A Transition Probability Model for Amino Acid Substitutions from Blocks

A Transition Probability Model for Amino Acid Substitutions from Blocks

Substitution matrices have been useful for sequence alignment and protein sequence comparisons. The BLOSUM series of matrices, which had been derived from a database of alignments of protein blocks, improved the accuracy of alignments previously obtained from the PAM-type matrices estimated from only closely related sequences. Although BLOSUM matrices are scoring matrices now widely used for pr...

Amino acid substitution matrices from protein blocks.

Methods for alignment of protein sequences typically measure similarity by using a substitution matrix with scores for all possible exchanges of one amino acid with another. The most widely used matrices are based on the Dayhoff model of evolutionary rates. Using a different approach, we have derived substitution matrices from about 2000 blocks of aligned sequence segments characterizing more t...

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