Side-chain Modeling Research Articles

Mercedes Benz model of neutral amino-acid side chains

We present a 2-d coarse-grain model of polar and non-polar amino-acid side chains, and investigate their thermodynamic and structural properties in solution. The molecules interact via a Lennard-Jones potential and a local treatment of the hydrogen bond energy. Such a form allows very fast highly converged calculations. Estimates of the Gibbs free energy of hydration (GFEH) of the solutes show good qualitative agreement with experiments. We find moreover that contributions to the GFEH are linked to the perturbations of the solvent hydration shell structure. For large hydrophobic solutes, unfavorable GFEH results mainly from an increase of the water–water energy contribution, while for hydrophilic solutes the increase in solvent energy is compensated by the solute–solvent energy. The model appears therefore to capture the main features of non-charged amino-acids hydration.

Membrane protein simulations with a united-atom lipid and all-atom protein model:lipid–protein interactions, side chain transfer free energies and model proteins

We have reparameterized the dihedral parameters in a commonly used united-atom lipidforce field so that they can be used with the all-atom OPLS force field for proteinsimplemented in the molecular dynamics simulation software GROMACS. Simulations withthis new combination give stable trajectories and sensible behaviour of both lipids andprotein. We have calculated the free energy of transfer of amino acid side chains betweenwater and ‘lipid-cyclohexane’, made of lipid force field methylene groups, as ahydrophobic mimic of the membrane interior, for both the OPLS-AA and a modifiedOPLS-AA force field which gives better hydration free energies under simulationconditions close to those preferred for the lipid force field. The average error is4.3 kJ mol−1 for water–‘lipid-cyclohexane’ compared to3.2 kJ mol−1 for OPLS-AAcyclohexane and 2.4 kJ mol−1 for the modified OPLS-AA water–‘lipid-cyclohexane’. We have also investigated the effectof different methods to combine parameters between the united-atom lipid force field andthe united-atom protein force field ffgmx. In a widely used combination, the strength ofinteractions between hydrocarbon lipid tails and proteins is significantly overestimated,causing a decrease in the area per lipid and an increase in lipid ordering. Using straightcombination rules improves the results. Combined, we suggest that using OPLS-AAtogether with the united-atom lipid force field implemented in GROMACS is areasonable approach to membrane protein simulations. We also suggest that usingpartial volume information and free energies of transfer may help to improve theparameterization of lipid–protein interactions and point out the need for accurateexperimental data to validate and improve force field descriptions of such interactions.

Advances in homology protein structure modeling.

Homology modeling plays a central role in determining protein structure in the structural genomics project. The importance of homology modeling has been steadily increasing because of the large gap that exists between the overwhelming number of available protein sequences and experimentally solved protein structures, and also, more importantly, because of the increasing reliability and accuracy of the method. In fact, a protein sequence with over 30% identity to a known structure can often be predicted with an accuracy equivalent to a low-resolution X-ray structure. The recent advances in homology modeling, especially in detecting distant homologues, aligning sequences with template structures, modeling of loops and side chains, as well as detecting errors in a model, have contributed to reliable prediction of protein structure, which was not possible even several years ago. The ongoing efforts in solving protein structures, which can be time-consuming and often difficult, will continue to spur the development of a host of new computational methods that can fill in the gap and further contribute to understanding the relationship between protein structure and function.

Partial molar volumes and heat capacities of the N-acetyl amide derivatives of the amino acids asparagine, glutamine, tyrosine, and lysine monohydrochloride in aqueous solution at temperatures from T = 288.15 K to T = 328.15 K

The partial molar volumes, V 2 ∘ , and partial molar heat capacities, C p , 2 ∘ , at infinite dilution have been determined for the compounds N-acetylasparaginamide, N-acetylglutaminamide, N-acetyltyrosinamide, and N-acetyllysinamide monohydrochloride in aqueous solution at T = (288.15, 298.15, 313.15, and 328.15) K. These results, along with the literature data for the compound N-acetylglycinamide, have been used to calculate the amino acid side-chain contributions to the thermodynamic properties. These side-chain contributions are compared with those obtained using small peptides as side-chain model compounds.

Intrinsic Relative Stabilities of the Neutral Tautomers of Arginine Side-Chain Models.

The specific protonation state of amino acids is crucial for the physicochemical properties of proteins and their biological functions. These protonation states influence, for instance, properties related to hydrogen bonding, solubility, and folding. pKa calculations for proteins are, therefore, important and require, in principle, a specification of the most stable protonated and deprotonated forms of each titratable group. This is complicated by the existence of multiple tautomers, like the five neutral tautomers of the guanidine moiety in arginine. In this study, the compounds N-methyl-guanidine and N-ethyl-guanidine were used to model the charged and all neutral protonation states of the arginine side chain. The relative stabilities of all five neutral tautomers were investigated systematically for the first time, using quantum-mechanical calculations. These relative stabilities were obtained in vacuo, water and chloroform, by combining the quantum-mechanical calculations with a continuum solvation model. The water model was used to represent arginines exposed to an aqueous solution, whereas the chloroform model has a polarity representative of a protein core or a membrane. This allowed determining the relative pKa's associated with each neutral tautomer in these environments. A key result is that significant differences in stability are found between the neutral tautomers, in both water and chloroform. Some tautomers are consistently found to be the most stable. These findings will be helpful to refine pKa calculations in proteins.

SPACE: a suite of tools for protein structure prediction and analysis based on complementarity and environment

We describe a suite of SPACE tools for analysis and prediction of structures of biomolecules and their complexes. LPC/CSU software provides a common definition of inter-atomic contacts and complementarity of contacting surfaces to analyze protein structure and complexes. In the current version of LPC/CSU, analyses of water molecules and nucleic acids have been added, together with improved and expanded visualization options using Chime or Java based Jmol. The SPACE suite includes servers and programs for: structural analysis of point mutations (MutaProt); side chain modeling based on surface complementarity (SCCOMP); building a crystal environment and analysis of crystal contacts (CryCo); construction and analysis of protein contact maps (CMA) and molecular docking software (LIGIN). The SPACE suite is accessed at .

Determination of the Orientation of T4 Lysozyme Vectorially Bound to a Planar-Supported Lipid Bilayer Using Site-Directed Spin Labeling

Site-directed spin labeling is used to investigate the structure of adsorbed T4 lysozyme (T4L). A monolayer of T4L is prepared by tethering the protein selectively via a His-tag to the chelating headgroups (NTA Ni) of a planar quartz-supported lipid bilayer. This results in a vectorially oriented ensemble of proteins on the surface, which gives rise to angular-dependent electron paramagnetic resonance spectra. Similar measurements of spin-labeled lipid bilayers were used to characterize the structure and dynamics of the supports. Electron paramagnetic resonance line shape was analyzed using the stochastic Liouville equation approach developed by Freed and co-workers. The simulations reveal a conservation of the secondary and tertiary structure of T4L upon adsorption although slight conformational changes in the presence of the surface can be detected by probing tertiary contact sites. The orientation of the entire protein was deduced on the basis of an anisotropic motional model for the spin-labeled side chain. In addition, a polar order but azimuthal disorder of the molecules was assumed to fit the data. These results demonstrate the utility of site-directed spin labeling in combination with spectral simulation to study not only the secondary and tertiary structure of adsorbed proteins in monolayer coverage but also their orientation with respect to the surface.

Improved side‐chain modeling for protein–protein docking

Success in high-resolution protein-protein docking requires accurate modeling of side-chain conformations at the interface. Most current methods either leave side chains fixed in the conformations observed in the unbound protein structures or allow the side chains to sample a set of discrete rotamer conformations. Here we describe a rapid and efficient method for sampling off-rotamer side-chain conformations by torsion space minimization during protein-protein docking starting from discrete rotamer libraries supplemented with side-chain conformations taken from the unbound structures, and show that the new method improves side-chain modeling and increases the energetic discrimination between good and bad models. Analysis of the distribution of side-chain interaction energies within and between the two protein partners shows that the new method leads to more native-like distributions of interaction energies and that the neglect of side-chain entropy produces a small but measurable increase in the number of residues whose interaction energy cannot compensate for the entropic cost of side-chain freezing at the interface. The power of the method is highlighted by a number of predictions of unprecedented accuracy in the recent CAPRI (Critical Assessment of PRedicted Interactions) blind test of protein-protein docking methods.

Side‐chain flexibility in protein–ligand binding: The minimal rotation hypothesis

The goal of this work is to learn from nature about the magnitudes of side-chain motions that occur when proteins bind small organic molecules, and model these motions to improve the prediction of protein-ligand complexes. Following analysis of protein side-chain motions upon ligand binding in 63 complexes, we tested the ability of the docking tool SLIDE to model these motions without being restricted to rotameric transitions or deciding which side chains should be considered as flexible. The model tested is that side-chain conformational changes involving more atoms or larger rotations are likely to be more costly and less prevalent than small motions due to energy barriers between rotamers and the potential of large motions to cause new steric clashes. Accordingly, SLIDE adjusts the protein and ligand side groups as little as necessary to achieve steric complementarity. We tested the hypothesis that small motions are sufficient to achieve good dockings using 63 ligands and the apo structures of 20 different proteins and compared SLIDE side-chain rotations to those experimentally observed. None of these proteins undergoes major main-chain conformational change upon ligand binding, ensuring that side-chain flexibility modeling is not required to compensate for main-chain motions. Although more frugal in the number of side-chain rotations performed, this model substantially mimics the experimentally observed motions. Most side chains do not shift to a new rotamer, and small motions are both necessary and sufficient to predict the correct binding orientation and most protein-ligand interactions for the 20 proteins analyzed.

A Vibrational Spectral Maker for Probing the Hydrogen-Bonding Status of Protonated Asp and Glu Residues

Hydrogen bonding is a fundamental element in protein structure and function. Breaking a single hydrogen bond may impair the stability of a protein. We report an infrared vibrational spectral marker for probing the hydrogen-bond number for buried, protonated Asp or Glu residues in proteins. Ab initio computational studies were performed on hydrogen-bonding interactions of a COOH group with a variety of side-chain model compounds of polar and charged amino acids in vacuum using density function theory. For hydrogen-bonding interactions with polar side-chain groups, our results show a strong correlation between the C O stretching frequency and the hydrogen bond number of a COOH group: ∼1759–1776 cm −1 for zero, ∼1733–1749 cm −1 for one, and 1703–1710 cm −1 for two hydrogen bonds. Experimental evidence for this correlation will be discussed. In addition, we show an approximate linear correlation between the C O stretching frequency and the hydrogen-bond strength. We propose that a two-dimensional infrared spectroscopy, C O stretching versus O-H stretching, may be employed to identify the specific type of hydrogen-bonding interaction. This vibrational spectral marker for hydrogen-bonding interaction is expected to enhance the power of time-resolved Fourier transform infrared spectroscopy for structural characterization of functionally important intermediates of proteins.

Raman signature of the non-hydrogen-bonded tryptophan side chain in proteins: experimental and ab initio spectra of 3-methylindole in the gas phase

3-Methylindole (3MI), which serves as a structural model for the tryptophan side chain in proteins, has been investigated using vapor phase Raman spectroscopy. The vapor phase spectrum of 3MI identifies the Raman signature of the indolyl moiety free of intermolecular interaction and extends previously reported solution Raman studies of 3MI and related tryptophan derivatives. The Raman spectrum of 3MI vapor is also complemented here with newly obtained vapor phase infrared data and ab initio calculations to refine and extend previous vibrational assignments. The present results provide an improved basis for assessing the dependence of the indolyl Raman signature on the local environment of the tryptophan side chain of proteins. The principal conclusions of this work are the following. (i) The vapor phase 3MI molecule exhibits Raman bands at 3506, 1585, 1409, 1349/1341 (Fermi doublet) and 881cm−1, which differ greatly from their counterparts in the Raman spectrum of 3MI liquid and thus serve as spectral markers of the indolyl ring environment. (ii) The Fermi doublet relative intensity ratio (I1/I2, where I1 and I2 are, respectively, the Raman intensities of the higher and lower wavenumber components of the doublet) is highly sensitive to the state of 3MI condensation, consistent with the previously reported sensitivity of I1/I2 to solvent polarity. The maximum value of the intensity ratio (I1/I2=3.0) is observed for 3MI vapor, while the minimum value (I1/I2=0.43) is observed for 3MI in CHCl3 solution. Implications of the present results for Raman analysis of hydrogen bonding states, hydrophilic interactions and hydrophobic interactions of tryptophan residues in proteins are considered.

Computational Models for the Helix Tilt Angle

The concept of hydrophobic imbalance and that of hydrophobic and hydrophilic centers are used along with side chain models in the computation of helix orientation and tilt angle in or near a membrane. Rotamer statistics are used to infer typical side chain positions and chain length for each amino acid, and the results are used in fast computation of helix orientation. Sliding windows are used to compute local tilt angles on long alpha-helices that defy idealized modeling and generate tilt angle profiles. Seven different procedures based on different formulas and hydrophobicity scales are used for comparison. These procedures generated very similar tilt angle profiles. These profiles provide insights into helix deformation, membrane destabilization, and similarity and differences between membrane proteins.

Development of the force field parameters for phosphoimidazole and phosphohistidine.

Phosphorylation of histidine-containing proteins is a key step in the mechanism of many phosphate transfer enzymes (kinases, phosphatases) and is the first stage in a wide variety of signal transduction cascades in bacteria, yeast, higher plants, and mammals. Studies of structural and dynamical aspects of such enzymes in the phosphorylated intermediate states are important for understanding the intimate molecular mechanisms of their functioning. Such information may be obtained via molecular dynamics and/or docking simulations, but in this case appropriate force field parameters for phosphohistidine should be explicitly defined. In the present article we describe development of the GROMOS96 force field parameters for phosphoimidazole molecule--a realistic model of the phosphohistidine side chain. The parameterization is based on the results of ab initio quantum chemical calculations with subsequent refinement and testing using molecular mechanics and molecular dynamics simulations. The set of force constants and equilibrium geometry is employed to derive force field for the phosphohistidine moiety. Resulting parameters and topology are incorporated into the molecular modeling package GROMACS and used in molecular dynamics simulations of a phosphohistidine-containing protein in explicit solvent.

Partial molar isentropic and isothermal compressibilities of some N-acetyl amino acid amides in aqueous solution at 298.15 K

The partial molar isentropic compressibilities at infinite dilution, K°S,2, have been determined for eight N-acetyl amino acid amides and four N-acetyl-N′-methyl amino acid amides in aqueous solution at 298.15 K. The partial molar isothermal compressibilities at infinite dilution, K°T,2, were derived from the K°S,2 results using partial molar expansibilities and heat capacities determined in previous work. The K°T,2 and K°S,2 results were used to calculate the contributions to the compressibility of the amino acid side-chains. These results are compared with those derived using alternative small solutes that have been proposed as models for the amino acid side-chains in proteins. The applicability of the various side-chain contributions in group additivity schemes for the calculation of the compressibilities of poylpeptides and proteins is discussed.

Advantages of fine-grained side chain conformer libraries.

We compare the modelling accuracy of two common rotamer libraries, the Dunbrack-Cohen and the 'Penultimate' rotamer libraries, with that of a novel library of discrete side chain conformations extracted from the Protein Data Bank. These side chain conformer libraries are extracted automatically from high-quality protein structures using stringent filters and maintain crystallographic bond lengths and angles. This contrasts with traditional rotamer libraries defined in terms of chi angles under the assumption of idealized covalent geometry. We demonstrate that side chain modelling onto native and near-native main chain conformations is significantly more successful with the conformer libraries than with the rotamer libraries when solely considering excluded-volume interactions. The rotamer libraries are inadequate to model side chains without atomic clashes on over 20% of targets if the backbone is held fixed in the native conformation. An algorithm is described for simultaneously modelling both main chain and side chain atoms during discrete ab initio sampling. The resulting models have equivalent root mean square deviations from the experimentally determined protein loops as models from backbone-only ensembles, indicating that all-atom modelling does not detract from the accuracy of conformational sampling.

Molecular Simulation Study of the Potentials of Mean Force for the Interactions between Models of Like-Charged and between Charged and Nonpolar Amino Acid Side Chains in Water

The purpose of this study was to determine the potentials of mean force (PMF) of the interactions between models of like-charged and between models of charged and nonpolar amino acid side chains in water to design improved side chain−side chain interaction potentials for our united residue UNRES force field for protein-structure prediction. Restrained molecular dynamics with the AMBER force field, the TIP3P model of water, and the Ewald summation were used to carry out simulations, and the weighted histogram analysis method (WHAM) was used to calculate the PMFs as functions of solute−solute distances. The following types of systems were considered to model the interactions between like-charged side chains and the interactions between charged and nonpolar side chains: (i) a pair of positively charged ions (potassium, ammonium, and guanidine, respectively); (ii) a pair of negatively charged ions (chloride and acetate, respectively), and (iii) pairs of methane with potassium, ammonium, and chloride ions, re...

Vitamin E models. Shortened sidechain models of α, β, γ and δ tocopherol and tocotrienol—a density functional study

Model compounds of α-, β-, γ-, and δ-tocopherol and Tocotrienol, as well as their sulphur and selenium congeners, were subjected to density functional analysis. The mono methyl substitution either stabilized or destabilized the ring structures to a small extent as assessed in terms of isodesmic reactions. In general, multiple methyl substitutions destabilized the ring. Dimethyl para-substitution results in electronic stabilization and steric repulsion being nearly additive. This was not the case for ortho-dimethyl derivatives, whereby steric repulsions dominate; the meta-substituted models reflect the same trend to a lesser degree. Structurally, the phenolic hydroxyl orientation was approximately planar, with the hydroxyl proton oriented away from the adjacent Me group whenever the structure permitted such an orientation.

Toward direct determination of conformations of protein building units from multidimensional NMR experiments. V. NMR chemical shielding analysis of N-formyl-serinamide, a model for polar side-chain containing peptides.

Knowledge of chemical shift-structure relationships could greatly facilitate the NMR chemical shift assignment and structure refinement processes that occur during peptide/protein structure determination via NMR spectroscopy. To determine whether such correlations exist for polar side chain containing amino acid residues the serine dipeptide model, For-L-Ser-NH(2), was studied. Using the GIAO-RHF/6-31+G(d) and GIAO-RHF/TZ2P levels of theory the NMR chemical shifts of all hydrogen ((1)H(N), (1)H(alpha), (1)H(beta1), (1)H(beta2)), carbon ((13)C(alpha), (13)C(beta), (13)C') and nitrogen ((15)N) atoms have been computed for all 44 stable conformers of For-L-Ser-NH(2). An attempt was made to establish correlation between chemical shift of each nucleus and the major conformational variables (omega(0), phi, psi, omega(1), chi,(1) and chi(2)). At both levels of theory a linear correlation can be observed between (1)H(alpha)/phi, (13)C(alpha)/phi, and (13)C(alpha)/psi. These results indicate that the backbone and side-chain structures of For-L-Ser-NH(2) have a strong influence on its chemical shifts.

Approximate protein folding in the HP side chain model on extended cubic lattices

One of the most important open problems in computational biology is the prediction of the conformation of a protein based on its amino acid sequence. In this paper, we design approximation algorithms for protein structure prediction in the so-called HP side chain model. The major drawback of the standard HP side chain model is the bipartiteness of the cubic lattice. To eliminate this drawback, we introduce the extended cubic lattice that extends the cubic lattice by diagonals in the plane. For this lattice, we present two linear algorithms with approximation ratios of 59/70 and 37/42, respectively. The second algorithm is designed for a ‘natural’ subclass of proteins, which covers more than 99.5% of all sequenced proteins. This is the first time that a protein structure prediction algorithm is designed for a ‘natural’ subclass of all combinatorial possible sequences.

Automated side-chain model building and sequence assignment by template matching.

An algorithm is described for automated building of side chains in an electron-density map once a main-chain model is built and for alignment of the protein sequence to the map. The procedure is based on a comparison of electron density at the expected side-chain positions with electron-density templates. The templates are constructed from average amino-acid side-chain densities in 574 refined protein structures. For each contiguous segment of main chain, a matrix with entries corresponding to an estimate of the probability that each of the 20 amino acids is located at each position of the main-chain model is obtained. The probability that this segment corresponds to each possible alignment with the sequence of the protein is estimated using a Bayesian approach and high-confidence matches are kept. Once side-chain identities are determined, the most probable rotamer for each side chain is built into the model. The automated procedure has been implemented in the RESOLVE software. Combined with automated main-chain model building, the procedure produces a preliminary model suitable for refinement and extension by an experienced crystallographer.