suggests possible experiments that might provide further insights into the structural origins of the unusual flexibility of the DNA.

Biophysics↗

PubMed2006

A simple clustering algorithm can be accurate enough for use in calculations of pKs in macromolecules.

Structure and function of macromolecules depend critically on the ionization states of their acidic and basic groups. Most current structure-based theoretical methods that predict pK of ionizable groups in macromolecules include, as one of the key steps, a computation of the partition sum (Boltzmann average) over all possible protonation microstates. As the number of these microstates depends exponentially on the number of ionizable groups present in the molecule, direct computation of the sum is not realistically feasible for many typical proteins that may have tens or even hundreds of ionizable groups. We have tested a simple and robust approximate algorithm for computing these partition sums for macromolecules. The method subdivides the interacting sites into independent clusters, based upon the strength of site-site electrostatic interaction. The resulting partition function is factorizable into computationally manageable components. Two variants of the approach are presented and validated on a representative test set of 602 proteins, by comparing the pK(1/2) values computed by the proposed method with those obtained by the standard Monte Carlo approach used as a reference. With 95% confidence, the relative error introduced by the more accurate of the two methods is less than 0.25 pK units. The algorithms are one to two orders of magnitude faster than the Monte Carlo method, with the typical settings. A graphical representation is introduced that visualizes the clusters of strong site-site interactions in the context of the three-dimensional (3D) structure of the macromolecule, facilitating identification of functionally important clusters of ionizable groups; the approach is exemplified on two proteins, bacteriorhodopsin and myoglobin.

Algorithms↗

PubMed2006

Analytical electrostatics for biomolecules: beyond the generalized Born approximation.

The modeling and simulation of macromolecules in solution often benefits from fast analytical approximations for the electrostatic interactions. In our previous work [G. Sigalov et al., J. Chem. Phys. 122, 094511 (2005)], we proposed a method based on an approximate analytical solution of the linearized Poisson-Boltzmann equation for a sphere. In the current work, we extend the method to biomolecules of arbitrary shape and provide computationally efficient algorithms for estimation of the parameters of the model. This approach, which we tentatively call ALPB here, is tested against the standard numerical Poisson-Boltzmann (NPB) treatment on a set of 579 representative proteins, nucleic acids, and small peptides. The tests are performed across a wide range of solvent/solute dielectrics and at biologically relevant salt concentrations. Over the range of the solvent and solute parameters tested, the systematic deviation (from the NPB reference) of solvation energies computed by ALPB is 0.5-3.5 kcal/mol, which is 5-50 times smaller than that of the conventional generalized Born approximation widely used in this context. At the same time, ALPB is equally computationally efficient. The new model is incorporated into the AMBER molecular modeling package and tested on small proteins.

Algorithms↗

PubMed2005

H++: a server for estimating pKas and adding missing hydrogens to macromolecules.

The structure and function of macromolecules depend critically on the ionization (protonation) states of their acidic and basic groups. A number of existing practical methods predict protonation equilibrium pK constants of macromolecules based upon their atomic resolution Protein Data Bank (PDB) structures; the calculations are often performed within the framework of the continuum electrostatics model. Unfortunately, these methodologies are complex, involve multiple steps and require considerable investment of effort. Our web server http://biophysics.cs.vt.edu/H++ provides access to a tool that automates this process, allowing both experts and novices to quickly obtain estimates of pKs as well as other related characteristics of biomolecules such as isoelectric points, titration curves and energies of protonation microstates. Protons are added to the input structure according to the calculated ionization states of its titratable groups at the user-specified pH; the output is in the PQR (PDB + charges + radii) format. In addition, corresponding coordinate and topology files are generated in the format supported by the molecular modeling package AMBER. The server is intended for a broad community of biochemists, molecular modelers, structural biologists and drug designers; it can also be used as an educational tool in biochemistry courses.

Databases, Protein↗

PubMed2005

Incorporating variable dielectric environments into the generalized Born model.

A generalized Born (GB) model is proposed that approximates the electrostatic part of macromolecular solvation free energy over the entire range of the solvent and solute dielectric constants. The model contains no fitting parameters, and is derived by matching a general form of the GB Green function with the exact Green's function of the Poisson equation for a random charge distribution inside a perfect sphere. The sphere is assumed to be filled uniformly with dielectric medium epsilon(in), and is surrounded by infinite solvent of constant dielectric epsilon(out). This model is as computationally efficient as the conventional GB model based on the widely used functional form due to Still et al. [J. Am. Chem. Soc. 112, 6127 (1990)], but captures the essential physics of the dielectric response for all values of epsilon(in) and epsilon(out). This model is tested against the exact solution on a perfect sphere, and against the numerical Poisson-Boltzmann (PB) treatment on a set of macromolecules representing various structural classes. It shows reasonable agreement with both the exact and the numerical solutions of the PB equation (where available) considered as reference, and is more accurate than the conventional GB model over the entire range of dielectric values.

Journal Article↗

PubMed2005

The Amber biomolecular simulation programs.

We describe the development, current features, and some directions for future development of the Amber package of computer programs. This package evolved from a program that was constructed in the late 1970s to do Assisted Model Building with Energy Refinement, and now contains a group of programs embodying a number of powerful tools of modern computational chemistry, focused on molecular dynamics and free energy calculations of proteins, nucleic acids, and carbohydrates.

Algorithms↗

PubMed2004

Exploring protein native states and large-scale conformational changes with a modified generalized born model.

Implicit solvation models provide, for many applications, a reasonably accurate and computationally effective way to describe the electrostatics of aqueous solvation. Here, a popular analytical Generalized Born (GB) solvation model is modified to improve its accuracy in calculating the solvent polarization part of free energy changes in large-scale conformational transitions, such as protein folding. In contrast to an earlier GB model (implemented in the AMBER-6 program), the improved version does not overstabilize the native structures relative to the finite-difference Poisson-Boltzmann continuum treatment. In addition to improving the energy balance between folded and unfolded conformers, the algorithm (available in the AMBER-7 and NAB molecular modeling packages) is shown to perform well in more than 50 ns of native-state molecular dynamics (MD) simulations of thioredoxin, protein-A, and ubiquitin, as well as in a simulation of Barnase/Barstar complex formation. For thioredoxin, various combinations of input parameters have been explored, such as the underlying gas-phase force fields and the atomic radii. The best performance is achieved with a previously proposed modification to the torsional potential in the Amber ff99 force field, which yields stable native trajectories for all of the tested proteins, with backbone root-mean-square deviations from the native structures being approximately 1.5 A after 6 ns of simulation time. The structure of Barnase/Barstar complex is regenerated, starting from an unbound state, to within 1.9 A relative to the crystal structure of the complex.

Bacterial Proteins↗

PubMed2004

Performance comparison of generalized born and Poisson methods in the calculation of electrostatic solvation energies for protein structures.

This study compares generalized Born (GB) and Poisson (PB) methods for calculating electrostatic solvation energies of proteins. A large set of GB and PB implementations from our own laboratories as well as others is applied to a series of protein structure test sets for evaluating the performance of these methods. The test sets cover a significant range of native protein structures of varying size, fold topology, and amino acid composition as well as nonnative extended and misfolded structures that may be found during structure prediction and folding/unfolding studies. We find that the methods tested here span a wide range from highly accurate and computationally demanding PB-based methods to somewhat less accurate but more affordable GB-based approaches and a few fast, approximate PB solvers. Compared with PB solvation energies, the latest, most accurate GB implementations were found to achieve errors of 1% for relative solvation energies between different proteins and 0.4% between different conformations of the same protein. This compares to accurate PB solvers that produce results with deviations of less than 0.25% between each other for both native and nonnative structures. The performance of the best GB methods is discussed in more detail for the application for force field-based minimizations or molecular dynamics simulations.

Hydrogen Bonding↗

PubMed2003

Proton affinity changes driving unidirectional proton transport in the bacteriorhodopsin photocycle.

Bacteriorhodopsin is the smallest autonomous light-driven proton pump. Proposals as to how it achieves the directionality of its trans-membrane proton transport fall into two categories: accessibility-switch models in which proton transfer pathways in different parts of the molecule are opened and closed during the photocycle, and affinity-switch models, which focus on changes in proton affinity of groups along the transport chain during the photocycle. Using newly available structural data, and adapting current methods of protein protonation-state prediction to the non-equilibrium case, we have calculated the relative free energies of protonation microstates of groups on the transport chain during key conformational states of the photocycle. Proton flow is modeled using accessibility limitations that do not change during the photocycle. The results show that changes in affinity (microstate energy) calculable from the structural models are sufficient to drive unidirectional proton transport without invoking an accessibility switch. Modeling studies for the N state relative to late M suggest that small structural re-arrangements in the cytoplasmic side may be enough to produce the crucial affinity change of Asp96 during N that allows it to participate in the reprotonation of the Schiff base from the cytoplasmic side. Methodologically, the work represents a conceptual advance compared to the usual calculations of pK(a) using macroscopic electrostatic models. We operate with collective states of protonation involving all key groups, rather than the individual-group pK(a) values traditionally used. When combined with state-to-state transition rules based on accessibility considerations, a model for non-equilibrium proton flow is obtained. Such methods should also be applicable to other active proton-transport systems.

Aspartic Acid↗

PubMed2003

Structural details, pathways, and energetics of unfolding apomyoglobin.

Protein folding is often difficult to characterize experimentally because of the transience of intermediate states, and the complexity of the protein-solvent system. Atomistic simulations, which could provide more detailed information, have had to employ highly simplified models or high temperatures, to cope with the long time scales of unfolding; direct simulation of folding is even more problematic. We report a fully atomistic simulation of the acid-induced unfolding of apomyoglobin in which the protonation of acidic side-chains to simulate low pH is sufficient to induce unfolding at room temperature with no added biasing forces or other unusual conditions; and the trajectory is validated by comparison to experimental characterization of intermediate states. Novel insights provided by their analysis include: characterization of a dry swollen globule state forming a barrier to initial unfolding or final folding; observation of cooperativity in secondary and tertiary structure formation and its explanation in terms of dielectric environments; and structural details of the intermediate and the completely unfolded states. These insights involve time scales and levels of structural detail that are presently beyond the range of experiment, but come within reach through the simulation methods described here. An implicit solvation model is used to analyze the energetics of protein folding at various pH and ionic strength values, and a reasonable estimate of folding free energy is obtained. Electrostatic interactions are found to disfavor folding.

Apoproteins↗

PubMed2002

Effective Born radii in the generalized Born approximation: the importance of being perfect.

Generalized Born (GB) models provide, for many applications, an accurate and computationally facile estimate of the electrostatic contribution to aqueous solvation. The GB models involve two main types of approximations relative to the Poisson equation (PE) theory on which they are based. First, the self-energy contributions of individual atoms are estimated and expressed as "effective Born radii." Next, the atom-pair contributions are estimated by an analytical function f(GB) that depends upon the effective Born radii and interatomic distance of the atom pairs. Here, the relative impacts of these approximations are investigated by calculating "perfect" effective Born radii from PE theory, and enquiring as to how well the atom-pairwise energy terms from a GB model using these perfect radii in the standard f(GB) function duplicate the equivalent terms from PE theory. In tests on several biological macromolecules, the use of these perfect radii greatly increases the accuracy of the atom-pair terms; that is, the standard form of f(GB) performs quite well. The remaining small error has a systematic and a random component. The latter cannot be removed without significantly increasing the complexity of the GB model, but an alternative choice of f(GB) can reduce the systematic part. A molecular dynamics simulation using a perfect-radii GB model compares favorably with simulations using conventional GB, even though the radii remain fixed in the former. These results quantify, for the GB field, the importance of getting the effective Born radii right; indeed, with perfect radii, the GB model gives a very good approximation to the underlying PE theory for a variety of biomacromolecular types and conformations.

Macromolecular Substances↗