in this report, we describe a procedure for in-silico design of a novel haloalkane dehalogenase protein that exhibits luciferase property which can be potentially used in biosensor applications. from a pdb blast search, the selected haloalkane dehalogenase (pdb code: 1ede) had a close structural homology with a lucifearse (pdb code: 2psj chain a) sharing an identity of 33%. initially, the amino...

aim :  to evaluate the association of dnmt1 and mgmt amino acid substitution polymorphisms and colorectal cancer in iranian population. background : the mgmt and dnmt1 are two important methyltransferase enzymes. amino acid substitution polymorphisms in mgmt and dnmt1 genes may be associated with the genetic susceptibility to sporadic colorectal cancer. patients and methods : we assessed eight ...

GNPKVKAH Here we discuss standard ways of assigning a score to each amino acid pair, i.e., to each possible column of a gap-free pairwise protein alignment. Examples of such scoring matrices include the PAM30, PAM70, BLOSUM80, BLOSUM62 and BLOSUM45 matrices that are available on NCBI’s blastp server. Such scores are appropriate for comparing two sequences about which we have no other informatio...

GNPKVKAH Here we discuss standard ways of assigning a score to each amino acid pair, i.e., to each possible column of a gap-free pairwise protein alignment. Examples of such scoring matrices include the PAM30, PAM70, BLOSUM80, BLOSUM62 and BLOSUM45 matrices that are available on NCBI’s blastp server. Such scores are appropriate for comparing two sequences about which we have no other informatio...

The BLOSUM (BLOck SUbstitution Matrices) matrices were derived by Steven and Jorja Henikoff in 1992 1. They were based on a much larger data set than the PAM matrices, and used conserved local alignments or “blocks,” rather than global alignments of very closely related sequences. In order to account for different degrees of sequence divergence, the Henikoffs used clustering rather than an expl...

• Biophysical properties of residues: Amino acids differ in size and charge. Some are acidic, some are basic, some have aromatic side chains. Generally, replacement of an amino acid with another amino acid with similar properties is less likely to break the protein or cause dramatic changes in function than replacement with an amino acid with different properties. A substitution matrix should r...

We searched for novel Chinese hamster ovary (CHO) cell mutants defective in peroxisome biogenesis by an improved method using peroxisome targeting sequence (PTS) of Pex3p (amino acid residues 1–40)-fused enhanced green fluorescent protein (EGFP). From mutagenized TKaEG3(1–40) cells, the wild-type CHO-K1 stably expressing rat Pex2p and of rat Pex3p(1–40)-EGFP, numerous cell colonies resistant to...

we searched for novel chinese hamster ovary (cho) cell mutants defective in peroxisome biogenesis by an improved method using peroxisome targeting sequence (pts) of pex3p (amino acid residues 1–40)-fused enhanced green fluorescent protein (egfp). from mutagenized tkaeg3(1–40) cells, the wild-type cho-k1 stably expressing rat pex2p and of rat pex3p(1–40)-egfp, numerous cell colonies resistant to...

• Biophysical properties of residues: Amino acids differ in size and charge. Some are acidic, some are basic, some have aromatic side chains. Generally, replacement of an amino acid with another amino acid with similar properties is less likely to break the protein or cause a dramatic change in function than replacement with an amino acid with different properties. A substitution matrix should ...