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ePub Bioinformatic analysis of Beta barrel porins: Structural Analysis of Outer Membrane Beta-stranded Porins using Temperature Factor download

by Abhishek Kumar

ePub Bioinformatic analysis of Beta barrel porins: Structural Analysis of Outer Membrane Beta-stranded Porins using Temperature Factor download
Author:
Abhishek Kumar
ISBN13:
978-3639244502
ISBN:
3639244508
Language:
Publisher:
VDM Verlag Dr. Müller (March 14, 2010)
Category:
Subcategory:
Biological Sciences
ePub file:
1410 kb
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1878 kb
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4.5
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using temperature factor. Abhishek Kumar & Sankaran Krishnaswamy Structures of six porins (four 16 stranded beta barrel porins and two 8 stranded beta barrel porins) were taken from the PDB fo. .

using temperature factor. Abhishek Kumar & Sankaran Krishnaswamy. School of Biotechnology, Madurai Kamaraj University, Madurai, Tamilnadu, India. Outer membrane beta-stranded porins form a diverse and complex set of proteins which allow passage of molecules across the membrane interface have been analyzed here from a biophysical and structural perspective using atomic temperature factors or B-factors. Structures of six porins (four 16 stranded beta barrel porins and two 8 stranded beta barrel porins) were taken from the PDB for the analysis based on resolution (better than . Å) and R-factor (< . 3).

Outer membrane beta-stranded porins form a diverse and complex set of proteins which allow passage of molecules .

Outer membrane beta-stranded porins form a diverse and complex set of proteins which allow passage of molecules across the membrane interface have been analyzed here from a biophysical and structural perspective using atomic temperature factors or B-factors. The residue distribution and mobility distribution was found to be characteristic of each of the porins.

A beta barrel is a beta-sheet composed of tandem repeats that twists and coils to form a closed toroidal structure in which the first strand is bonded to the last strand (hydrogen bond). Beta-strands in many beta-barrels are arranged in an antiparallel fashion. Beta barrel structures are named for resemblance to the barrels used to contain liquids. Most of them are water-soluble proteins and frequently bind hydrophobic ligands in the barrel center, as in lipocalins

Thesis: Structural Analysis of Outer Membrane Beta-stranded Porins using. Structures of six porins (Four 16-stranded beta barrel porins and two 8-stranded beta barrel porins) were taken from the PDB for the analysis based on resolution and R-factor.

Thesis: Structural Analysis of Outer Membrane Beta-stranded Porins using. Programs and scripts were written for extracting the temperature factors for the beta strands, loops and turns so that the analysis could be done for different atom-types and residue-types.

The analysis on the amino acid sequences of transmembrane beta barrel proteins (TMBs) provides deep insights about their structure and function. We found that the occurrence of Ser, Asn and Gln is significantly higher in TMBs than globular proteins, which might be due to their importance in the formation of β-barrel structures in the membrane, stability of binding pockets and the function of TMBs

cle{tureOB, title {Architecture of beta-barrel membrane proteins: analysis of.We have analyzed the known three-dimensional structures of trimeric porins from bacterial outer membranes.

cle{tureOB, title {Architecture of beta-barrel membrane proteins: analysis of trimeric porins. author {Kothandaraman Seshadri and R Garemyr and Emelie Wallin and Gunnar von Heijne and Arne Elofsson}, journal {Protein science : a publication of the Protein Society}, year {1998}, volume {7 9}, pages {. The distribution of surface-exposed residues in a direction perpendicular to the membrane is similar to that in helical membrane proteins, with aliphatic residues concentrated in the central 20 A of the bilayer.

Recently solved outer membrane protein structures include the smallest and largest known beta-barrel structures, with functions distinct from the general and specific porins

Recently solved outer membrane protein structures include the smallest and largest known beta-barrel structures, with functions distinct from the general and specific porins. Both protein expressed in outer membranes and protein deposited as cytoplasmic aggregates have been used for the structure determinations. As most beta-barrel proteins can be overexpressed in an aggregated form (inclusion bodies) and refolded to the native state, this provides an alternative to membrane-targeted expression strategies and yields sufficient quantities of protein for future structural studies

Porins are integral membrane proteins found in the outer membrane of.

Porins are integral membrane proteins found in the outer membrane of bacteria, mitochondria and chloroplasts. We have explored and extended the intrinsic motilities within porins using selected six porins structures.

membrane in the cynobacteria where they have the protein components to harvest light (from AP BIO MICHELLE) o Carboxysomes: CO2 treating system o Inclusion o Nanotubes. The rate of transcription is ~ 40-50 nt/second, which is about the same rate as translation (15 amino acids/ second; 45 nt of RNA/ second). Transcription is much slower than DNA synthesis (~800 bp/sec).

Key-Words: - outer membrane proteins, beta barrel, Markov chains, bioinformatics

Key-Words: - outer membrane proteins, beta barrel, Markov chains, bioinformatics. They are located in the outer membrane of amphipathicity. The β-barrel outer membrane gram-negative bacteria, and presumably in the outer proteins perform a wide variety of functions such as membrane of chloroplasts and mitochondria.

Outer membrane beta-stranded porins form a diverse and complex set of proteins which allow passage of molecules across the membrane interface have been analyzed here from a biophysical and structural perspective using atomic temperature factors or B-factors. Structures of six porins (four 16 stranded beta barrel porins and two 8 stranded beta barrel porins) were taken from the PDB for the analysis based on resolution (better than 3.0 Å) and R-factor (< 0.23). The residue distribution and mobility distribution was found to be characteristic of each of the porins. The mobility and residue distribution amongst the secondary structural elements were found to follow the level of homology at the sequence and structural level. For both the 16 stranded and the 8 stranded barrels it was found one part of the barrel was more rigid and the other half of the barrel showed more mobility as seen from the temperature factors. This seems to be an intrinsic structural component of the beta barrels.