Xylanase homology modeling using the inverse protein folding approach

Xylanase homology modeling using the inverse protein folding approach.

Xylanase has been used in wood pulp bleaching in an effort to reduce chlorine release into the environment and pollution associated with paper production. The three-dimensional structure of xylanase is important to enable better understanding of the enzyme mechanism and to help design a more thermostable xylanase mutant. At the time this work was begun, there was no sequence homologous protein ...

Feasibility in the inverse protein folding protocol.

Methods for protein structure (3D)-sequence (1D) compatibility evaluation (threading) have been developed during the past decade. The protocol in which a sequence can recognize its compatible structure in the structural library (i.e., the fold recognition or the forward-folding search) is available for the structure prediction of new proteins. However, the reverse protocol, in which a structure...

Towards Solving the Inverse Protein Folding Problem

Accurately assigning folds for divergent protein sequences is a major obstacle to structural studies and underlies the inverse protein folding problem. Herein, we outline our theories for fold-recognition in the “twilight-zone” of sequence similarity (<25% identity). Our analyses demonstrate that structural sequence profiles built using Position-Specific Scoring Matrices (PSSMs) significantly o...

Probabilistic protein homology modeling

Modeling Protein Folding Pathways

Proteins fold through a series of intermediate states called a pathway. Protein folding pathways have been modeled using either simulations or a heirarchy of statistical models. Here we present a series of related statistical models that attempt to predict early, middle and late intermediates along the folding pathway. Isites motifs are discrete models for folding initiation sites. HMMSTR is a ...