Prediction of protein side chain conformations: a study on the influence of backbone accuracy on conformation stability in the rotamer space

We have studied the effect of backbone inaccuracy on the efficiency of protein side chain conformation prediction using rotamer libraries. The backbones were generated by randomly perturbing the crystallographic conformation of 12 proteins and exhibit C alpha r.m.s.d.s of up to 2 A. Our results show that, even for a perturbation of the backbone fully compatible with the temperature factors of the proteins, the predicted side chain conformations of approximately 10% of the buried side chains remain variable. This fraction increases further for larger backbone deviations. However, for backbone deviations of up to 2 A r.m.s.d., the predicted side chain r.m.s.d. varies only in a ratio of < 1.4. Moreover, a possible strategy for obtaining side chain conformations close to the experimental ones consists of extracting the consensus conformations of the side chains from a series of backbone conformations. Such a procedure allows the computation of the side chain conformations with no loss of accuracy for backbones exhibiting r.m.s.d.s of up to 1 A from the crystallographic coordinates. For larger backbone deviations (up to 2 A r.m.s.d.) the r.m.s.d. of the buried side chains increases from 1.33 up to 1.60 A. We also discuss the influence of the size of the rotamer library on the quality of the prediction.      

Refinement of protein cores and protein-peptide interfaces using a potential scaling approach

Refinement of side chain conformations in protein model structures and at the interface of predicted protein-protein or protein-peptide complexes is an important step during protein structural modelling and docking. A common approach for side chain prediction is to assume a rigid protein main chain for both docking partners and search for an optimal set of side chain rotamers to optimize the steric fit. However, depending on the target-template similarity in the case of comparative protein modelling and on the accuracy of an initially docked complex, the main chain template structure is only an approximation of a realistic target main chain. An inaccurate rigid main chain conformation can in turn interfere with the prediction of side chain conformations. In the present study, a potential scaling approach (PS-MD) during a molecular dynamics (MD) simulation that also allows the inclusion of explicit solvent has been used to predict side chain conformations on semi-flexible protein main chains. The PS-MD method converges much faster to realistic protein-peptide interface structures or protein core structures than standard MD simulations. Depending on the accuracy of the protein main chain, it also gives significantly better results compared with the standard rotamer search method.     

Correlation between side chain mobility and conformation in protein structures

Thermal factors of protein atoms as determined by X-ray crystallographic techniques show a tendency to be larger in side chains with unfavourable local conformations rather than in those displaying conformational energy minima. It follows that side chain atoms are more mobile if they are in a non-rotameric configuration and that the stereochemistry of protein structures cannot be fully assessed or simulated without consideration of thermal factors that monitor flexibility in various regions of the protein. The observations should also prove useful in protein folding and design.      

Prediction of protein side-chain conformations by principal component analysis for fixed main-chain atoms

A method of side-chain prediction without calculating the potential function is introduced. It is based on the assumption that similar side- chain conformations have a similar structural environment around the side chains. The environment information is represented by vectors that were obtained from principle component analysis and represented by the variance of positions of main-chain atoms around side chains. This information was added to the side-chain library (rotamer library) made from X-ray structures. Side-chain conformations were constructed using this side-chain library without using potential functions. An optimal solution was determined by comparing environmental information with the backbone conformation around the side chain to be predicted and native ones in the library. The method was performed for 15 proteins whose structures were known. The result for the root-mean-square deviation between the predicted and X-ray side-chain conformations was approximately 1.5 A (the value for core residues was approximately 1.1 A) and the percentage of predicted chi 1 angles correct within 40 degrees was approximately 65% (75% for the core). The computational time was short (approximately 60 s for the prediction of proteins with 200 amino acid residues). About 70% of the side-chain conformations were constructed by location of the main-chain atoms around the central C beta atom and the average of r.m.s.d. was approximately 1.4 A (for core residues the average was approximately 1.0 A).      

Constructing side chains on near-native main chains for ab initio protein structure prediction

Is there value in constructing side chains while searching proteinconformational space during an ab initio simulation? If so,what is the most computationally efficient method for constructingthese side chains? To answer these questions, four publishedapproaches were used to construct side chain conformations ona range of near-native main chains generated by ab initio proteinstructure prediction methods. The accuracy of these approacheswas compared with a naive approach that selects the most frequentlyobserved rotamer for a given amino acid to construct side chains.An all-atom conditional probability discriminatory functionis useful at selecting conformations with overall low all-atomroot mean square deviation (r.m.s.d.) and the discriminationimproves on sets that are closer to the native conformation.In addition, the naive approach performs as well as more sophisticatedmethods in terms of the percentage of     

Effect of secondary structure on the conformations and folding behaviors of protein-like chains

We present a new model considering the effects of secondary structure on the conformations and folding process of protein-like chains in three-dimensional simple cubic lattice in this paper. The properties such as chain dimensions, shape, average contacts and chain average energy with different helical energy of a helix (ε_hel=0, −0.75, −1.5, and −3 in the unit of kT) are discussed here. Unlike conventional polymers, protein-like chains are much compact. We also find that the ability to form helix of residue is different under the condition of different helical energy of a helix. The energy distribution for protein-like chains with different length and the conformation changes in the process of folding of proteins are discussed. Comparisons with real protein chains are also made.     

The Effect of the Structural Elements on the Properties of Side Chain Mesomorphic Polymers

The thermal properties of mesomorphic polymers depend on the relative amounts of the different structural elements (hard core, flexible chains, main chain) of the polymer. Literature data are compared with the conclusions obtained from the three-component thermodynamic model of side chain mesomorphic polymers. The effects of the different soft elements (main chain, spacer and p-alkyl or alkoxy chain) depend first of all on the length of the spacer and its interaction with the main chain. The thermal properties of the polymer can be well regulated by varying the different structural elements of the homo- and co-polymers. The glass transition temperature (T_g) of the polymer can be reduced by building O and N atoms into the main chain and/or by binding the side chains on 3rd, 4th, etc. atoms of the main chain. The T_g can be further reduced by increasing the length of the spacer. If the spacers are long enough, the layer type structures are favored, with p-alkoxy chains behaving also as a plasticizer of the main chain. The clearing point can be influenced by copolymerization of monomers with different hard cores. The three-component thermodynamic model of side-chain mesomorphic polymers well explains the effect of different structural elements on the structure and properties of these polymers.     

Hydration of amino acid side chains: dependence on secondary structure

Energy calculations have been used to study the hydration sitesaround the polar groups of serine, threonine and tyrosine sidechains. These hydration sites depend not only on the hybridizationof the polar group but also on the local secondary structure,the X₁ side chain torsion angle and the position of the hydroxylhydrogen atom. For tyrosine side chains, two solvent sites arefound approximately in the plane of the ring. Even for serineand threonine side chains only two minimum energy sites arefound in general of which one is in an expected position withinhydrogen bonding of the hydroxyl hydrogen atom (unless thisis blocked from interaction with solvent molecules by, for example,O_i–4 or O_i–3. The position of the second of thesesites depends not only on the position of the hydroxyl oxygenbut also on neighbouring main chain atoms to which it can alsohydrogen bond. There is good agreement with the solvent distributionsobtained from crystallographic data.     

Protein dynamics determined by backbone conformation and atom packing

To study the factors determining the collective motions in thermal, conformational fluctuations of a globular protein, molecular dynamics simulations were performed with a backbone model and an atomic-level model. In the backbone model, only the C alpha atoms were explicitly treated with two types of pairwise interactions assigned between the C alpha atoms; atom-packing interactions to take into account the effect of tight atom packing in the protein interior and chain-restoring interactions to maintain the backbone around the native conformation. A quasi-harmonic method was used to decompose the overall fluctuations into independent, collective modes. The modes assigned to large conformational fluctuations showed a good correlation between the backbone and atomic-level models. From this study, it was suggested that the collective modes were motions in which a protein fluctuates, keeping the tertiary structure around the native one and avoiding backbone overlap and, hence, rough aspects of the collective modes can be derived without details of the atomic interactions. The backbone model is useful in obtaining the overall backbone motions of a protein without heavy simulations, even though the simulation starts from a poorly determined conformation of experiments and in sampling main chain conformations, from which the side chain conformations may be predicted.      

Interaction of cyclodextrins with side chains of water soluble polymers: A simple model for biological molecular recognition and its utilization for stimuli-responsive systems

This article demonstrates that the interaction of cyclodextrins (CDs) with side chains of water soluble polymers is useful not only as simple models for biological molecular recognition but also as building blocks in nanotechnological applications. In the interaction of CDs with polymer side chains, the selectivity of CDs was enhanced by the steric effect of the polymer main chain and by interaction at multi-sites (i.e., collectivity). Utilizing the interaction of CDs with polymer side chains, stimuli-responsive systems were constructed from simple components.     

Self-Consistent Field Analysis of Molecular Bottle-Brushes with Primary and Secondary Side Chains: Induced Persistence Length and Lateral Thickness

Macromolecules may feature liquid crystalline behavior when the chain aspect ratio, that is the ratio between the chain persistence length and the cross-sectional thickness of its segments, is large. Scaling theory suggests that for molecular bottle-brushes under good solvent condition the induced persistence length does not depend on the chain architecture but only on the amount of segments in the side chains per unit length of the backbone. Numerical self-consistent field results are presented for macromolecular bottle-brushes with side chains of variable architecture attached at regular intervals along the backbone chain. We consider side chains (flexible “flagstaffs”), which feature one branch-point onto which secondary side chains (the “flag”) emanate. We varied the distance of this branch-point from the main chain as our tuning parameter, resembling the “raising of the flag.” For a given height of the flags, that is when the mass-distribution along a side chain is architecturally fixed, the induced persistence length is a function of the branching parameter (ratio between the length of the longest path and the total number of segments in the graft). We found that the induced persistence length and hence the chain aspect ratio, vary non-monotonically with the height of the flags. The lowest aspect ratio is found when the flag is raised to about a quarter of the full height of the flagstaff. The induced persistence length is independent of this height when upon bending the translocation of the side chains from compressed to expanded regions is artificially suppressed, which leads us to speculate that the non-monotonic behavior of aspect ratio is related to the efficiency of side chains to partly translocate themselves upon bending.     

The application of hydrogen bonding analysis in X-ray crystallography to help orientate asparagine, glutamine and histidine side chains

Protein X-ray crystallography produces an electron density mapthat rarely detects individual hydrogen atoms or distinguishesbetween carbon, nitrogen and oxygen atoms in the electron density.This makes it difficult to orientate the side chains of Asn,Gln and His, which appear symmetrical in the electron density;their orientation is usually judged on the basis of hydrogenbonding. Based on the observation that almost all buried donorsand acceptors are satisfied, we have developed a simple algorithmto compare the alternative conformations of these residues and,where possible, identify the most favourable. In a cross-sectionof protein structures we found a few side chains (15.0% of Asnand Gln and 9.9% of His) which would be more favourable in thealternative orientation. We have also found that this proportionrises slightly with worsening resolution.     

Quantitative calculation of the orientation angles of adsorbed polyamides nanofilms

Polyamides (PA) PA66, 610 and 612 were adsorbed as thin films on functionalized substrates. The conformational changes after adsorption are studied. New conformations due to the rotation of diamine/diacid planes were evidenced by infrared reflection absorption spectroscopy (IRRAS) and polarization modulation IRRAS (PM-IRRAS). The study of some infrared vibrators, which have a well defined transition moment direction with respect to the principal chain axis, allows us to access a qualitative information on the molecular orientation of PA chains. In this paper, we will discuss the possibility to obtain quantitative data on polyamide conformations on the basis of PM-IRRAS experiments. Values of orientation angles of diamine/diacid planes versus surface plane were determined. Similar angles are found in the four cases of gold, OH, NH₂ and COOH functionalized substrates, and for the three PA. Twist angle of about 20° is found between diamine and diacid planes. The chain orientation angles and conformations obtained do not depend on the substrate functionality and thus suggest that they are only the consequence of an adsorption effect.     

Secondary Structures of the Transmembrane Domain of SARS-CoV-2 Spike Protein in Detergent Micelles

Spike protein of SARS-CoV-2 contains a single-span transmembrane (TM) domain and plays roles in receptor binding, viral attachment and viral entry to the host cells. The TM domain of spike protein is critical for viral infectivity. Herein, the TM domain of spike protein of SARS-CoV-2 was reconstituted in detergent micelles and subjected to structural analysis using solution NMR spectroscopy. The results demonstrate that the TM domain of the protein forms a helical structure in detergent micelles. An unstructured linker is identified between the TM helix and heptapeptide repeat 2 region. The linker is due to the proline residue at position 1213. Side chains of the three tryptophan residues preceding to and within the TM helix important for the function of S-protein might adopt multiple conformations which may be critical for their function. The side chain of W1212 was shown to be exposed to solvent and the side chains of residues W1214 and W1217 are buried in micelles. Relaxation study shows that the TM helix is rigid in solution while several residues have exchanges. The secondary structure and dynamics of the TM domain in this study provide insights into the function of the TM domain of spike protein.     

Novel method to detect a motif of local structures in different protein conformations

In order to detect a motif of local structures in different protein conformations, the Delaunay tessellation is applied to protein structures represented by C(alpha) atoms only. By the Delaunay tessellation the interior space of the protein is uniquely divided up into Delaunay tetrahedra whose vertices are the C(alpha) atom positions. Some edges of the tetrahedra are virtual bonds connecting adjacent residues' C(alpha) atoms along the polypeptide chain and others indicate interactions between residues nearest neighbouring in space. The rules are proposed to assign a code, i.e., a string of digits, to each tetrahedron to characterize the local structure constructed by the vertex residues of one relevant tetrahedron and four surrounding it. Many sets comprised of the local structures with the same code are obtained from 293 proteins, each of which has relatively low sequence similarity with the others. The local structures in each set are similar enough to each other to represent a motif. Some of them are parts of secondary or supersecondary structures, and others are irregular, but definite structures. The method proposed here can find motifs of local structures in the Protein Data Bank much more easily and rapidly than other conventional methods, because they are represented by codes. The motifs detected in this method can provide more detailed information about specific interactions between residues in the local structures, because the edges of the Delaunay tetrahedra are regarded to express interactions between residues nearest neighbouring in space.      

The transfer matrix method for lattice proteins—an application with cooperative interactions

The transfer matrix method for generating lattice conformations of proteins is explained and applied to lattice proteins having high-level cooperativity to represent hydrophobic interactions. The main advantage of the method is the extremely efficient attrition-free generation and enumeration of compact conformations. We review the application of the method for the generation and complete, exact enumeration of all conformation for linear and cyclic chains in 2D on the square lattice and in 3D on the cubic lattice. We show for compact conformations that the growth of the chain in a piecewise way, cross-section by cross-section, is much more efficient than the traditional linear chain growth. We discuss an extension of the method by including information about the amino acid sequence. We develop a Zimm-Bragg [J Chem Phys 31 (1959) 476-85]-like theory of hydrophobic cluster formation by using the transfer matrix method. We show that the transfer matrix approach to the generation and averaging over chain conformations can be formulated as an algebraic problem. We show also how the transfer matrix method can be extended to off-lattice proteins.     

Structure refinement of α-poly(l-methionine): X-ray and conformational analysis

Using the agreement function between observed and calculated X-ray intensities of the fibre pattern as a constraint in the packing energy minimization, a structure is proposed for the α-helix of poly(L-methionine). This structure has a negative packing energy, is in good agreement with X-ray data, and consists of three different side chain conformations. A model for the packing of randomly up and down pointing polypeptide chains is proposed.     

Hydrogen bonds and salt bridges across protein-protein interfaces

To understand further, and to utilize, the interactions across protein- protein interfaces, we carried out an analysis of the hydrogen bonds and of the salt bridges in a collection of 319 non-redundant protein- protein interfaces derived from high-quality X-ray structures. We found that the geometry of the hydrogen bonds across protein interfaces is generally less optimal and has a wider distribution than typically observed within the chains. This difference originates from the more hydrophilic side chains buried in the binding interface than in the folded monomer interior. Protein folding differs from protein binding. Whereas in folding practically all degrees of freedom are available to the chain to attain its optimal configuration, this is not the case for rigid binding, where the protein molecules are already folded, with only six degrees of translational and rotational freedom available to the chains to achieve their most favorable bound configuration. These constraints enforce many polar/charged residues buried in the interface to form weak hydrogen bonds with protein atoms, rather than strongly hydrogen bonding to the solvent. Since interfacial hydrogen bonds are weaker than the intra-chain ones to compete with the binding of water, more water molecules are involved in bridging hydrogen bond networks across the protein interface than in the protein interior. Interfacial water molecules both mediate non-complementary donor-donor or acceptor- acceptor pairs, and connect non-optimally oriented donor-acceptor pairs. These differences between the interfacial hydrogen bonding patterns and the intra-chain ones further substantiate the notion that protein complexes formed by rigid binding may be far away from the global minimum conformations. Moreover, we summarize the pattern of charge complementarity and of the conservation of hydrogen bond network across binding interfaces. We further illustrate the utility of this study in understanding the specificity of protein-protein associations, and hence in docking prediction and molecular (inhibitor) design.      

Orientation-dependent coarse-grained potentials derived by statistical analysis of molecular structural databases

We present results obtained for anisotropic potentials for protein simulations extracted from the continually growing databases of protein structures. This work is based on the assumption that the detailed information on molecular conformations can be used to derive statistical (a.k.a. ‘knowledge-based’) potentials that can describe on a coarse-grained level the side chain-side chain interactions in peptides and proteins. The complexity of inter-residue interactions is reflected in a high degree of orientational anisotropy for the twenty amino acids. By including in this coarse-grained interaction model the possibility of quantifying the backbone-backbone and backbone-side chain interactions, important improvements are obtained in characterizing the native protein states. Results obtained from tests that involve the identification of native-like conformations from large sets of decoy structures are presented. The method for deriving orientation-dependent statistical potentials is also applied to obtain water-water interactions. Monte Carlo simulations using the new coarse-grained water model show that the locations of the minima and maxima of the oxygen-oxygen radial distribution function correspond well with experimental measurements.     

On Surface Modification of Polymeric Biomaterials

Surface modification with hydrophilic polymers has been beneficial in improving blood compatibility of biomaterials. Formation of dense and tightly-bonded surface layers may prevent plasma protein adsorption owing to steric repulsion. General conditions for formation of layers, protecting blood components from direct contacts with the surface, are discussed. It seems to be necessary to ensure a delicate balance between adsorption energy of the attached chains and their length. The crucial point is to get a high grafting density which is more influential than high chain length. Length should be calibrated to the size of protein molecules to meet both effective repulsion and high density of the protecting chains and to avoid chain displacement by plasma proteins.