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Spatial chemical conservation of hot spot interactions in protein-protein complexes.

ABSTRACT: Conservation of the spatial binding organizations at the level of physico-chemical interactions is important for the formation and stability of protein-protein complexes as well as protein and drug design. Due to the lack of computational tools for recognition of spatial patterns of interactions shared by a set of protein-protein complexes, the conservation of such interactions has not been addressed previously.We performed extensive spatial comparisons of physico-chemical interactions common to different types of protein-protein complexes. We observed that 80% of these interactions correspond to known hot spots. Moreover, we show that spatially conserved interactions allow prediction of hot spots with a success rate higher than obtained by methods based on sequence or backbone similarity. Detection of spatially conserved interaction patterns was performed by our novel MAPPIS algorithm. MAPPIS performs multiple alignments of the physico-chemical interactions and the binding properties in three dimensional space. It is independent of the overall similarity in the protein sequences, folds or amino acid identities. We present examples of interactions shared between complexes of colicins with immunity proteins, serine proteases with inhibitors and T-cell receptors with superantigens. We unravel previously overlooked similarities, such as the interactions shared by the structurally different RNase-inhibitor families.The key contribution of MAPPIS is in discovering the 3D patterns of physico-chemical interactions. The detected patterns describe the conserved binding organizations that involve energetically important hot spot residues and are crucial for the protein-protein associations.

SUBMITTER: Shulman-Peleg A

PROVIDER: S-EPMC2231411 | biostudies-literature | 2007 Oct

REPOSITORIES: biostudies-literature

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Spatial chemical conservation of hot spot interactions in protein-protein complexes.

Shulman-Peleg Alexandra A Shatsky Maxim M Nussinov Ruth R Wolfson Haim J HJ

BMC biology 20071009

<h4>Background</h4>Conservation of the spatial binding organizations at the level of physico-chemical interactions is important for the formation and stability of protein-protein complexes as well as protein and drug design. Due to the lack of computational tools for recognition of spatial patterns of interactions shared by a set of protein-protein complexes, the conservation of such interactions has not been addressed previously.<h4>Results</h4>We performed extensive spatial comparisons of phys ...[more]

PMID: 17925020

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Project description:In this paper, ReaxFF force field combined with molecular dynamics method was used to study the ignition, deflagration, and detonation of pentaerythritol tetranitrate (PETN) induced by hot spots. The hot spot is 5.6% of the total volume. When the hot spot temperature is 1000 K, the deflagration and detonation of PETN cannot be observed in the simulation time of 200 ps. When the hot spot temperature is 2000 K, it corresponds to the heating time of 20 to 50 ps, deflation and detonation were observed. During hot spot ignition, the products of decomposition of the condensed phase PETN are dominated by NO2 and HONO. The energy required for the C-C bond and C-ONO2 bond cleavage in PETN is high, resulting in only a small amount of CH2O and NO3 during the reaction. Small nitrogen-containing molecules (such as NO2, NO3, HONO, HNO3, etc.) mainly exist during thermal equilibrium, while the number of N2 increases sharply during the thermal runaway stage, and a small amount of NH3 and NH2 are also produced. H2O molecules are formed before CO2 and N2 are produced, and the number always dominates. During the thermal runaway, the entire system can maintain a spontaneous reaction, resulting in a sharp rise in temperature of about 2500 K in 20 ps. During this phase, the catalytic effect of H2O accelerates the formation of CO2 and N2 due to the near Chapman-Jouguet point in the crystal. PETN is a weak oxygen balance explosive that results in a small amount of CO and H2 production during the thermal instability phase. When the reaction is balanced, the relative molecular mass is close to or exceeds that of PETN. The product is only less than 1% of the total mass fraction, while the small molecule product is as high as 78%, and some relative molecular masses are [75,225]. The intermediates account for about 21%. Rapid and complex reaction events make it difficult to accurately predict the structure of these intermediates by existing experiments and calculations, which will be the focus of future research.

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Spatial chemical conservation of hot spot interactions in protein-protein complexes.

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Spatial chemical conservation of hot spot interactions in protein-protein complexes.

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