Conservation and production of solvent accessibility in protein families pdf

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conservation and production of solvent accessibility in protein families pdf

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Protein structure prediction is the inference of the three-dimensional structure of a protein from its amino acid sequence—that is, the prediction of its secondary and tertiary structure from primary structure. Structure prediction is different from the inverse problem of protein design. Protein structure prediction is one of the most important goals pursued by computational biology ; and it is important in medicine for example, in drug design and biotechnology for example, in the design of novel enzymes.

ResBoost: characterizing and predicting catalytic residues in enzymes

Protein thermal stability is an important factor considered in medical and industrial applications. Many structural characteristics related to protein thermal stability have been elucidated, and increasing salt bridges is considered as one of the most efficient strategies to increase protein thermal stability. However, the accurate simulation of salt bridges remains difficult. In this study, a novel method for salt-bridge design was proposed based on the statistical analysis of 10, surface salt bridges on 6, X-ray protein structures. Pairing preferences generalized from statistical analysis were used to construct a salt-bridge pair index and utilized in a weighted electrostatic attraction model to find the effective pairings for designing salt bridges.

For each protein of known 3-D structure from the Protein Data Bank PDB , the database has a multiple sequence alignment of all available homologues and a sequence profile characteristic of the family. The list of homologues is the result of a database search in SwissProt using a position-weighted dynamic programming method for sequence profile alignment MaxHom. The database is updated frequently. The listed homologues are very likely to have the same 3-D structure as the PDB protein to which they have been aligned. HSSP h omology-derived s tructure s of p roteins is a derived database merging information from 3-D structures and 1-D sequences of proteins. The added value in the database stems from the evolutionary observation that protein sequences can vary considerably while maintaining the same overall 3-D structure. One can therefore group sequence-similar proteins into families of structural homologues.

Metrics details. Identifying the catalytic residues in enzymes can aid in understanding the molecular basis of an enzyme's function and has significant implications for designing new drugs, identifying genetic disorders, and engineering proteins with novel functions. Since experimentally determining catalytic sites is expensive, better computational methods for identifying catalytic residues are needed. We propose ResBoost, a new computational method to learn characteristics of catalytic residues. The method effectively selects and combines rules of thumb into a simple, easily interpretable logical expression that can be used for prediction.

The Dundee Resource for Sequence Analysis and Structure Prediction

Either your web browser doesn't support Javascript or it is currently turned off. In the latter case, please turn on Javascript support in your web browser and reload this page. In current protein X-ray structures, however, the SRD is not resolved and assumed to be disordered. Here, we combined secondary structure annotation and domain threading followed by long molecular dynamics MD simulations and showed that the SRD possesses well-defined secondary structure elements. The concept of conservation of secondary structure elements SSEs Rost, in families can be used to identify proteins only distantly related in sequence, which may, however, still share a higher degree of conservation of SSEs. However, repeats 1, 3, and 4 deviate from the canonical 33 amino acid repeat unit.

Structural modeling of the N-terminal signal–receiving domain of IκBα

For each protein of known 3-D structure from the Protein Data Bank PDB , the database has a multiple sequence alignment of all available homologues and a sequence profile characteristic of the family. The list of homologues is the result of a database search in SwissProt using a position-weighted dynamic programming method for sequence profile alignment MaxHom. The database is updated frequently. The listed homologues are very likely to have the same 3-D structure as the PDB protein to which they have been aligned. HSSP h omology-derived s tructure s of p roteins is a derived database merging information from 3-D structures and 1-D sequences of proteins.

A cationic terminal extension or tail is a common feature of many DNA-binding proteins. Enhanced conformational sampling of these representative peptides using accelerated molecular dynamic simulations supported by circular dichroism spectroscopy and nuclear magnetic resonance studies demonstrates the role of frequent and interspersed prolines in augmenting conformational heterogeneity of the peptide backbone. Analysis of circular variance of backbone dihedral angles indicates alternating regions of relative rigidity and flexibility along the peptide sequence due to prolines. Preferred placement of lysines in the regions of higher backbone flexibility might improve DNA-binding by conformational selection.

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Protein structure prediction

Identifying the catalytic residues in enzymes can aid in understanding the molecular basis of an enzyme's function and has significant implications for designing new drugs, identifying genetic disorders, and engineering proteins with novel functions. Since experimentally determining catalytic sites is expensive, better computational methods for identifying catalytic residues are needed. We propose ResBoost, a new computational method to learn characteristics of catalytic residues. The method effectively selects and combines rules of thumb into a simple, easily interpretable logical expression that can be used for prediction. We formally define the rules of thumb that are often used to narrow the list of candidate residues, including residue evolutionary conservation, 3D clustering, solvent accessibility, and hydrophilicity. ResBoost builds on two methods from machine learning, the AdaBoost algorithm and Alternating Decision Trees, and provides precise control over the inherent trade-off between sensitivity and specificity.

DRSASP resources are available through conventional web interfaces and APIs but are also integrated into the Jalview sequence analysis workbench, which enables the composition of multitool interactive workflows. New resources are being developed that enable the analysis of population genetic data in evolutionary and 3D structural contexts. Existing resources are actively developed to exploit new technologies and maintain parity with evolving web standards. The flood of sequence data across all species continues to grow in rate and volume. While there are many challenges in managing these large datasets, the major hurdle is to use the raw sequence data to inform our knowledge and understanding of biological systems. In order to achieve this goal, accurate and reliable software tools are required to make structural and functional predictions from the sequence data.


Abstract Currently, the prediction of three‐dimensional (3D) protein structure from sequence alone is an exceedingly difficult task. As an intermediate step.


Background

SDR enzymes have critical roles in lipid, amino acid, carbohydrate, cofactor, hormone and xenobiotic metabolism as well as in redox sensor mechanisms. The conservation of this element and an active site, often with an Asn-Ser-Tyr-Lys tetrad, provides a platform for enzymatic activities encompassing several EC classes, including oxidoreductases, epimerases and lyases. The common mechanism is an underlying hydride and proton transfer involving the nicotinamide and typically an active site tyrosine residue, whereas substrate specificity is determined by a variable C-terminal segment. Relationships exist with bacterial haloalcohol dehalogenases, which lack cofactor binding but have the active site architecture, emphasizing the versatility of the basic fold in also generating hydride transfer-independent lyases. The conserved fold and nucleotide binding emphasize the role of SDRs as scaffolds for an NAD P H redox sensor system, of importance to control metabolic routes, transcription and signalling.

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