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Influence of Medium and Long Range Interactions in (?/?)(8) Barrel Proteins.

ABSTRACT: The residue-residue contacts and the role of medium and long rangeinteractions in 36 (?/?)(8) barrel proteins have beenanalysed. The influence of long range contacts in the formation ofphysico-chemically similar clusters, and the preference of amino acidresidues towards long range contacts have also been studied. Theresults reveal a nearly uniform level of medium and long rangecontacts in most of the proteins. The residues Gln and Ala havehighest medium range contacts and the residue Pro has the lowestmedium range contacts. The residue Cys has the highest long rangecontact followed by other hydrophobic residues namely Val, Ile andLeu. In the physico-chemically similar clusters identified in theseproteins, 25-40 percent residues are influenced by long rangecontacts, and the residues Cys, Ile, Val and Met are the mostpreferred ones.

SUBMITTER: Gromiha MM

PROVIDER: S-EPMC3456500 | biostudies-other | 1997 Dec

REPOSITORIES: biostudies-other

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Influence of Medium and Long Range Interactions in (α/β)(8) Barrel Proteins.

Gromiha M M MM Selvaraj S S

Journal of biological physics 19971201 4

The residue-residue contacts and the role of medium and long rangeinteractions in 36 (α/β)(8) barrel proteins have beenanalysed. The influence of long range contacts in the formation ofphysico-chemically similar clusters, and the preference of amino acidresidues towards long range contacts have also been studied. Theresults reveal a nearly uniform level of medium and long rangecontacts in most of the proteins. The residues Gln and Ala havehighest medium range contacts and the residue Pro has the ...[more]

PMID: 23345662

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Project description:Chemotaxis enables cells to systematically approach distant targets that emit a diffusible guiding substance. However, the visual observation of an encounter between a cell and a target does not necessarily indicate the presence of a chemotactic approach mechanism, as even a blindly migrating cell can come across a target by chance. To distinguish between the chemotactic approach and blind migration, we present an objective method that is based on the analysis of time-lapse recorded cell migration trajectories: For each movement step of a cell relative to the position of a potential target, we compute a p value that quantifies the likelihood of the movement direction under the null-hypothesis of blind migration. The resulting distribution of p values, pooled over all recorded cell trajectories, is then compared to an ensemble of reference distributions in which the positions of targets are randomized. First, we validate our method with simulated data, demonstrating that it reliably detects the presence or absence of remote cell-cell interactions. In a second step, we apply the method to data from three-dimensional collagen gels, interspersed with highly migratory natural killer (NK) cells that were derived from two different human donors. We find for one of the donors an attractive interaction between the NK cells, pointing to a cooperative behavior of these immune cells. When adding nearly stationary K562 tumor cells to the system, we find a repulsive interaction between K562 and NK cells for one of the donors. By contrast, we find attractive interactions between NK cells and an IL-15-secreting variant of K562 tumor cells. We therefore speculate that NK cells find wild-type tumor cells only by chance, but are programmed to leave a target quickly after a close encounter. We provide a freely available Python implementation of our p value method that can serve as a general tool for detecting long-range interactions in collective systems of self-driven agents.

Dataset Information

Influence of Medium and Long Range Interactions in (?/?)(8) Barrel Proteins.

Publications

Influence of Medium and Long Range Interactions in (α/β)(8) Barrel Proteins.

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