Favored and suppressed patterns of hydrophobic and nonhydrophobic amino acids in protein sequences.

Vazquez, Stephen; Thomas, Christopher A.; Lew, Robert A.; Humphreys, Robert E.

doi:10.1073/pnas.90.19.9100

Cited by 17 publications

(18 citation statements)

References 24 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…However, this does not exclude the possibility that some distribution patterns of certain amino acids exist in the zero‐pentat pool. Indeed, it is known that certain patterns of hydrophobic and nonhydrophobic amino acids are favored in α‐helices (Vazquez et al 1993). Similarly, binary patterns of polar and nonpolar amino acids are favored in α‐helices and solvent‐exposed β‐strands (West and Hecht 1995), whose biological significance is at least partially known (Broome and Hech 2000; Mandel‐Gutfreund and Gregoret 2002).…”

Section: Resultsmentioning

confidence: 99%

Availability of short amino acid sequences in proteins

et al. 2005

View full text Add to dashboard Cite

Much attention is being paid to protein databases as an important information source for proteome research. Although used extensively for similarity searches, protein databases themselves have not fully been characterized. In a systematic attempt to reveal protein-database characters that could contribute to revealing how protein chains are constructed, frequency distributions of all possible combinatorial sets of three, four, and five amino acids ("triplets," "quartets," and "pentats"; collectively called constituent sequences) have been examined in the nonredundant (nr) protein database, demonstrating the existence of nonrandom bias in their "availability" at the population level. Nonexistent short sequences of pentats were found that showed low availability in biological proteins against their expected probabilities of occurrence. Among them, six representative ones were successfully synthesized as peptides with reasonably high yields in a conventional Fmoc method, excluding the possibility that a putative physicochemical energy barrier in forming them could be a direct cause for the low availability. They were also expressed as soluble fusion proteins in a conventional Escherichia coli BL21Star(DE3) system with reasonably high yield, again excluding a possible difficulty in their biological synthesis. Together, these results suggest that information on threedimensional structures and functions of proteins exists in the context of connections of short constituent sequences, and that proteins are composed of evolutionarily selected constituent sequences, which are reflected in their availability differences in the database. These results may have biological implications for protein structural studies.

show abstract

Section: Resultsmentioning

confidence: 99%

Availability of short amino acid sequences in proteins

et al. 2005

View full text Add to dashboard Cite

show abstract

“…101011 is found as a cluster 3419 times in a bank of 32,886 sequences and 45,746 times as a common motif). In contrast, they hold far more specific information, as already demonstrated [10] and observed in recent presentations of ordinary pattern properties [17,18]. Indeed, the 2D h-helical plot hydrophobic clusters best match the observed h or i regular secondary structures of globular proteins.…”

Section: Reviewmentioning

confidence: 87%

Deciphering protein sequence information through hydrophobic cluster analysis (HCA): current status and perspectives

Callebaut¹,

Labesse²,

Durand³

et al. 1997

Cellular and Molecular Life Sciences (CMLS)

459

453

View full text Add to dashboard Cite

Ten years after the idea of hydrophobic cluster analysis (HCA) was conceived and first published, theoretical and practical experience has shown this unconventional method of protein sequence analysis to be particularly efficient and sensitive, especially with families of sequences sharing low levels of sequence identity. This extreme sensitivity has made it possible to predict the functions of genes whose sequence similarities are hardly if at all detectable by current one-dimensional (1D) methods alone, and offers a new way to explore the enormous amount of data generated by genome sequencing. HCA also provides original tools to understand fundamental features of protein stability and folding. Since the last review of HCA published in 1990 [1], significant improvements have been made and several new facets have been addressed. Here we wish to update and summarize this information.

show abstract

“… for a review). On the other hand, several studies have also shown that binary patterns are major determinants of the types of secondary structures, in addition to the fact that they generally deviate from randomness . In this respect, binary patterns typical of α‐helices are more favored than those typical of β‐strands, an observation which was suggested to correlate with the necessity of avoiding aggregation of partially folded intermediates during intracellular folding.…”

Section: Resultsmentioning

confidence: 99%

The respective roles of polar/nonpolar binary patterns and amino acid composition in protein regular secondary structures explored exhaustively using hydrophobic cluster analysis

et al. 2016

View full text Add to dashboard Cite

Several studies have highlighted the leading role of the sequence periodicity of polar and nonpolar amino acids (binary patterns) in the formation of regular secondary structures (RSS). However, these were based on the analysis of only a few simple cases, with no direct mean to correlate binary patterns with the limits of RSS. Here, HCA-derived hydrophobic clusters (HC) which are conditioned binary patterns whose positions fit well those of RSS, were considered. All the HC types, defined by unique binary patterns, which were commonly observed in three-dimensional (3D) structures of globular domains, were analyzed. The 180 HC types with preferences for either α-helices or β-strands distinctly contain basic binary units typical of these RSS. Therefore a general trend supporting the "binary pattern preference" assumption was observed. HC for which observed RSS are in disagreement with their expected behavior (discordant HC) were also examined. They were separated in HC types with moderate preferences for RSS, having "weak" binary patterns and versatile RSS and HC types with high preferences for RSS, having "strong" binary patterns and then displaying nonpolar amino acids at the protein surface. It was shown that in both cases, discordant HC could be distinguished from concordant ones by well-differentiated amino acid compositions. The obtained results could, thus, help to complement the currently available methods for the accurate prediction of secondary structures in proteins from the only information of a single amino acid sequence. This can be especially useful for characterizing orphan sequences and for assisting protein engineering and design.

show abstract

Favored and suppressed patterns of hydrophobic and nonhydrophobic amino acids in protein sequences.

Cited by 17 publications

References 24 publications

Availability of short amino acid sequences in proteins

Availability of short amino acid sequences in proteins

Deciphering protein sequence information through hydrophobic cluster analysis (HCA): current status and perspectives

The respective roles of polar/nonpolar binary patterns and amino acid composition in protein regular secondary structures explored exhaustively using hydrophobic cluster analysis

Contact Info

Product

Resources

About