A Survey of Left-handed Helices in Protein Structures

Novotný, Marián; Kleywegt, Gerard J.

doi:10.1016/j.jmb.2005.01.037

Cited by 86 publications

(120 citation statements)

References 66 publications

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“…The chiral overturn of part of the fumarase a-helices upon bismuth binding seemed to indicate the reorganization of the local environment around the bismuthbinding site. This may represent the incorrect interpretation of the CD data by CDPro software, as left-handed a-helix (Novotny and Kleywegt 2005) exist exclusively in peptides containing D-amino acids (Anil et al 2004) and in poly-Gly strands (Hovmoller et al 2002), which is not the case for fumarase. On the basis of the crystal structure of E. coli fumarase C and sequence homology alignment, the fumarase structure was simulated and the modeled structure consists of 455 amino acids (residues 4-458) in three domains (Fig.…”

Section: Structural Characterizations Of Fumarase Upon Bismuth-bindingmentioning

confidence: 99%

Inhibition of fumarase by bismuth(III): implications for the tricarboxylic acid cycle as a potential target of bismuth drugs in Helicobacter pylori

Chen

Zhou

2011

Biometals

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Helicobacter pylori causes various gastric diseases, such as gastritis, peptic ulcerations and gastric cancer. Triple therapy combining bismuth compounds with two antibiotics is the cornerstone of the treatment of H. pylori infections. Up to now, the molecular mechanisms by which bismuth inhibits the growth of H. pylori are far from clear. In the bacterial tricarboxylic acid (TCA) cycle, fumarase catalyses the reversible hydration of fumarate to malic acid. Our previous proteomic work indicated that fumarase was capable of bismuth-binding. The interactions as well as the inhibitory effects of bismuth to fumarase have been characterized in this study. The titration of bismuth showed that each fumarase monomer binds one mol equiv of Bi(3+), with negligible secondary structural change. Bismuth-binding results in a near stoichiometric inactivation of the enzyme, leading to an apparent non-competitive mechanism as reflected by the Lineweaver-Burk plots. Our collective data indicate that the TCA cycle is a potential molecular target of bismuth drugs in H. pylori.

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Section: Structural Characterizations Of Fumarase Upon Bismuth-bindingmentioning

confidence: 99%

Inhibition of fumarase by bismuth(III): implications for the tricarboxylic acid cycle as a potential target of bismuth drugs in Helicobacter pylori

Chen

Zhou

2011

Biometals

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“…A notable feature emerging from this study is the propensity of proteins' active sites to populate rare sequence motif, akin to the notion that rare structural motifs co-localize with functionally important sites [21-23]. This selectivity suggests that enzymes tend to recruit such distinctive/rare sequences at their active sites to increase their specificity, consistent with the higher information content associated with rare events.…”

Section: Introductionmentioning

confidence: 67%

“…Petock et al [22] showed that 9-residue fragments of rare backbone conformations often form parts of ligand-binding sites, protein-protein interactions, and domain-domain contacts. Likewise, Novotny and Kleywegt [23] found that, even thought left-handed helices are rare, when they do occur, they are structurally or functionally significant. The present analysis shows that not only structural motifs, but sequence motifs as well, tend to be highly distinctive at active sites.…”

Section: Resultsmentioning

confidence: 99%

Recruitment of rare 3-grams at functional sites: Is this a mechanism for increasing enzyme specificity?

Tobi

Bahar

2007

BMC Bioinformatics

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Background: A wealth of unannotated and functionally unknown protein sequences has accumulated in recent years with rapid progresses in sequence genomics, giving rise to ever increasing demands for developing methods to efficiently assess functional sites. Sequence and structure conservations have traditionally been the major criteria adopted in various algorithms to identify functional sites. Here, we focus on the distributions of the 20 3 different types of 3-grams (or triplets of sequentially contiguous amino acid) in the entire space of sequences accumulated to date in the UniProt database, and focus in particular on the rare 3-grams distinguished by their high entropy-based information content.

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“…Rotating anti-axially 360°, the spiralled thread exits the heart, winding behind the stream of the truncus arteriosus and into upper gill arches to reach the dorsal aorta to complete a 'loop-in-loop' trajectory. Across nature, symmetry-breaking action is typically left-handed [25][26][27].…”

Section: Mechanism Of Transformationmentioning

confidence: 99%

Basic Science Model of Blood as an Electron-Delivery Circuit Describes the Evolution of the Human Circulation

Peters¹

2017

Hum Genet Embryol

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A basic science model of the closed one-way circulation of redoxing haem in vertebrates is detailed. The adaptive, mechanistic model is of an electron-delivery circuit bounded by the geomagnetic field and electromagnetic radiation and it accounts for a quantum conformational change in circulatory topography from fish to human via a transitionary reptilian circulation. The model is nested within a macro-evolutionary view of plants and animals as countervailing poles of a light-enabled redoxing biosphere. The model is reconciled with human embryogenesis and evolution. If proven broadly applicable, this basic science model will allow for a greater understanding of vertebrate embryogenesis and circulatory physiology.The author acknowledges the support of Prof.

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A Survey of Left-handed Helices in Protein Structures

Cited by 86 publications

References 66 publications

Inhibition of fumarase by bismuth(III): implications for the tricarboxylic acid cycle as a potential target of bismuth drugs in Helicobacter pylori

Inhibition of fumarase by bismuth(III): implications for the tricarboxylic acid cycle as a potential target of bismuth drugs in Helicobacter pylori

Recruitment of rare 3-grams at functional sites: Is this a mechanism for increasing enzyme specificity?

Basic Science Model of Blood as an Electron-Delivery Circuit Describes the Evolution of the Human Circulation

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