Amino acid pairs distinguishing

It was also shown that the four interaction indexes introduced (surface contact, relative solvation, electrostatics and the relative propensity of amino acid pairs to interact) can be conveniently combined into an effective interaction potential function, able to distinguish native from non-native binding modes and to propose a limited set of plausible candidate models of protein complexes. For every complex tested (except for the two where the correct solutions were excluded from the ones retained by BoGIE), a near-correct docked structure was found within the five top-ranked solutions indicated by the global interaction function. 

In the latter implementation, the residue interaction potentials measure the propensities P l °j (dij) of amino acid pairs at positions / and j along the sequence to be separated by a given spatial distance d. Residue pairs are partitioned according to the number of positions / — j that separates them along the polypeptide sequence. In order to try and distinguish between local contributions associated with secondary structure propensities and nonlocal tertiary interactions, pairs of consecutive residues are not considered, because their spatial distance is roughly constant. For pairs separated by 2-8 sequence positions (1 < f — j < 8), probabilities are computed for each separation individually, yielding seven... 

Allele One form of a genetic locus, distinguished from other forms (= alleles) by its particular nucleotide or its coded amino acid sequence. Single nucleotide polymorphisms are biallelic, i.e., one base pair is exchanged with just one other base pair. In such a case, only two different alleles exist in the population for such a gene locus. However, several different alleles may exist in the population if the locus is defined by more than one nucleotide (i.e., microsatelhtes, haplotypes). Thus,... 

In a series of works, Nishikawa and colleagues have shown that intracellular and extracellular proteins can be distinguished by their amino acid composition. In their recent work, they also used the residue pair frequency (not only the neighboring ones, but also pairs with some spacers) and reported a considerable improvement in prediction accuracy (Nakashima and Nishikawa, 1994). 

His1 0 and orients it for its catalytic function [54], The putative catalytic thiolate-imldazollum pair at the active site of bromelain is thus, by comparison of the amino acid sequence of bromelain with other cysteine protein ases, likely to have a different conformation from that in (he cysteine proteinases (hat aie tightly inhibited by cystatin [45]. Bromelain also distinguishes itself from other cysteine protein ases by its slow inhibition by the irreversible inhibitor of cysteine oroteinases E-64 rW-ft 3-fraw-cari)OKVOxiran-2 BrboiwlVL-leucvn-amido 4-... 

Together with the criteria set by the pairs of amino acids whose molar ratios were constant, the n/K ratios offered distinguishing features that characterized the system found in the serum from other proteins picked at random. This would be expected, because while the total aspartic and glutamic acids may provide the principal source of negativity, other proteins may contain the two amino acids in differing proportions, and the alanine would not necessarily be in the same ratio to glutamic acid as is found in all of the serum proteins. Figure 2 shows... 

Transfer RNA molecules are the adaptors that associate an amino acid with its correct base sequence. Transfer RNA molecules are structurally similar to one another each adopts a three-dimensional cloverleaf pattern of base-paired groups (Figure 2,10). Subtle differences in structure enable the protein-synthesis machinery to distinguish transfer RNA molecules with different amino acid specificities. 

In the similarity framework one can easily distinguish among the different possible mismatches and also among different kinds of matches. For example, a match between two Tryptophanes is usually seen to be more important than a match between two Alanines. Likewise, the pairing of two hydrophobic amino acids like Leucine and Isoleucine is preferable to the pairing of a hydrophobic with a hydrophilic residue. Scores are used to de-... 

For the tris(amino acidato)metal(III) complexes four geometrical and chiral isomers are possible, as shown in Scheme 2, where NO is the chelated amino acid anion, mer and fac refer to the meridional and facial geometrical isomers and A and A refer to the configuration at the metal centre. For the glycine complexes A and A are an enantiomeric pair, while for the optically pure forms of the other amino acids they form a diastereomeric pair and hence are easier to separate. For most of the simple bidentate amino acids of the kinetically inert metal ions Cr" , Co " and Rh ", the four isomers have been obtained. The isomers are distinguishable by their UV/visible, CD and NMR spectra. Not all the isomers can be found in certain cases, for example, with L-proline the k-fac isomer could not be prepared, a fact which was predicted on steric grounds." ... 

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