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A fresh look at the Ramachandran plot and the occurrence of standard structures in proteins.

ABSTRACT: The Ramachandran plot is among the most central concepts in structural biology, seen in publications and textbooks alike. However, with the increasing numbers of known protein-structures and greater accuracy of ultra-high resolution protein structures, we are still learning more about the basic principles of protein structure. Here we use high fidelity conformational information to explore novel ways, such a geo-style and wrapped Ramachandran plots, to convey some of the basic aspects of the Ramachandran plot and of protein conformation. We point out the pressing need for a standard nomenclature for peptide conformation and propose such a nomenclature. Finally, we summarize some recent conceptual advances related to the building blocks of protein structure. The results for linear groups imply the need for substantive revisions in how the basics of protein structure are handled.

SUBMITTER: Hollingsworth SA

PROVIDER: S-EPMC3061398 | biostudies-literature | 2010 Oct

REPOSITORIES: biostudies-literature

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A fresh look at the Ramachandran plot and the occurrence of standard structures in proteins.

Hollingsworth Scott A SA Karplus P Andrew PA

Biomolecular concepts 20101001 3-4

The Ramachandran plot is among the most central concepts in structural biology, seen in publications and textbooks alike. However, with the increasing numbers of known protein-structures and greater accuracy of ultra-high resolution protein structures, we are still learning more about the basic principles of protein structure. Here we use high fidelity conformational information to explore novel ways, such a geo-style and wrapped Ramachandran plots, to convey some of the basic aspects of the Ram ...[more]

PMID: 21436958

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Project description:Mechanical stress from haemodynamic perturbations or interventional manipulation of epicardial coronary atherosclerotic plaques with inflammatory destabilization can release particulate debris, thrombotic material and soluble substances into the coronary circulation. The physical material obstructs the coronary microcirculation, whereas the soluble substances induce endothelial dysfunction and facilitate vasoconstriction. Coronary microvascular obstruction and dysfunction result in patchy microinfarcts accompanied by an inflammatory reaction, both of which contribute to progressive myocardial contractile dysfunction. In clinical studies, the benefit of protection devices to retrieve atherothrombotic debris during percutaneous coronary interventions has been modest, and the treatment of microembolization has mostly relied on antiplatelet and vasodilator agents. The past 25 years have witnessed a relative proportional increase in non-ST-segment elevation myocardial infarction in the presentation of acute coronary syndromes. An associated increase in the incidence of plaque erosion rather than rupture has also been recognized as a key mechanism in the past decade. We propose that coronary microembolization is a decisive link between plaque erosion at the culprit lesion and the manifestation of non-ST-segment elevation myocardial infarction. In this Review, we characterize the features and mechanisms of coronary microembolization and discuss the clinical trials of drugs and devices for prevention and treatment. In this Review, Kleinbongard and Heusch characterize the features and mechanisms of coronary microembolization and discuss the clinical trials of drugs and devices for the prevention and treatment of this phenomenon. Key points Coronary microembolization results from spontaneous or interventional erosion or rupture of an epicardial coronary atherosclerotic plaque. Atherothrombotic plaque debris causes physical obstruction of coronary microvessels and results in microinfarcts with an inflammatory response. The surviving myocardium around the patchy microinfarcts has reduced contractile function as a result of inflammatory signal transduction leading to myofibrillar oxidation. Atherosclerotic plaque erosion or rupture releases soluble substances that induce coronary microvascular endothelial dysfunction, vasoconstriction, platelet aggregation and coagulation. Routine use of interventional protection devices does not improve patient outcomes but these devices are indicated in cases of high atherothrombotic plaque burden. Plaque stabilization with statins and canakinumab prevents coronary microembolization, whereas platelet inhibitors, vasodilators and interleukin antagonists attenuate coronary microvascular impairment.

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A fresh look at the Ramachandran plot and the occurrence of standard structures in proteins.

Publications

A fresh look at the Ramachandran plot and the occurrence of standard structures in proteins.

Similar Datasets

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