The Influence of the Amino Acid Side Chains on the Raman Optical Activity Spectra of Proteins

The Raman optical activity (ROA) spectra of proteins show distinct patterns arising from the secondary structure. It is generally believed that the spectral contributions of the side-chains largely cancel out because of their flexibility and the occurrence of many side-chains with different conformations. Yet, the influence of the side-chains on the ROA patterns assigned to different secondary structures is unknown. Here, the first systematic study of the influence of all amino acid side-chains on the ROA patterns is presented based on density functional theory (DFT) calculations of an extensive collection of peptide models that include many different side-chain and secondary structure conformations. It was shown that the contributions of the side-chains to a large extent average out with conformational flexibility. However, specific side-chain conformations can have significant contributions to the ROA patterns. It was also shown that α-helical structure is very sensitive to both the exact backbone conformation and the side-chain conformation. Side-chains with χ₁≈−60° generate ROA patterns alike those in experiment. Aromatic side-chains strongly influence the amide III ROA patterns. Because of the huge structural sensitivity of ROA, the spectral patterns of proteins arise from extensive conformational averaging of both the backbone and the side-chains. The averaging results in the fine spectral details and relative intensity differences observed in experimental spectra.     

Critical assessment of side-chain conformational space sampling procedures designed for quantifying the effect of side-chain environment

We introduce a family of procedures designed to sample side-chain conformational space at particular locations in protein structures. These procedures (CRSP) use intensive cycles of random assignment of side-chain conformations followed by minimization to determine all the conformations that a group of side-chains can adopt simultaneously. First, we consider a procedure evolving in the dihedral space (dCRSP). Our results suggest that it can accurately map low-energy conformations adopted by clusters of side-chains of a protein. dCRSP is relatively insensitive to various important parameters, and it is sufficiently accurate to capture efficiently the constraint induced by the environment on the conformations a particular side-chain can adopt. Our results show that dCRSP, compared with molecular dynamics (MD), can overcome the problem of the limited set of conformations reached in a reasonable amount of simulations. Next, we introduce procedures (vCRSP) in which valence angles are relaxed, and we assess how efficiently they quantify the conformational entropy of side-chains in the protein native state. For simple peptides, entropies obtained with vCRSP are fully compatible with those obtained with a Monte Carlo procedure. For side-chains in a protein environment, however, vCRSP appears of limited use. Finally, we consider a two-step procedure that combines dCRSP and vCRSP. Our tests suggest that it is able to overcome the limitations of vCRSP. We also note that dCRSP provides a reasonable initial approximation. This family of procedures offers promise in quantifying the contribution of conformational entropy to the energetics of protein structures.     

A genetic algorithm encoded with the structural information of amino acids and dipeptides for efficient conformational searches of oligopeptides

The genetic algorithm (GA) is an intelligent approach for finding minima in a highly dimensional parametric space. However, the success of GA searches for low energy conformations of biomolecules is rather limited so far. Herein an improved GA scheme is proposed for the conformational search of oligopeptides. A systematic analysis of the backbone dihedral angles of conformations of amino acids (AAs) and dipeptides is performed. The structural information is used to design a new encoding scheme to improve the efficiency of GA search. Local geometry optimizations based on the energy calculations by the density functional theory are employed to safeguard the quality and reliability of the GA structures. The GA scheme is applied to the conformational searches of Lys, Arg, Met‐Gly, Lys‐Gly, and Phe‐Gly‐Gly representative of AAs, dipeptides, and tripeptides with complicated side chains. Comparison with the best literature results shows that the new GA method is both highly efficient and reliable by providing the most complete set of the low energy conformations. Moreover, the computational cost of the GA method increases only moderately with the complexity of the molecule. The GA scheme is valuable for the study of the conformations and properties of oligopeptides. © 2016 Wiley Periodicals, Inc.     

A B3LYP investigation of the conformational and environmental sensitivity of carbon�Cdeuterium frequencies of aryl-perdeuterated phenylalanine and tryptophan

Carbon?Cdeuterium labeled amino acids can serve as sensitive probes for biophysical characterization. Although multiple research groups have used infrared spectroscopy in conjunction with alkyl backbone or side-chain deuterated amino acids for the biophysical characterization of conformational and/or environmental changes, it was not entirely clear to the authors that perdeuterated aryl rings would demonstrate a similar sensitivity toward conformational or environmental changes. In an effort to evaluate the sensitivity of aryl carbon?Cdeuterium (C?CD) IR frequencies, a B3LYP investigation of the sensitivity of aryl C?CD frequencies toward conformational and environmental changes was conducted for phenylalanine (Phe) and tryptophan (Trp). To compensate for the low molar absorptivity of C?CD frequencies, perdeuterated aryl rings were investigated, which are commercially available and can be readily compared to experimental data. B3LYP results suggest that aryl-deuterated Phe and Trp will exhibit moderate sensitivities toward conformational and environmental changes with frequency shifts upward of 13 and 26?cm^?1 for Phe and Trp, respectively. B3LYP predicts that conformational sensitivity arises from dipole changes and not orbital alignment changes. In an effort to mimic what might be observed experimentally, simulated IR spectra were created and show absorption band changes with conformational and environmental changes, which indicate that IR characterization of perdeuterated aryl rings in amino acids could serve as a biophysical tool.     

Accounting for non-optimal interactions in molecular recognition: a study of ion-π complexes using a QM/MM model with a dipole-polarisable MM region

For a quantitative understanding of molecular structure, interaction and dynamics, accurate modelling of the energetics of both near-equilibrium and less optimal contacts is important. In this work, we explore the potential energy surfaces of representative ion-π complexes. We examine the performance of a semi-empirical QM/MM approach and the corresponding QM/MMpol model, where inducible point dipoles are additionally employed in the MM region. The predicted potential energy surfaces of cation-benzene complexes are improved by inclusion of explicit MM polarisation of the π-molecule. For cation-formamide complexes, inducible dipoles appreciably improve energetic estimates at geometries forming non-optimal interactions. Energetic component analysis suggests that the implicit MM polarisation of the fixed charge QM/MM model mirrors the behaviour of the QM/MMpol dipole model for the energetics of near-equilibrium conformations. However, for complexes at less optimal orientations, the QM/MM model exhibits higher errors than the QM/MMpol approach, being unable to capture orientation-dependent variations in polarisation energy.     

Characterization of structural transitions from aqueous solution to a lipid phase for α-MSH

Fluorescence spectroscopy results show that the α-melanocyte-stimulating hormone peptide (α-MSH) interacts with acidic lipid vesicles. Detectable structural changes are concomitant with the passage of a tryptophan residue from aqueous to lipidic media. The observed multiexponential decay of fluorescence, rationalized as originating from three rotameric populations of the tryptophan residue, has been used together with a matrix algorithm to find the most probable conformational families of α-MSH in water and lipid environments. A model is discussed in which the same conformational families occur in various phases, although with different probabilities. A conformational family in which χ₁ of the Trp9 side chain is in the trans-rotameric conformation is shown to have structural features highly appropriate to interact with negatively charged biological membranes, which are also in accordance with previous molecular dynamics simulations and with structures engineered in α-MSH analogs that show an increased potency in biological essays. The gauche minus and gauche plus side-chain conformations of Trp9, on the other hand, yield conformations more likely to predominate in aqueous solution. NMR spectroscopy measurements of α-MSH analogs indicate the existence in aqueous solution of a β strand in the vicinity of Trp9. A similar structural feature was found in the present conformational analysis for the gauche minus and gauche plus side-chain rotamers of Trp9. © 1995 John Wiley & Sons, Inc.     

Closing the side-chain gap in protein loop modeling

The success of structure-based drug design relies on accurate protein modeling where one of the key issues is the modeling and refinement of loops. This study takes a critical look at modeled loops, determining the effect of re-sampling side-chains after the loop conformation has been generated. The results are evaluated in terms of backbone and side-chain conformations with respect to the native loop. While models can contain loops with high quality backbone conformations, the side-chain orientations could be poor, and therefore unsuitable for ligand docking and structure-based design. In this study, we report on the ability to model loop side-chains accurately using a variety of commercially available algorithms that include rotamer libraries, systematic torsion scans and knowledge-based methods. Electronic supplementary material  The online version of this article (doi:) contains supplementary material, which is available to authorized users.     

Fine grained sampling of residue characteristics using molecular dynamics simulation

In a fine-grained computational analysis of protein structure, we investigated the relationships between a residue's backbone conformations and its side-chain packing as well as conformations. To produce continuous distributions in high resolution, we ran molecular dynamics simulations over a set of protein folds (dynameome). In effect, the dynameome dataset samples not only the states well represented in the PDB but also the known states that are not well represented in the structural database. In our analysis, we characterized the mutual influence among the backbone ?,ψ angles with the first side-chain torsion angles (χ₁) and the volumes occupied by the side-chains. The dependencies of these relationships on side-chain environment and amino acids are further explored. We found that residue volumes exhibit dependency on backbone 2° structure conformation: side-chains pack more densely in extended β-sheet than in α-helical structures. As expected, residue volumes on the protein surface were larger than those in the interior. The first side-chain torsion angles are found to be dependent on the backbone conformations in agreement with previous studies, but the dynameome dataset provides higher resolution of rotamer preferences based on the backbone conformation. All three gauche^?, gauche⁺, and trans rotamers show different patterns of ?,ψ dependency, and variations in χ₁ value are skewed from their canonical values to relieve the steric strains. By demonstrating the utility of dynameomic modeling on the native state ensemble, this study reveals details of the interplay among backbone conformations, residue volumes and side-chain conformations.     

Investigation of aromatic-backbone amide interactions in the model peptide acetyl-Phe-Gly-Gly-N-methyl amide using molecular dynamics simulations and protein database search.

Weakly polar interactions between the side-chain aromatic rings and hydrogens of backbone amides (Ar-HN) are found in unique conformational regions. To characterize these conformational regions and to elucidate factors that determine the conformation of the Ar-HN interactions, four 4-ns molecular dynamics simulations were performed using four different low-energy conformations obtained from simulated annealing and one extended conformation of the model tripeptide Ac-Phe-Gly-Gly-NH-CH(3) as starting structures. The Ar(i)-HN(i+1) interactions were 4 times more frequent than were Ar(i)-HN(i+2) interactions. Half of the conformations with Ar(i)-HN(i+2) interactions also contained an Ar(i)-HN(i+1) interaction. The solvent access surface area of the Phe side chain and of the amide groups of Phe1, Gly2, and Gly3 involved in Ar-HN interactions was significantly smaller than in residues not involved in such interactions. The number of hydrogen bonds between the solvent and Phe1, Gly2, and Gly3 amide groups was also lower in conformations with Ar-HN interactions. For each trajectory, structures that contained Ar(i)-HN(i), Ar(i)-HN(i+1), and Ar(i)-HN(i+2) interactions were clustered on the basis of similarity of selected torsion angles. Attraction energies between the aromatic ring and the backbone amide in representative conformations of the clusters ranged from -1.98 to -9.24 kJ mol(-1) when an Ar-HN interaction was present. The most representative conformations from the largest clusters matched well with the conformations from the Protein Data Bank of Phe-Gly-Gly protein fragments containing Ar-HN interactions.     

Gas-phase models of gamma turns: effect of side-chain/backbone interactions investigated by IR/UV spectroscopy and quantum chemistry

The conformations of laser-desorbed jet-cooled short peptide chains Ac-Phe-Xxx-NH2 (Xxx=Gly, Ala, Val, and Pro) have been investigated by IR/UV double resonance spectroscopy and density-functional-theory (DFT) quantum chemistry calculations. Singly gamma-folded backbone conformations (betaL-gamma) are systematically observed as the most stable conformers, showing that in these two-residue peptide chains, the local conformational preference of each residue is retained (betaL for Phe and gamma turn for Xxx). Besides, beta turns are also spontaneously formed but appear as minor conformers. The theoretical analysis suggests negligible inter-residue interactions of the main conformers, which enables us to consider these species as good models of gamma turns. In the case of valine, two similar types of gamma turns, differing by the strength of their hydrogen bond, have been found both experimentally and theoretically. This observation provides evidence for a strong flexibility of the peptide chain, whose minimum-energy structures are controlled by side-chain/backbone interactions. The qualitative conformational difference between the present species and the reversed sequence Ac-Xxx-Phe-NH2 is also discussed.     

Understanding the Sequence Preference of Recurrent RNA Building Blocks using Quantum Chemistry: The Intrastrand RNA Dinucleotide Platform

Folded RNA molecules are shaped by an astonishing variety of highly conserved noncanonical molecular interactions and backbone topologies. The dinucleotide platform is a widespread recurrent RNA modular building submotif formed by the side-by-side pairing of bases from two consecutive nucleotides within a single strand, with highly specific sequence preferences. This unique arrangement of bases is cemented by an intricate network of noncanonical hydrogen bonds and facilitated by a distinctive backbone topology. The present study investigates the gas-phase intrinsic stabilities of the three most common RNA dinucleotide platforms - 5'-GpU-3', ApA, and UpC - via state-of-the-art quantum-chemical (QM) techniques. The mean stability of base-base interactions decreases with sequence in the order GpU > ApA > UpC. Bader's atoms-in-molecules analysis reveals that the N2(G)…O4(U) hydrogen bond of the GpU platform is stronger than the corresponding hydrogen bonds in the other two platforms. The mixed-pucker sugar-phosphate backbone conformation found in most GpU platforms, in which the 5'-ribose sugar (G) is in the C2'-endo form and the 3'-sugar (U) in the C3'-endo form, is intrinsically more stable than the standard A-RNA backbone arrangement, partially as a result of a favorable O2'…O2P intra-platform interaction. Our results thus validate the hypothesis of Lu et al. (Lu Xiang-Jun, et al. Nucleic Acids Res. 2010, 38, 4868-4876), that the superior stability of GpU platforms is partially mediated by the strong O2'…O2P hydrogen bond. In contrast, ApA and especially UpC platform-compatible backbone conformations are rather diverse and do not display any characteristic structural features. The average stabilities of ApA and UpC derived backbone conformers are also lower than those of GpU platforms. Thus, the observed structural and evolutionary patterns of the dinucleotide platforms can be accounted for, to a large extent, by their intrinsic properties as described by modern QM calculations. In contrast, we show that the dinucleotide platform is not properly described in the course of atomistic explicit-solvent simulations. Our work also gives methodological insights into QM calculations of experimental RNA backbone geometries. Such calculations are inherently complicated by rather large data and refinement uncertainties in the available RNA experimental structures, which often preclude reliable energy computations.     

Accurate assessment of the strain energy in a protein-bound drug using QM/MM X-ray refinement and converged quantum chemistry

An ongoing question regarding the energetics of protein‐ligand binding has been; what is the strain energy that a ligand pays (if any) when binding to its protein target? The traditional method to estimate strain energy uses force fields to calculate the energy difference between the ligand bound conformation and its nearest local minimum/global minimum on the gas‐phase or aqueous phase potential energy surface. This makes the implicit assumption that the underlying force field as well as the reference crystal structure is accurate. Herein, we use ibuprofen as a test case and compare MMFF and ab initio QM methods to identify the local and global minimum conformations. Nine low energy conformations were identified with HF/6‐31G* geometry optimization in vacuo. We also obtained highly accurate relative energies for ibuprofen's conformational energy surface based on M06/aug‐cc‐pVXZ (X = D and T), MP2/aug‐cc‐pVXZ (X = D and T) and the MP2/CBS method (with and without solvent corrections). Moreover, we curate and re‐refine the ibuprofen‐protein complex (PDB 2BXG) using QM/MM X‐ray refinement approaches (HF/6‐31G* was the QM method and the MM model was the AMBER force field ff99sb), which were compared with the low energy conformers to calculate the strain energy. The result indicates that there was an 88% reduction in ibuprofen conformation strain using the QM/MM refined structure versus the original PDB ibuprofen conformations. Furthermore, our results indicate that, due to its inherent limitations in estimating electrostatic interactions, force fields are not suitable to gauge strain energy for charged drug molecules like ibuprofen. The present work offers a carefully validated conformational potential energy surface for a drug molecule as well as a reliable QM/MM re‐refined X‐ray structure that can be used to test current structure‐based drug design approaches. © 2011 Wiley Periodicals, Inc. J Comput Chem, 2011     

Effect of side chains on competing pathways for beta-scission reactions of peptide-backbone alkoxyl radicals

High-level quantum chemistry calculations have been carried out to investigate beta-scission reactions of alkoxyl radicals located at the alpha-carbon of a peptide backbone. This type of alkoxyl radical may undergo three possible beta-scission reactions, namely C-C beta-scission of the backbone, C-N beta-scission of the backbone, and C-R beta-scission of the side chain. We find that the rates for the C-C beta-scission reactions are all very fast, with rate constants of the order 10(12) s(-1) that are essentially independent of the side chain. The C-N beta-scission reactions are all slow, with rate constants that range from 10(-0.7) to 10(-4.5) s(-1). The rates of the C-R beta-scission reactions depend on the side chain and range from moderately fast (10(7) s(-1)) to very fast (10(12) s(-1)). The rates of the C-R beta-scission reactions correlate well with the relative stabilities of the resultant side-chain product radicals (*R), as reflected in calculated radical stabilization energies (RSEs). The order of stabilities for the side-chain fragment radicals for the natural amino acids is found to be Ala < Glu < Gln approximately Leu approximately Met approximately Lys approximately Arg < Asp approximately Ile approximately Asn approximately Val < Ser approximately Thr approximately Cys < Phe approximately Tyr approximately His approximately Trp. We predict that for side-chain C-R beta-scission reactions to effectively compete with the backbone C-C beta-scission reactions, the side-chain fragment radicals would generally need an RSE greater than approximately 30 kJ mol(-1). Thus, the residues that may lead to competitive side-chain beta-scission reactions are Ser, Thr, Cys, Phe, Tyr, His, and Trp.     

Structure of isolated tyrosyl-glycyl-glycine tripeptide. A comparative conformational study with peptides containing an aromatic ring

The potential energy surface (PES) of tyrosyl-glycyl-glycine (YGG) tripeptide in solution was explored using EDMC (Electrostatically Driven Monte Carlo) and in the gas-phase by means of ab initio quantum chemical calculations. The theoretical computational analysis revealed that this tripeptide possesses a significant molecular flexibility. A C₇ backbone conformation was the most energetically preferred for the central Gly residue, using both methodologies. Some new stable conformers that have not been previously reported were identified in the gas phase as well. This study points out the interplay of backbone and side-chain contributions in determining the relative stabilities of energy minima. In addition, the peptide backbone of YGG was compared with other small peptides containing aromatic side-chains (Phe-Gly-Gly and Trp-Gly-Gly). The comparison with experimental X-ray results was also satisfactory.      

A new method for side-chain conformation prediction using a Hopfield network and reproduced rotamers

We present a new side-chain prediction method based on energy minimization using a Hopfield network, focusing on the buried residues of proteins. In this method, the network is composed of automata assigned to each rotamer to restrict side-chain conformational space. We reproduced a rotamer library that enabled us to more widely cover the space for side-chain conformations than those previously produced. The accuracy of the side-chain modeling was estimated by three standards: root mean square deviations (rmsds) between the modeled and the crystal structures, the percentages of correctly predicted side-chain torsion angles, and the percentages of correctly predicted hydrogen bonds. The average rmsd for buried side chains of 21 proteins was 1.10 Å. The value was almost always improved relative to the previous works. The percentage of side-chain X₁ angles for buried residues was 87.3%. By considering the hydrogen bond energy, the average percentage of correctly predicted hydrogen bonds rose from 33% without hydrogen bond energy to 52% with the bond energy. We applied this method to homology modeling, where the protein backbone used to predict side-chain conformations deviates from the correct conformation, and could predict side-chain conformations as correctly as those using the correct backbones. © 1996 by John Wiley & Sons, Inc.     

Peptide models XVI. The identification of selected HCO—L—SER—NH2 conformers via a systematic grid search using ab initio potential energy surfaces

Multidimensional conformational analysis (MDCA) predicted the existence of nine stable backbone conformations (α_L, α_D, β_L, γ_L, γ_D, δ_L, δ_D, ϵ_L, and ϵ_D) on the 2D-Ramachandran map, E = E(ϕ, ψ), for a single amino acid diamide (HCONH-CHR-CONH₂). The potential energy hypersurfaces (E = E[ϕ, ψ, χ₁, χ₂]) of For-L-Ser-NH₂ associated with the α_L-, bgr;_L-, γ_L-, δ_L-, and ϵ_L-type stable backbone orientations are investigated in this article. An appropriate number of side-chain rotamers is associated with each of the backbone conformers. In the case of serine, where R = −CH₂OH, the two sidechain torsional angles (χ₁, χ₂) should lead to 3 * 3 = 9 different sidechain orientations according to MDCA. For certain backbone structures, some of the sidechain conformations were nonexistent. © 1996 by John Wiley & Sons, Inc.     

Structural and pathway complexity of beta-strand reorganization within aggregates of human transthyretin(105-115) peptide

Interstrand conformational rearrangements of human transthyretin peptide (TTR(105-115)) within dimeric aggregates were simulated by means of molecular dynamics (MD) with implicit solvation model for a total length of 48 micros. The conformations sampled in the MD simulations were clustered to identify free energy minima without any projections of free energy surface. A connected graph was constructed with nodes (=clusters) and edges corresponding to free energy minima and transitions between nodes, respectively. This connected graph which reflects the complexity of the free energy surface was used to extract the transition disconnectivity graph, which reflects the overall free energy barriers between pairs of free energy minima but does not contain information on transition paths. The routes of transitions between important free energy minima were obtained by further processing the original graph and the MD data. We have found that both parallel and antiparallel aggregates are populated. The parallel aggregates with different alignment patterns are separated by nonnegligible free energy barriers. Multiroutes exist in the interstrand conformational reorganization. Most visited routes do not dominant the kinetics, while less visited routes contribute a little each but they are numerous and their total contributions are actually dominant. There are various kinds of reptation motions, including those through a beta-bulge, side-chain aided reptation, and flipping or rotation of a hairpin formed by one strand.     

Intrinsic conformational preferences of C(alpha,alpha)-dibenzylglycine

The intrinsic conformational preferences of C (alpha,alpha)-dibenzylglycine, a symmetric alpha,alpha-dialkylated amino acid bearing two benzyl substituents on the alpha-carbon atom, have been determined using quantum chemical calculations at the B3LYP/6-31+G(d,p) level. A total of 46 minimum energy conformations were found for the N-acetyl- N'-methylamide derivative, even though only nine of them showed a relative energy lower than 5.0 kcal/mol. The latter involves C 7, C 5, and alpha' backbone conformations stabilized by intramolecular hydrogen bonds and/or N-H...pi interactions. Calculation of the conformational free energies in different environments (gas-phase, carbon tetrachloride, chloroform, methanol, and water solutions) indicates that four different minima (two C 5 and two C 7) are energetically accessible at room temperature in the gas phase, while in methanol and aqueous solutions one such minimum (C 5) becomes the only significant conformation. Comparison with results recently reported for C (alpha,alpha)-diphenylglycine indicates that substitution of phenyl side groups by benzyl enhances the conformational flexibility leading to (i) a reduction of the strain of the peptide backbone and (ii) alleviating the repulsive interactions between the pi electron density of the phenyl groups and the lone pairs of the carbonyl oxygen atoms.     

Revised algorithms for the build-up procedure for predicting protein conformations by energy minimization

The build-up procedure for predicting low-energy conformations of polypeptides has been extended to cover the case of peptides in aqueous solutions. The revised procedure consists of five steps to be applied to each stage of the build-up. I. All low-energy minima of each of the two fragments to be joined are combined as starting points for energy minimization of the enlarged fragment, and those minima of the enlarged fragment within a certain upper bound of the lowest energy are retained. II. Whenever one of the combinations in Step I leads to an atomic overlap, the minimization is started again using a pseudoenergy function which remains finite everywhere and becomes equal to the standard energy function when no atoms overlap. III. The minima generated in Steps I and II are culled by ignoring side-chain conformations and retaining only those minima whose backbone conformations differ significantly. IV. The rotameric states of the side chains are optimized, by testing their energy of interaction with the rest of the molecule, and subjecting the whole molecule to a further round of energy minimization if the test indicates that this would reduce the energy. V. The energies of all minima are recomputed with inclusion of a term for solvation and with a smaller upper bound as the criterion for retention. The original build-up procedure consisted of Steps I and III only. Examples are presented showing the effectiveness of the new Steps II and IV in locating low-energy minima, and the problems that remain to be solved, chiefly concerning Step V, are discussed.