A Global Taxonomy of Loops in Globular Proteins

Kwasigroch, Jean-Marc; Chomilier, Jacques; Mornon, Jean‐Paul

doi:10.1006/jmbi.1996.0363

Cited by 86 publications

(86 citation statements)

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“…Other authors combined such loop motifs into "supra families" (Donate et al, 1996). The hexapeptide linking two helices H-L6-H is found to contain two major clusters, which have not been described previously (Donate et al, 1996;Kwasigroch et al, 1996). In the first cluster, the fourth residue of the linker has a preference for Gly and the last residue has a preference for Asp and Ser/Thr/Pro.…”

Section: Linkers Of Length Greater Than Three Residuesmentioning

confidence: 58%

“…2, region L). This distribution was found to contribute to the irregularity of the linkers (Kwasigroch et al, 1996). Antiparallel sheets (Fig.…”

Section: Resultsmentioning

confidence: 91%

“…In earlier studies of loops and turns, painvise sequence identity of as much as 50% was allowed (Sibanda & Thornton, 1985;Cohen et al, 1993;Chelvanayagam et al, 1994;Mattos et al, 1994;Kwasigroch et al, 1996). Various linkers of size ranging from two to eight residues (Ln, n = 2-8), connecting different secondary structures, are clustered here (see the Materials and methods).…”

Section: Resultsmentioning

confidence: 99%

“…Description of linker motifs clearly depends upon the method of classification of the secondary structural elements and their termini. Arecent taxonomy of loops (Kwasigroch et al, 1996) has considered the end-to-end distances and an axial descriptor using virtual positions to identify families of clusters. That method combines linkers of same length irrespective of the flanking elements.…”

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confidence: 99%

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Linkers of secondary structures in proteins

Geetha¹,

Munson²

1997

Protein Science

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Linkers that connect repeating secondary structures fall into conformational classes based on distance and main-chain torsion clustering. A data set of 300 unique protein chains with low painvise sequence identity was clustered into only a few groups representing the preferred motifs. The linkers of two to eight residues for the nonredundant data set are designated H-Ln-H, H-Ln-E, E-Ln-H, E-Ln-E, where n is the length, H stands for a-helices, and E for P-strands. Most of the clusters identified here corroborate earlier findings. However, 19 new clusters are identified in this paper, with many of them having seven and eight residue linkers. In our first analysis, the secondary structures flanking the linkers are both interacting and noninteracting and there is no precise angle of orientation between them. A second analysis was performed on a set of proteins with restricted orientations for the flanking elements, namely, mainly a class of proteins with orthogonal architecture. Two definite clusters are identified, one corresponding to linkers of orthogonal helices and the other to linkers of antiparallel helices. Loops forming binding sites or involved in catalytic activity are important determinants of the function of proteins. Although the structural conservation of the residues around the catalytic triad of serine proteases has been studied widely, there has not been a systematic analysis of the conformation of the loops that contain them. Residues of the catalytic triad reside in the linkers of &strands, with varying lengths of more than eight residues. Here, we analyze the structural conservation of such linkers by superposition, and observe a conserved structural feature of the linkers incorporating each of the three residues of the catalytic triad.

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Section: Linkers Of Length Greater Than Three Residuesmentioning

confidence: 58%

“…2, region L). This distribution was found to contribute to the irregularity of the linkers (Kwasigroch et al, 1996). Antiparallel sheets (Fig.…”

Section: Resultsmentioning

confidence: 91%

Section: Resultsmentioning

confidence: 99%

mentioning

confidence: 99%

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Linkers of secondary structures in proteins

Geetha¹,

Munson²

1997

Protein Science

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“…Reverse turns and loops, which allow the reversal of the direction of peptide sequences, are important secondary structure elements for the formation of globular protein structures [1][2][3][4][5][6][7][8][9][10].…”

Section: Introductionmentioning

confidence: 99%

How many hydrogen-bonded α-turns are possible?

2010

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The formation of -turns is a possibility to reverse the direction of peptide sequences via five amino acids. In this paper, a systematic conformational analysis was performed to find the possible isolated -turns with a hydrogen bond between the first and fifth amino acid employing the methods of ab initio MO theory in vacuum (HF/6-31G*, B3LYP/6-311+G*) and in solution (CPCM/HF/6-31G*). Only few -turn structures with glycine and alanine backbones fulfill the geometry criteria for the i(i+4) hydrogen bond satisfactorily. The most stable representatives agree with structures found in the Protein Data Bank. There is a general tendency to form additional hydrogen bonds for smaller pseudocycles corresponding to -and -turns with better hydrogen bond geometries. Sometimes, this competition weakens or even destroys the i(i+4) hydrogen bond leading to very stable double -turn structures. This is also the reason why an "ideal" -turn with three central amino acids having the perfect backbone angle values of an -helix could not be localized. There are numerous hints for stable -turns with a distance between the C  -atoms of the first and fifth amino acid smaller than 6-7 Å, but without an i(i+4) hydrogen bond.

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A new soft-core potential function for molecular dynamics applied to the prediction of protein loop conformations

Tappura¹,

Lahtela‐Kakkonen²,

Teleman³

2000

J. Comput. Chem.

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We have developed a new soft‐core potential function for the conformational search of complex systems with molecular dynamics. The potential function was designed to maintain the main equilibrium properties of the original force field, which means that the soft‐core potential gives physically realistic performance also without additional restraints, different from most of the previous soft‐core potential functions. The performance of the method was demonstrated by applying it to the problem of finding native conformations for protein loops. Short loops from neocarzinostatin and parvalbumin were used as the first test cases. The use of the new soft‐core potential function was shown to improve significantly the performance of molecular dynamics in the search of the native conformation of protein loops. © 2000 John Wiley & Sons, Inc. J Comput Chem 21: 388–397, 2000

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A Global Taxonomy of Loops in Globular Proteins

Cited by 86 publications

References 0 publications

Linkers of secondary structures in proteins

Linkers of secondary structures in proteins

How many hydrogen-bonded α-turns are possible?

A new soft-core potential function for molecular dynamics applied to the prediction of protein loop conformations

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