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Register a new userProperties of contact matrices induced by pairwise interactions in proteins
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The total conformational energy is assumed to consist of pairwise interaction energies between atoms or residues, each of which is expressed as a product of a conformation-dependent function (an element of a contact matrix, C-matrix) and a sequence-dependent energy parameter (an element of a contact energy matrix, E-matrix). Such pairwise interactions in proteins force native C-matrices to be in a relationship as if the interactions are a Go-like potential [N. Go, Annu. Rev. Biophys. Bioeng. 12. 183 (1983)] for the native C-matrix, because the lowest bound of the total energy function is equal to the total energy of the native conformation interacting in a Go-like pairwise potential. This relationship between C- and E-matrices corresponds to (a) a parallel relationship between the eigenvectors of the C- and E-matrices and a linear relationship between their eigenvalues, and (b) a parallel relationship between a contact number vector and the principal eigenvectors of the C- and E-matrices; the E-matrix is expanded in a series of eigenspaces with an additional constant term, which corresponds to a threshold of contact energy that approximately separates native contacts from non-native ones. These relationships are confirmed in 182 representatives from each family of the SCOP database by examining inner products between the principal eigenvector of the C-matrix, that of the E-matrix evaluated with a statistical contact potential, and a contact number vector. In addition, the spectral representation of C- and E-matrices reveals that pairwise residue-residue interactions, which depends only on the types of interacting amino acids but not on other residues in a protein, are insufficient and other interactions including residue connectivities and steric hindrance are needed to make native structures the unique lowest energy conformations.
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We analytically derive the lower bound of the total conformational energy of a protein structure by assuming that the total conformational energy is well approximated by the sum of sequence-dependent pairwise contact energies. The condition for the native structure achieving the lower bound leads to the contact energy matrix that is a scalar multiple of the native contact matrix, i.e., the so-called Go potential. We also derive spectral relations between contact matrix and energy matrix, and approximations related to one-dimensional protein structures. Implications for protein structure prediction are discussed.
Molecular dynamics studies within a coarse-grained structure based model were used on two similar proteins belonging to the transcarbamylase family to probe the effects in the native structure of a knot. The first protein, N-acetylornithine transcarbamylase, contains no knot whereas human ormithine transcarbamylase contains a trefoil knot located deep within the sequence. In addition, we also analyzed a modified transferase with the knot removed by the appropriate change of a knot-making crossing of the protein chain. The studies of thermally- and mechanically-induced unfolding processes suggest a larger intrinsic stability of the protein with the knot.
Stochastic simulations of coarse-grained protein models are used to investigate the propensity to form knots in early stages of protein folding. The study is carried out comparatively for two homologous carbamoyltransferases, a natively-knotted N-acetylornithine carbamoyltransferase (AOTCase) and an unknotted ornithine carbamoyltransferase (OTCase). In addition, two different sets of pairwise amino acid interactions are considered: one promoting exclusively native interactions, and the other additionally including non-native quasi-chemical and electrostatic interactions. With the former model neither protein show a propensity to form knots. With the additional non-native interactions, knotting propensity remains negligible for the natively-unknotted OTCase while for AOTCase it is much enhanced. Analysis of the trajectories suggests that the different entanglement of the two transcarbamylases follows from the tendency of the C-terminal to point away from (for OTCase) or approach and eventually thread (for AOTCase) other regions of partly-folded protein. The analysis of the OTCase/AOTCase pair clarifies that natively-knotted proteins can spontaneously knot during early folding stages and that non-native sequence-dependent interactions are important for promoting and disfavoring early knotting events.
Computational elucidation of membrane protein (MP) structures is challenging partially due to lack of sufficient solved structures for homology modeling. Here we describe a high-throughput deep transfer learning method that first predicts MP contacts by learning from non-membrane proteins (non-MPs) and then predicting three-dimensional structure models using the predicted contacts as distance restraints. Tested on 510 non-redundant MPs, our method has contact prediction accuracy at least 0.18 better than existing methods, predicts correct folds for 218 MPs (TMscore at least 0.6), and generates three-dimensional models with RMSD less than 4 Angstrom and 5 Angstrom for 57 and 108 MPs, respectively. A rigorous blind test in the continuous automated model evaluation (CAMEO) project shows that our method predicted high-resolution three-dimensional models for two recent test MPs of 210 residues with RMSD close to 2 Angstrom. We estimated that our method could predict correct folds for between 1,345 and 1,871 reviewed human multi-pass MPs including a few hundred new folds, which shall facilitate the discovery of drugs targeting at membrane proteins.
We perform theoretical studies of stretching of 20 proteins with knots within a coarse grained model. The knots ends are found to jump to well defined sequential locations that are associated with sharp turns whereas in homopolymers they diffuse around and eventually slide off. The waiting times of the jumps are increasingly stochastic as the temperature is raised. Larger knots do not return to their native locations when a protein is released after stretching.
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