A new type of secondary structure: mobile conformation of polypeptide chain. Data bank for protein structures

As a result of statistical analysis of Protein Data Bank a new type of secondary structure was found in globular proteins. It is mobile (M) conformation, characterised by noncooperative hydration and the increased dynamical properties of the chain. Percentage distribution of amino acid residues between the main secondary structure types is 42.7% for alpha-helix, 19.6% for beta-structure and 19.1% for M-conformation. The most frequently occurring amino acids for M-conformation are proline, cysteine and serine. Fragments of mobile conformation seem to play a major part in local and domain dynamics of protein globule.     

Third type of secondary structure: noncooperative mobile conformation. Protein Data Bank analysis

Analysis of 68 proteins from Protein Data Bank disclosed a new widely spread type of the secondary structure that is designated as mobile (M-) conformation. Helical parameters of M-conformation are close to the poly-L-proline II type helix. Its occurrence in globular proteins approximates that of the beta-sheet. The angles corresponding to the position of the M-conformation maximum in distribution of amino acid residues on a conformational map are phi: -65 degrees, psi: 140 degrees. Unique features and high occurrence in proteins make it possible to distinguish the M-conformation as an independent third type of the secondary structure in globular proteins, that should be included in the present classification.     

Conformational preference functions for predicting helices in membrane proteins

A suite of FORTRAN programs, PREF, is described for calculating preference functions from the data base of known protein structures and for comparing smoothed profiles of sequence-dependent preferences in proteins of unknown structure. Amino acid preferences for a secondary structure are considered as functions of a sequence environment. Sequence environment of amino acid residue in a protein is defined as an average over some physical, chemical, or statistical property of its primary structure neighbors. The frequency distribution of sequence environments in the data base of soluble protein structures is approximately normal for each amino acid type of known secondary conformation. An analytical expression for the dependence of preferences on sequence environment is obtained after each frequency distribution is replaced by corresponding Gaussian function. The preference for the α-helical conformation increases for each amino acid type with the increase of sequence environment of buried solvent-accessible surface areas. We show that a set of preference functions based on buried surface area is useful for predicting folding motifs in α-class proteins and in integral membrane proteins. The prediction accuracy for helical residues is 79% for 5 integral membrane proteins and 74% for 11 α-class soluble proteins. Most residues found in transmembrane segments of membrane proteins with known α-helical structure are predicted to be indeed in the helical conformation because of very high middle helix preferences. Both extramembrane and transmembrane helices in the photosynthetic reaction center M and L subunits are correctly predicted. We point out in the discussion that our method of conformational preference functions can identify what physical properties of the amino acids are important in the formation of particular secondary structure elements. © 1993 John Wiley & Sons, Inc.     

A study of the preferred environment of amino acid residues in globular proteins

In the native folded conformation of a globular protein, amino acid residues distant along the polypeptide chain come together to form the compact structure. This spatial structure is such that most of the polar residues are on the surface and have contact with the solvent medium and the nonpolar residues buried in the interior which have contact with similar nonpolar side chains. This cooperativity and mutual interaction among the randomly aligned amino acid residues suggest that each type of residue may prefer to have a specific environment. To gain more insight into this aspect of residue-residue cooperativity, a detailed analysis of the preferred environment associated with each of the 20 different amino acid residues in a number of protein crystals has been carried out. The variation of nonpolar nature computed for different sizes of spheres shows that the spatial region between radii of 6 and 8 Å is more favored for hydrophobic interactions and indicates that the influence of each residue over the surrounding medium extends predominantly up to a distance of 8 Å. The analysis of the surrounding amino acid residues associated with each type of residue shows that there is a definite tendency for each type of residue to have association with specific residues. The variation in environment is found even within the polar group as well as in the nonpolar group of residues. The surrounding residues associated with isoleucine, leucine, and valine are purely nonpolar. Proline, a nonpolar residue, is often surrounded by polar residues. The surrounding nonpolar nature of the tryptophan and tyrosine residues implies that even a single polar atom in a nonpolar side chain is sufficient to reduce their hydrophobic environment. There exists a high degree of mutual residue-residue cooperativity between the pairs glutamic acid-lysine, methionine-arginine, asparagine-tryptophan, and glutamine-proline, and the mutual residue-residue noncooperativity is high for the pairs methionine-aspartic acid, cysteine-glutamic acid, histidine-glutamine, and leucine-asparagine. The formation of secondary and tertiary structures is discussed in terms of the preferred environment and mutual cooperativity among various types of amino acid residues.     

The interrelationships of side-chain and main-chain conformations in proteins

The accurate determination of a large number of protein structures by X-ray crystallography makes it possible to conduct a reliable statistical analysis of the distribution of the main-chain and side-chain conformational angles, how these are dependent on residue type, adjacent residue in the sequence, secondary structure, residue-residue interactions and location at the polypeptide chain termini. The interrelationship between the main-chain (phi, psi) and side-chain (chi 1) torsion angles leads to a classification of amino acid residues that simplify the folding alphabet considerably and can be a guide to the design of new proteins or mutational studies. Analyses of residues occurring with disallowed main-chain conformation or with multiple conformations shed some light on why some residues are less favoured in thermophiles.     

Distribution of amino acid residues and residue-residue contacts in molecular chaperones.

The amino acid distribution and residue-residue contacts in molecular chaperones are different when compared to normal globular proteins. The study of molecular chaperones reveals a different surrounding environment to exist for the residues Cys, Trp, and His which may play an important role in determining the chaperone structures. Unlike globular proteins, it has been observed that a one-to-one correspondence between the amino acid distribution in a sequence and the structures of molecular chaperones. The preference of amino acid residues surrounding all 20 types of residues in secondary structures and their accessible surface areas have been analysed.     

Structural principles of the globular organization of protein chains. A stereochemical theory of globular protein secondary structure

The paper reveals the types of amino acid sequences of polypeptide chain regions of globular protein which form a regular (α or β) or irregular conformation in the native globule. The study was made taking into account general “architectural” principles of packing of polypeptide chains in globular proteins and considering the interactions of proteins with water molecules. An a priori theory is developed which permits the identification, in good agreement with experiment, of α-helical and β-structural regions in globular proteins from their primary structure.     

A computer model to dynamically simulate protein folding: studies with crambin

The current work describes a simplified representation of protein structure with uses in the simulation of protein folding. The model assumes that a protein can be represented by a freely rotating rigid chain with a single atom approximating the effect of each side chain. Potentials describing the attraction or repulsion between different types of amino acids are determined directly from the distribution of amino acids in the database of known protein structures. The optimization technique of simulated annealing has been used to dynamically sample the conformations available to this simple model, allowing the protein to evolve from an extended, random coil into a compact globular structure. Many characteristics expected of true proteins, such as the sequence-dependent formation of secondary structure, the partitioning of hydrophobic residues, and specific disulfide pairing, are reproduced by the simulation, suggesting the model may accurately simulate the folding process.     

Distribution of amino acid residues in the primary protein structure

The amino acid composition and sequence in primary structure of 180 proteins have been studied. It is shown that the distribution of amino acid residues is near to a random one, i.e. it is determined by the amino acid composition. The ratio between statistical and unique character of protein primary structures has been discussed. The amino acid sequence is suggested to be unique in fibrous proteins. In contrast the amino acid sequence in globular proteins is a statistical one. The statistical character of amino acids distribution in globular proteins explains the possibility of sensible text generation under the frame shift mutations, deletions and insertions.     

Spatial constraints and group behaviour in globular proteins

A comparative analysis has been attempted on the spatial placement of amino acid residues derived from radial, ellipsoidal and exposure arrangements. The group behaviour of residues and their restraining influence in protein folding have been brought out. A study is also made on the geometry of proteins, the exposure arrangement of residues and the spatial distribution of the physical properties of the residues in globular proteins. It has been shown that the group constraints along with the information on the shape of the globular proteins would be highly useful in assigning the spatial and exposure arrangements of residues in globular proteins.     

Evaluation of short-range interactions as secondary structure energies for protein fold and sequence recognition.

Short-range interactions for secondary structures of proteins are evaluated as potentials of mean force from the observed frequencies of secondary structures in known protein structures which are assumed to have an equilibrium distribution with the Boltzmann factor of secondary structure energies. A secondary conformation at each residue position in a protein is described by a tripeptide, including one nearest neighbor on each side. The secondary structure potentials are approximated as additive contributions from neighboring residues along the sequence. These are part of an empirical potential to provide a crude estimate of protein conformational energy at a residue level. Unlike previous works, interactions are decoupled into intrinsic potentials of residues, potentials of backbone-backbone interactions, and of side chain-backbone interactions. Also interactions are decoupled into one-body, two-body, and higher order interactions between peptide backbone and side chain and between backbones. These decouplings are essential to correctly evaluate the total secondary structure energy of a protein structure without overcounting interactions. Each interaction potential is evaluated separately by taking account of the correlation in the amino acid order of protein sequences. Interactions among side chains are neglected, because of the relatively limited number of protein structures. Proteins 1999;36:347-356. Published 1999 Wiley-Liss, Inc.     

A new approach for the calculation of the energy of van der Waals interactions in macromolecules of globular proteins

Van der Waals interaction energy in globular proteins is presented by the interaction energies between regions of protein spatial structure with homogenous medium density distribution. We introduce a notion of the local medium permittivity as a function of absorptance of molecular groups with particular conformation. Proposed theory avoids shortcomings which are typical for the calculations on the basis of the pairwise additive approximation. The approach takes into account local peculiarities of protein spatial structure and physical-chemical characteristics of amino acid residues and molecular groups.     

Protein packing: dependence on protein size, secondary structure and amino acid composition

We have used the occluded surface algorithm to estimate the packing of both buried and exposed amino acid residues in protein structures. This method works equally well for buried residues and solvent-exposed residues in contrast to the commonly used Voronoi method that works directly only on buried residues. The atomic packing of individual globular proteins may vary significantly from the average packing of a large data set of globular proteins. Here, we demonstrate that these variations in protein packing are due to a complex combination of protein size, secondary structure composition and amino acid composition. Differences in protein packing are conserved in protein families of similar structure despite significant sequence differences. This conclusion indicates that quality assessments of packing in protein structures should include a consideration of various parameters including the packing of known homologous proteins. Also, modeling of protein structures based on homologous templates should take into account the packing of the template protein structure.     

Identification of amino acids involved in protein structural uniqueness: implication for de novo protein design

Structural uniqueness is characteristic of native proteins and is essential to express their biological functions. The major factors that bring about the uniqueness are specific interactions between hydrophobic residues and their unique packing in the protein core. To find the origin of the uniqueness in their amino acid sequences, we analyzed the distribution of the side chain rotational isomers (rotamers) of hydrophobic amino acids in protein tertiary structures and derived deltaS(contact), the conformational-entropy changes of side chains by residue-residue contacts in each secondary structure. The deltaS(contact) values indicate distinct tendencies of the residue pairs to restrict side chain conformation by inter-residue contacts. Of the hydrophobic residues in alpha-helices, aliphatic residues (Leu, Val, Ile) strongly restrict the side chain conformations of each other. In beta-sheets, Met is most strongly restricted by contact with Ile, whereas Leu, Val and Ile are less affected by other residues in contact than those in alpha-helices. In designed and native protein variants, deltaS(contact) was found to correlate with the folding-unfolding cooperativity. Thus, it can be used as a specificity parameter for designing artificial proteins with a unique structure.     

The effect of distribution of adjacent amino acids in primary structures on the possibility of mutation substitutions in globular proteins

Frequency distributions of adjacent ARs in the primary structures of 320 globular proteins out of different superfamilies were investigated. ARs of every type were compared with the occurrence frequencies of 20 canonic residues at the distances of 1-20 residues according to their primary structure. Amino acid residues were found to be divided into groups of interchangeable residues in the course of globular protein evolution according to the distribution kinds and in terms of Euclidean distances. The use of pancreatic RNases of mammals showed that the approximate preservation of frequency adjacent (1-4 residues according to their primary structure) and characteristics in 5-15 residues mid-interactions may be used in studying the supposed amino acid substitutions in globular protein.     

To be folded or to be unfolded?

The lack of ordered structure in “natively unfolded” proteins raises a general question: Are there intrinsic properties of amino acid residues that are responsible for the absence of fixed structure at physiological conditions? In this article, we demonstrate that the competence of a protein to be folded or to be unfolded may be determined by the property of amino acid residues to form a sufficient number of contacts in a globular state. The expected average number of contacts per residue calculated from the amino acid sequence alone (using the average number of contacts for 20 amino acid residues in globular proteins) can be used as one of the simple indicators of natively unfolded proteins. The prediction accuracy for the sets of 80 folded and 90 natively unfolded proteins reaches 89% if the expected average number of contacts is used as a parameter and 83% in the case of hydrophobicity. An optimal set of artificial parameters for 20 amino acid residues obtained by Monte Carlo algorithm to maximally separate the sets of 90 natively unfolded and 80 folded proteins demonstrates the upper limit for prediction accuracy, which is 95%.     

Identification of conserved residue patterns in small beta-barrel proteins

Our abilities to predict three-dimensional conformation of a polypeptide, given its amino acid sequence, remain limited despite advances in structure analysis. Analysis of structures and sequences of protein families with similar secondary structural elements, but varying topologies, might help in addressing this problem. We have studied the small beta-barrel class of proteins characterized by four strands (n = 4) and a shear number of 8 (S = 8) to understand the principles of barrel formation. Multiple alignments of the various protein sequences were generated for the analysis. Positional entropy, as a measure of residue conservation, indicated conservation of non-polar residues at the core positions. The presence of a type II beta-turn among the various barrel proteins considered was another strikingly invariant feature. A conserved glycyl-aspartyl dipeptide at the beta-turn appeared to be important in guiding the protein sequence into the barrel fold. Molecular dynamics simulations of the type II beta-turn peptide suggested that aspartate is a key residue in the folding of the protein sequence into the barrel. Our study suggests that the conserved type II beta-turn and the non-polar residues in the barrel core are crucial for the folding of the protein's primary sequence into the beta-barrel conformation.     

A New Approach for the Calculation of the Energy of van der Waals Interactions in Macromolecules of Globular Proteins

Abstract

Van der Waals interaction energy in globular proteins is presented by the interaction energies between regions of protein spatial structure with homogenous medium density distribution. We introduce a notion of the local medium permittivity as a function of absorptance of molecular groups with particular conformation. Proposed theory avoids shortcomings which are typical for the calculations on the basis of the pairwise additive approximation. The approach takes into account local peculiarities of protein spatial structure and physical-chemical characteristics of amino acid residues and molecular groups.     

Conformational similarity among amino acid residues: 1. Analysis of protein crystal structure data

The probability distribution in the (?,ψ)-plane obtained for each amino acid residue from cyrstal structure data of globular proteins is compared. This has shown amino acid residues. Pro and Gly to be conformationally unique. Conformational similarity in the (?,ψ)-plane of amino acid reced does not necessarily mean that they will have the same chemical or biochemical properties or similar secondary structures. A set of amino acid residues are given which can adopt the conformations of other amino acid residues without much difficulty either in the whole (?,ψ)-plane or in regions, where the observed conformations are maximum.