Dosztanyi

PDB_TM is a database for transmembrane proteins with known structures. It aims to collect all transmembrane proteins that are deposited in the protein structure database (PDB) and to determine their membrane-spanning regions. These assignments are based on the TMDET algorithm, which uses only structural information to locate the most likely position of the lipid bilayer and to distinguish between transmembrane and globular proteins. This algorithm was applied to all PDB entries and the results were collected in the PDB_TM database...

The structure of integral membrane proteins is determined in the absence of the lipid bilayer; consequently the membrane localization of the protein is usually not specified in the corresponding PDB file. Recently, we have developed a new method called TMDET which determines the most possible localization of the membrane relative to the protein structure, and gives the annotation of the membrane embedded parts of the sequence. The entire Protein Data Bank has been scanned by the new TMDET algorithm resulting in the database of structurally determined transmembrane proteins (PDB_TM)...

MOTIVATION: Integral membrane proteins play important roles in living cells. Although these proteins are estimated to constitute 25% of proteins at a genomic scale, the Protein Data Bank (PDB) contains only a few hundred membrane proteins due to the difficulties with experimental techniques. The presence of transmembrane proteins in the structure data bank, however, is quite invisible, as the annotation of these entries is rather poor. Even if a protein is identified as a transmembrane one, the possible location of the lipid bilayer is not indicated in the PDB because these proteins are crystallized without their natural lipid bilayer, and currently no method is publicly available to detect the possible membrane plane using the atomic coordinates of membrane proteins...

Proteins are heteropolymers with evolutionary selected native sequences of residues. These native sequences code for unique and stable 3D structures indispensable for biochemical activity and for proteolysis resistance, the latter which guarantees an appropriate lifetime for the protein in the protease rich cellular environment. Cross-links between residues close in space but far in the primary structure are required to maintain the folded structure of proteins. Some of these cross-links are covalent, most frequently disulfide bonds, but the majority of the cross-links are sets of cooperative noncovalent long-range interactions...

We describe several algorithms and public servers that were developed to analyze and predict various features of protein structures. These servers provide information about the covalent state of cysteine (CYSREDOX), as well as about residues involved in non-covalent cross links that play an important role in the structural stability of proteins (SCIDE and SCPRED). We also discuss methods and servers developed to identify helical transmembrane proteins from large databases and rough genomic data, including two of the most popular transmembrane prediction methods, DAS and HMMTOP...

SUMMARY: SCide is a program to identify stabilization centers from known protein structures. These are residues involved in cooperative long-range contacts, which can be formed between various regions of a single polypeptide chain, or they can belong to different peptides or polypeptides in a complex. The server takes a PDB file as an input, and the result is presented in graphical or text format. AVAILABILITY: SCide is available on the web at https://www.enzim.hu/scide...

MOTIVATION: We propose a general method for deriving amino acid substitution matrices from low resolution force fields. Unlike current popular methods, the approach does not rely on evolutionary arguments or alignment of sequences or structures. Instead, residues are computationally mutated and their contribution to the total energy/score is collected. The average of these values over each position within a set of proteins results in a substitution matrix. RESULTS: Example substitution matrices have been calculated from force fields based on different philosophies and their performance compared with conventional substitution matrices...

Proteins must be stable to accomplish their biological function and to avoid enzymatic degradation. Constitutive proteolysis, however, is the main source of free amino acids used for de novo protein synthesis. In this paper the delicate balance of protein stability and degradability is discussed in the context of function of major histocompatibility complex (MHC) encoded protein. Classical MHC proteins are single-use peptide transporters that carry proteolytic degradation products to the cell surface for presenting them to T cells...

Most human adults carry the Epstein-Barr virus (EBV) and develop immunological memory against the structural and the virus-encoded cellular proteins. The EBV nuclear antigen 6 (EBNA6) elicits cytotoxic T cell responses and it also maintains a persistent antibody response. The majority of sera from EBV-seropositive individuals reacts with a synthetic peptide, p63, comprising 21 amino acids of a repetitive region of EBNA6. CD4(+) T lymphocytes, with specificity for p63, could be recalled from the T cell repertoire of EBV carriers that expressed certain HLA-DR allotypes which were identified as good binders of p63 by an in vitro flow cytometric assay...

Methods are presented to locate residues, stabilization center elements, which are expected to stabilize protein structures by preventing their decay with their cooperative long range interactions. Artificial neural network-based algorithms were developed to predict these residues from the primary structure of single proteins and from the amino acid sequences of homologous proteins. The prediction accuracy using only single sequence information is 65%, but the incorporation of evolutionary information in the form of multiple alignments and conservation scores raises the efficiency by 3%...

MOTIVATION: Secondary structure predictions based on the properties of individual residues, and sometimes on local interactions, usually fail to exceed 65% efficiency. Therefore, non-local, long-range interactions seem to be a significant cause of this limitation. RESULTS: In this paper, we apply approaches to localize highly interacting residues and clusters of residues involved in multiple non-local interactions, and test various secondary structure predictions on this separate subset to assess the effect of long-range interactions on the prediction efficiencies...

The free energy difference between folded and unfolded state is about the same for most proteins and it is not more than the energy of a few noncovalent interactions. In addition to the numerous noncovalent interactions, some proteins contain one or more disulfide bonds, which, as covalent crosslinks, significantly stabilize their tertiary structure. Correlation between the presence of disulfide bond(s), and the number noncovalent interresidue interactions of various kinds is analyzed here. The number of interactions per residue is almost the same for all protein...