Sequence diversity in the pore-forming motifs of the membrane-damaging protein toxins
Pore-forming proteins/toxins (PFPs/PFTs) are the distinct class of membrane-damaging
proteins. They act by forming oligomeric pores in the plasma membranes. PFTs and PFPs …
proteins. They act by forming oligomeric pores in the plasma membranes. PFTs and PFPs …
A method for probing the mutational landscape of amyloid structure
Motivation: Proteins of all kinds can self-assemble into highly ordered β-sheet aggregates
known as amyloid fibrils, important both biologically and clinically. However, the specific …
known as amyloid fibrils, important both biologically and clinically. However, the specific …
TMBpro: secondary structure, β-contact and tertiary structure prediction of transmembrane β-barrel proteins
Motivation: Transmembrane β-barrel (TMB) proteins are embedded in the outer membranes
of mitochondria, Gram-negative bacteria and chloroplasts. These proteins perform critical …
of mitochondria, Gram-negative bacteria and chloroplasts. These proteins perform critical …
TMBB-DB: a transmembrane β-barrel proteome database
TC Freeman Jr, WC Wimley - Bioinformatics, 2012 - academic.oup.com
Motivation: We previously reported the development of a highly accurate statistical algorithm
for identifying β-barrel outer membrane proteins or transmembrane β-barrels (TMBBs), from …
for identifying β-barrel outer membrane proteins or transmembrane β-barrels (TMBBs), from …
Bayesian models and algorithms for protein β-sheet prediction
Prediction of the 3D structure greatly benefits from the information related to secondary
structure, solvent accessibility, and nonlocal contacts that stabilize a protein's structure. We …
structure, solvent accessibility, and nonlocal contacts that stabilize a protein's structure. We …
[HTML][HTML] A multidomain outer membrane protein from Pasteurella multocida: modelling and simulation studies of PmOmpA
PmOmpA is a two-domain outer membrane protein from Pasteurella multocida. The N-
terminal domain of PmOmpA is a homologue of the transmembrane β-barrel domain of …
terminal domain of PmOmpA is a homologue of the transmembrane β-barrel domain of …
Modeling ensembles of transmembrane β‐barrel proteins
Transmembrane β‐barrel (TMB) proteins are embedded in the outer membrane of Gram‐
negative bacteria, mitochondria, and chloroplasts. Despite their importance, very few …
negative bacteria, mitochondria, and chloroplasts. Despite their importance, very few …
transFold: a web server for predicting the structure and residue contacts of transmembrane beta-barrels
Transmembrane β-barrel (TMB) proteins are embedded in the outer membrane of Gram-
negative bacteria, mitochondria and chloroplasts. The cellular location and functional …
negative bacteria, mitochondria and chloroplasts. The cellular location and functional …
Physical and genetic characterization of an outer-membrane protein (OmpM1) containing an N-terminal S-layer-like homology domain from the phylogenetically Gram …
Thin sectioning and freeze-fracture-etch of the ovine ruminal isolate Mitsuokella multacida
strain 46/5 (2) revealed a Gram-negative envelope ultra-structure consisting of a …
strain 46/5 (2) revealed a Gram-negative envelope ultra-structure consisting of a …
Comparative genomics and functional annotation of bacterial transporters
Transport proteins are difficult to study experimentally, and because of that their functional
characterization trails that of enzymes. The comparative genomic analysis is a powerful …
characterization trails that of enzymes. The comparative genomic analysis is a powerful …