The adaptability ofEscherichia colithioredoxin to non-conservative amino acid substitutions

Predicting HLA Class I Non-Permissive Amino Acid Residues Substitutions

Prediction of peptide binding to human leukocyte antigen (HLA) molecules is essential to a wide range of clinical entities from vaccine design to stem cell transplant compatibility. Here we present a new structure-based methodology that applies robust computational tools to model peptide-HLA (p-HLA) binding interactions. The method leverages the structural conservation observed in p-HLA complex...

Amino acid repeats avert mRNA folding through conservative substitutions and synonymous codons, regardless of codon bias

A significant number of proteins in all living species contains amino acid repeats (AARs) of various lengths and compositions, many of which play important roles in protein structure and function. Here, I have surveyed select homopolymeric single [(A)n] and double [(AB)n] AARs in the human proteome. A close examination of their codon pattern and analysis of RNA structure propensity led to the f...

Combinatorial codon-based amino acid substitutions.

Twenty Fmoc-protected trinucleotide phosphoramidites representing a complete set of codons for the natural amino acids were chemically synthesized for the first time. A pool of these reagents was incorporated into oligonucleotides at substoichiometric levels to generate two libraries of variants that randomly carry either few or many codon replacements on a region encoding nine amino acids of t...

Amino Acid Substitutions: Effects on Protein Stability

A living cell can be viewed as a biochemical factory, with as many as 100,000 distinct proteins providing the hardware to carry out cellular processes. The roles of these molecular machines include such diverse activities as pumping (e.g. voltage gated membrane channels), motor functions (e.g. flagella), amplification (e.g. cyclic AMP), and catalysis. The ability of a protein to function in one...

Amino Acid Properties and Consequences of Substitutions