Rapid refinement of protein interfaces incorporating solvation: application to the docking problem

Jackson, Richard M.; Gabb, Henry A.; Sternberg, Michael J.E.

doi:10.1006/jmbi.1997.1519

Cited by 226 publications

(206 citation statements)

References 54 publications

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“…Further refinement was performed using a MULTIDOCK program to minimize atom clashes and to improve bonding of the side chains of each interacting component (Jackson et al, 1998). In the resulting complexes, the electrostatic and shape complementarities of the individual molecules upon complexation were specifically assessed as 1) the difference of electrostatic potentials (E elect ) between the bound-unbound states using a finite difference Poisson-Boltzmann solver (Honig and Nicholls, 1995;Grant et al, 2001); and 2) the amount of buried area (BA) upon complexation calculated using the NACCES program (Hubbard et al, 1991).…”

Section: Computational Protein Dockingmentioning

confidence: 99%

Conserved Prefusion Protein Assembly in Regulated Exocytosis

Rickman

Jiménez

Graham

et al. 2006

MBoC

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The regulated release of hormones and neurotransmitters is a fundamental process throughout the animal kingdom. The short time scale for the calcium triggering of vesicle fusion in regulated secretion suggests that the calcium sensor synaptotagmin and the soluble N-ethylmaleimide-sensitive factor attachment protein receptor (SNARE) membrane fusion machinery are well ordered before the calcium signal. To gain insight into the organization of the prefusion protein assembly in regulated exocytosis, we undertook a structural/functional study of the vesicular synaptotagmin1 and the plasma membrane SNARE proteins, which copurify from the brain in the absence of calcium. Based on an evolutionary analysis, mutagenesis screens, and a computational protein docking approach, we now provide the first testable description of the supramolecular prefusion assembly. Perturbing the determined synaptotagmin/SNARE-interacting interface in several models of regulated exocytosis altered the secretion of hormones and neurotransmitters. These mutations also disrupted the constitutive synaptotagmin/SNARE link in full agreement with our model. We conclude that the interaction of synaptotagmin with preassembled plasma membrane SNARE proteins, before the action of calcium, can provide a precisely organized "tethering" scaffold that underlies regulated secretion throughout evolution. INTRODUCTIONIn regulated secretion, fusion of docked secretory vesicles with the plasma membrane is triggered by the rapid elevation of the intracellular calcium concentration (Katz and Miledi, 1967). The membrane fusion itself is brought about by the action of the three soluble N-ethylmaleimide-sensitive factor attachment protein receptor (SNARE) proteins, whereas the vesicular protein synaptotagmin (SYT) acts as the calcium sensor (Sollner et al., 1993;Sudhof and Scheller, 2001;Bonifacino and Glick, 2004). In neuroendocrine cells, the principal SNAREs are syntaxin1 and synaptosome-associated protein of 25 kDa (SNAP-25) on the plasma membrane (so-called target SNAREs or t-SNAREs), and vesicular synaptobrevin, also known as VAMP. Interaction between synaptobrevin and the two t-SNAREs leads to the formation of the ternary SNARE complex, a twisted parallel fourhelical bundle that probably drives membrane fusion (Sutton et al., 1998). With all the major players involved in vesicle fusion identified, it is becoming possible to tackle a central problem of this cellular process-how does calcium trigger vesicle fusion? Arguably, to understand the action of calcium it is essential to know 1) the extent of the assembly of the SNARE fusion proteins and 2) their organization in relation to the calcium sensor, SYT, before calcium-triggered events.It would be reasonable to assume that the SNAREs are at least partially preassembled, and the plasma membrane syntaxin and SNAP-25 are the first obvious candidates for being in such a ready state (An and Almers, 2004;Rickman et al., 2004b). Importantly, synaptobrevin binds syntaxin and SNAP-25 with high-affinity only when the two...

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Section: Computational Protein Dockingmentioning

confidence: 99%

Conserved Prefusion Protein Assembly in Regulated Exocytosis

Rickman

Jiménez

Graham

et al. 2006

MBoC

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“…This filtering step yielded six complexes for methylation site 1 with constraints ≤7 Å, three complexes for site 2 with constraints ≤10 Å, and seven complexes for site 3 with constraints ≤10 Å. The program MULTIDOCK (32) was used for refinement and rigid-body energy minimization of side chain conformations at the proteinprotein interface. The fifteen complexes cited above (one of which was common to both sites 2 and 3) were examined using the molecular graphics display program O (33).…”

Section: Computational Modeling Of Cher and Chemoreceptor Interactionmentioning

confidence: 99%

Discrimination between Different Methylation States of Chemotaxis Receptor Tar by Receptor Methyltransferase CheR

et al. 2004

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Bacterial chemotaxis receptors are posttranslationally modified by carboxyl methylation of specific glutamate residues within their cytoplasmic domains. This highly regulated, reversible modification counterbalances the signaling effects of ligand binding and contributes to adaptation. Based on the crystal structure of the γ-glutamyl-methyltransferase CheR, we have postulated that positively charged residues in helix α2 in the N-terminal domain of the enzyme may be complementary to the negatively charged methylation region of the methyltransferase substrates, the bacterial chemotaxis receptors. Several altered CheR proteins, in which positively charged arginine or lysine residues were substituted with alanines, were constructed and assayed for their methylation activities toward wild-type receptor and a series of receptor variants containing different glutamates available for methylation. One of the CheR mutant proteins (Arg53Ala) showed significantly lower activity toward all receptor constructs, suggesting that Arg53 may play a general role in catalysis of methyl transfer. The rest of the mutant proteins exhibited different patterns of relative methylation rates toward different receptor substrates, indicating specificity, probably through interaction of CheR with the receptor at sites distal to the specific site of methylation. The findings imply complementarity between positively charged residues of the α2 helix of CheR and the negatively charged glutamates of the receptor. It is likely that this complementarity is involved in discriminating different methylation states of the receptors.In enteric bacteria, chemotaxis is mediated by several homologous transmembrane receptors that sense changes in concentrations of attractant and repellent molecules (reviewed in refs. (1-4)). Ligand binding to the periplasmic domains of the receptors generates conformational signals that are transmitted to the cytoplasmic domains that regulate an associated twocomponent phosphotransfer signal transduction system. Alterations in ligand concentration evoke a cellular response involving a change in direction of flagellar rotation. Following a transient response, cells return to pre-stimulus behavior, a process known as adaptation. Adaptation is in part mediated by reversible covalent modification of the chemoreceptors. Changes in receptor ligand concentration are accompanied by changes in the level of methylation at several specific glutamate residues in the cytoplasmic domains of the † A

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“…The two regions of T4 CH at the interface correspond to the unique insertions compared with E.coli and T4 TSs (Figure 1). Prompted by this observation and the encouraging results of other investigators in deducing biologically relevant protein-protein interactions from an inspection of the crystal packing (Story et al, 1992;Rice and Steitz, 1994;Janin and Rodier, 1995;Shapiro et al, 1995), a hypothetical model of the complex between T4 CH and T4 TS was built using MULTIDOCK (Jackson et al, 1998). This model shown in Figure 6 is largely consistent with the proposal that three insertions and one deletion in the primary sequence, unique to T4 TS, possibly provide T4 TS-specific intermolecular interaction sites (FinerMoore et al, 1994).…”

Section: Catalysis Of Hydroxymethylation Reactionmentioning

confidence: 99%

Crystal structure of deoxycytidylate hydroxymethylase from bacteriophage T4, a component of the deoxyribonucleoside triphosphate-synthesizing complex

1999

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Bacteriophage T4 deoxycytidylate hydroxymethylase (EC 2.1.2.8), a homodimer of 246-residue subunits, catalyzes hydroxymethylation of the cytosine base in deoxycytidylate (dCMP) to produce 5-hydroxymethyldCMP. It forms part of a phage DNA protection system and appears to function in vivo as a component of a multienzyme complex called deoxyribonucleoside triphosphate (dNTP) synthetase. We have determined its crystal structure in the presence of the substrate dCMP at 1.6 Å resolution. The structure reveals a subunit fold and a dimerization pattern in common with thymidylate synthases, despite low (~20%) sequence identity. Among the residues that form the dCMP binding site, those interacting with the sugar and phosphate are arranged in a configuration similar to the deoxyuridylate binding site of thymidylate synthases. However, the residues interacting directly or indirectly with the cytosine base show a more divergent structure and the presumed folate cofactor binding site is more open. Our structure reveals a water molecule properly positioned near C-6 of cytosine to add to the C-7 methylene intermediate during the last step of hydroxymethylation. On the basis of sequence comparison and crystal packing analysis, a hypothetical model for the interaction between T4 deoxycytidylate hydroxymethylase and T4 thymidylate synthase in the dNTP-synthesizing complex has been built. Keywords: bacteriophage T4/deoxycytidylate hydroxymethylase/deoxyuridylate hydroxymethylase/ dNTP-synthesizing complex/thymidylate synthase

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Rapid refinement of protein interfaces incorporating solvation: application to the docking problem

Cited by 226 publications

References 54 publications

Conserved Prefusion Protein Assembly in Regulated Exocytosis

Conserved Prefusion Protein Assembly in Regulated Exocytosis

Discrimination between Different Methylation States of Chemotaxis Receptor Tar by Receptor Methyltransferase CheR

Crystal structure of deoxycytidylate hydroxymethylase from bacteriophage T4, a component of the deoxyribonucleoside triphosphate-synthesizing complex

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