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At least 631 records · Page 35Linked to original sources
PubMed2001

Cdc42p functions at the docking stage of yeast vacuole membrane fusion.

Membrane fusion reactions have been considered to be primarily regulated by Rab GTPases. In the model system of homotypic vacuole fusion in the yeast Saccharomyces cerevisiae, we show that Cdc42p, a member of the Rho family of GTPases, has a direct role in membrane fusion. Genetic evidence suggested a relationship between Cdc42p and Vtc1p/Nrf1p, a central part of the vacuolar membrane fusion machinery. Vacuoles from cdc42 temperature-sensitive mutants are deficient for fusion at the restrictive temperature. Specific amino acid changes on the Cdc42p protein surface in these mutants define the putative interaction domain that is crucial for its function in membrane fusion. Affinity-purified antibodies to this domain inhibited the in vitro fusion reaction. Using these antibodies in kinetic analyses and assays for subreactions of the priming, docking and post-docking phase of the reaction, we show that Cdc42p action follows Ypt7p-dependent tethering, but precedes the formation of trans-SNARE complexes. Thus, our data define an effector binding domain of Cdc42p by which it regulates the docking reaction of vacuole fusion.

Adenosine Triphosphatases↗
PubMed2006

GRAMM-X public web server for protein-protein docking.

Protein docking software GRAMM-X and its web interface (http://vakser.bioinformatics.ku.edu/resources/gramm/grammx) extend the original GRAMM Fast Fourier Transformation methodology by employing smoothed potentials, refinement stage, and knowledge-based scoring. The web server frees users from complex installation of database-dependent parallel software and maintaining large hardware resources needed for protein docking simulations. Docking problems submitted to GRAMM-X server are processed by a 320 processor Linux cluster. The server was extensively tested by benchmarking, several months of public use, and participation in the CAPRI server track.

Binding Sites↗
PubMed2003

Effect of local shape modifications of molecular surfaces on rigid-body protein-protein docking.

Geometric complementarity is the most dominant term in protein-protein docking and therefore, a good geometric representation of the molecules, which takes into account the flexibility of surface residues, is desirable. We present a modified geometric representation of the molecular surface that down-weighs the contribution of specified parts of the surface to the complementarity score. We apply it to the mobile ends of the most flexible side chains: lysines, glutamines and arginines (trimming). The new representation systematically reduces the complementarity scores of the false-positive solutions, often more than the scores of the correct solutions, thereby improving significantly our ability to identify nearly correct solutions in rigid-body docking of unbound structures. The effect of trimming lysine residues is larger than trimming of glutamine or arginine residues. It appears to be independent of the conformations of the trimmed residues but depends on the relative abundance of such residues at the interface and on the non-interacting surface. Combining the modified geometric representation with electrostatic complementarity further improves the docking results.

Arginine↗
PubMed2003

A protein-protein docking algorithm dependent on the type of complexes.

An efficient 'soft docking' algorithm is described to assist the prediction of protein-protein association using three-dimensional structures of molecules. The basic tools are the 'simplified protein' model and the docking algorithm of Wodak and Janin. The side chain flexibility of Arg, Lys, Asp, Glu and Met residues at the protein surface is taken into account. The complex type-dependent filtering technique on the basis of the geometric matching, hydrophobicity and electrostatic complementarity is used to select candidate binding modes. Subsequently, we calculate a scoring function which includes electrostatic and desolvation energy terms. In the 44 complexes tested including enzyme-inhibitor, antibody-antigen and other complexes, native-like structures were all found, of which 30 were ranked in the top 20. Thus, our soft docking algorithm has the potential to predict protein-protein recognition.

Algorithms↗
PubMed1993

Matching chemistry and shape in molecular docking.

We have added a chemical filter to the ligand placement algorithm of the molecular docking program DOCK. DOCK places ligands in receptors using local shape features. Here we label these shape features by chemical type and insist on complementary matches. We find fewer physically unrealistic complexes without reducing the number of complexes resembling the known ligand-receptor configurations. Approximately 10-fold fewer complexes are calculated and the new algorithm is correspondingly 10-fold faster than the previous shape-only matching. We tested the new algorithm's ability to reproduce three known ligand-receptor complexes: methotrexate in dihydrofolate reductase, deoxyuridine monophosphate in thymidylate synthase and pancreatic trypsin inhibitor in trypsin. The program found configurations within 1 A of the crystallographic mode, with fewer non-native solutions compared with shape-only matching. We also tested the program's ability to retrieve known inhibitors of thymidylate synthase and dihydrofolate reductase by screening molecular databases against the enzyme structures. Both algorithms retrieved many known inhibitors preferentially to other compounds in the database. The chemical matching algorithm generally ranks known inhibitors better than does matching based on shape alone.

Algorithms↗
PubMed2005

Incorporating intermolecular distance into protein-protein docking.

In this work, intermolecular distance was integrated into the docking of protein-protein complexes. To develop an efficient docking procedure, 22 enzyme-inhibitor targets and 15 antibody-antigen targets were taken from a benchmark set. A three-step approach was adopted, which included global sampling by FTDOCK, filtering by intermolecular distance and ranking by a composite scoring function. For the enzyme-inhibitor targets, the composite scoring function consists of geometry and energy terms. In the set composed of the approximately 100 highest ranked candidates for each target, correct complexes were identified for all of the 22 enzyme-inhibitor targets. This docking strategy also succeeded on the four test targets, of which three are CAPRI targets with the same receptor but different binding modes. Interestingly, all three binding modes were correctly predicted. For the antibody-antigen targets, CDR and physical energy were also used in the filtering process and informatics terms were added to the scoring function. The composite score had successful prediction for 13 of the 15 antibody-antigen targets.

Algorithms↗
PubMed2005

Modelling the structure of latexin-carboxypeptidase A complex based on chemical cross-linking and molecular docking.

We have determined the three-dimensional structure of the protein complex between latexin and carboxypeptidase A using a combination of chemical cross-linking, mass spectrometry and molecular docking. The locations of three intermolecular cross-links were identified using mass spectrometry and these constraints were used in combination with a speed-optimised docking algorithm allowing us to evaluate more than 3 x 10(11) possible conformations. While cross-links represent only limited structural constraints, the combination of only three experimental cross-links with very basic molecular docking was sufficient to determine the complex structure. The crystal structure of the complex between latexin and carboxypeptidase A4 determined recently allowed us to assess the success of this structure determination approach. Our structure was shown to be within 4 A r.m.s. deviation of Calpha atoms of the crystal structure. The study demonstrates that cross-linking in combination with mass spectrometry can lead to efficient and accurate structural modelling of protein complexes.

Algorithms↗
PubMed2006

Critical and distinct roles for key RET tyrosine docking sites in renal development.

Molecular mechanisms that lead to congenital anomalies of kidneys and the lower urinary tract (CAKUT) are poorly understood. To elucidate the molecular basis for signaling specificity of GDNF-mediated RET signaling in kidney development, we characterized mice that exclusively express either the human RET9 or RET51 isoform, or express these isoforms with individual mutations in docking tyrosines for PTB and SH2-domain-containing adaptors Src (Y981), PLCgamma (Y1015), and Shc (Y1062). Our results provide evidence for differential and isoform-specific roles of these docking sites in murine kidney development. Homozygous Ret(RET9) and Ret(RET51) mice were viable and show normally developed kidneys, indicating redundant roles of human RET isoforms in murine kidney development. In the context of the RET51 isoform, only mutation of the docking Tyr 1015 (Y1015F) resulted in severe renal anomalies. These included bilateral megaureters and multicystic kidneys that were caused by supernumerary ureteric buds that fail to separate from the wolffian duct as well as decreased branching morphogenesis. Similar kidney and ureter defects were observed in RET9(Y1015F) mice that contain the Y1015F mutation in the RET9 isoform. Interestingly, loss of RET9(Y1062)-mediated AKT/MAPK activation resulted in renal agenesis or kidney rudiments, whereas mutation of this residue in RET51 had no obvious effect on AKT/MAPK activity and renal development. These results reveal novel roles of key RET-dependent signaling pathways in embryonic kidney development and provide murine models and new insights into the molecular basis for CAKUT.

Animals↗
PubMed2006

Effect of crystal freezing and small-molecule binding on internal cavity size in a large protein: X-ray and docking studies of lipoxygenase at ambient and low temperature at 2.0 A resolution.

Flash-freezing is a technique that is commonly used nowadays to collect diffraction data for X-ray structural analysis. It can affect both the crystal and molecular structure and the molecule's surface, as well as the internal cavities. X-ray structural data often serve as a template for the protein receptor in docking calculations. Thus, the size and shape of the binding site determines which small molecules could be found as potential ligands in silico, especially during high-throughput rigid docking. Data were analyzed for wild soybean lipoxygenase-3 (MW 97 kDa) at 293 and 93 K and compared with the results from studies of its molecular complexes with known inhibitors, structures published by others for a derivative of the same enzyme (98 K) or a topologically close isozyme lipoxygenase-1 (at ambient temperature and 100 K). Analysis of these data allows the following conclusions. (i) Very small changes in the relative orientation of the molecules in the crystal can cause major changes in the crystal reciprocal lattice. (ii) The volume of the internal cavities can ;shrink' by several percent upon freezing even when the unit-cell and the protein molecular volume show changes of only 1-2%. (iii) Using a receptor structure determined based on cryogenic data as a target for computational screening requires flexible docking to enable the expansion of the binding-site cavity and sampling of the alternative conformations of the crucial residues.

Algorithms↗
PubMed2005

The orientations of cytochrome c in the highly dynamic complex with cytochrome b5 visualized by NMR and docking using HADDOCK.

The interaction of bovine microsomal ferricytochrome b5 with yeast iso-1-ferri and ferrocytochrome c has been investigated using heteronuclear NMR techniques. Chemical-shift perturbations for 1H and 15N nuclei of both cytochromes, arising from the interactions with the unlabeled partner proteins, were used for mapping the interacting surfaces on both proteins. The similarity of the binding shifts observed for oxidized and reduced cytochrome c indicates that the complex formation is not influenced by the oxidation state of the cytochrome c. Protein-protein docking simulations have been performed for the binary cytochrome b5-cytochrome c and ternary (cytochrome b5)-(cytochrome c)2 complexes using a novel HADDOCK approach. The docking procedure, which makes use of the experimental data to drive the docking, identified a range of orientations assumed by the proteins in the complex. It is demonstrated that cytochrome c uses a confined surface patch for interaction with a much more extensive surface area of cytochrome b5. Taken together, the experimental data suggest the presence of a dynamic ensemble of conformations assumed by the proteins in the complex.

Animals↗
PubMed2005

Improved side-chain modeling for protein-protein docking.

Success in high-resolution protein-protein docking requires accurate modeling of side-chain conformations at the interface. Most current methods either leave side chains fixed in the conformations observed in the unbound protein structures or allow the side chains to sample a set of discrete rotamer conformations. Here we describe a rapid and efficient method for sampling off-rotamer side-chain conformations by torsion space minimization during protein-protein docking starting from discrete rotamer libraries supplemented with side-chain conformations taken from the unbound structures, and show that the new method improves side-chain modeling and increases the energetic discrimination between good and bad models. Analysis of the distribution of side-chain interaction energies within and between the two protein partners shows that the new method leads to more native-like distributions of interaction energies and that the neglect of side-chain entropy produces a small but measurable increase in the number of residues whose interaction energy cannot compensate for the entropic cost of side-chain freezing at the interface. The power of the method is highlighted by a number of predictions of unprecedented accuracy in the recent CAPRI (Critical Assessment of PRedicted Interactions) blind test of protein-protein docking methods.

Models, Molecular↗
PubMed2006

Peptide deformylase is a potential target for anti-Helicobacter pylori drugs: reverse docking, enzymatic assay, and X-ray crystallography validation.

Colonization of human stomach by the bacterium Helicobacter pylori is a major causative factor for gastrointestinal illnesses and gastric cancer. However, the discovery of anti-H. pylori agents is a difficult task due to lack of mature protein targets. Therefore, identifying new molecular targets for developing new drugs against H. pylori is obviously necessary. In this study, the in-house potential drug target database (PDTD, http://www.dddc.ac.cn/tarfisdock/) was searched by the reverse docking approach using an active natural product (compound 1) discovered by anti-H. pylori screening as a probe. Homology search revealed that, among the 15 candidates discovered by reverse docking, only diaminopimelate decarboxylase (DC) and peptide deformylase (PDF) have homologous proteins in the genome of H. pylori. Enzymatic assay demonstrated compound 1 and its derivative compound 2 are the potent inhibitors against H. pylori PDF (HpPDF) with IC50 values of 10.8 and 1.25 microM, respectively. X-ray crystal structures of HpPDF and the complexes of HpPDF with 1 and 2 were determined for the first time, indicating that these two inhibitors bind well with HpPDF binding pocket. All these results indicate that HpPDF is a potential target for screening new anti-H. pylori agents. In addition, compounds 1 and 2 were predicted to bind to HpPDF with relatively high selectivity, suggesting they can be used as leads for developing new anti-H. pylori agents. The results demonstrated that our strategy, reverse docking in conjunction with bioassay and structural biology, is effective and can be used as a complementary approach of functional genomics and chemical biology in target identification.

Amidohydrolases↗
PubMed2002

Soft protein-protein docking in internal coordinates.

The association of two biological macromolecules is a fundamental biological phenomenon and an unsolved theoretical problem. Docking methods for ab initio prediction of association of two independently determined protein structures usually fail when they are applied to a large set of complexes, mostly because of inaccuracies in the scoring function and/or difficulties on simulating the rearrangement of the interface residues on binding. In this work we present an efficient pseudo-Brownian rigid-body docking procedure followed by Biased Probability Monte Carlo Minimization of the ligand interacting side-chains. The use of a soft interaction energy function precalculated on a grid, instead of the explicit energy, drastically increased the speed of the procedure. The method was tested on a benchmark of 24 protein-protein complexes in which the three-dimensional structures of their subunits (bound and free) were available. The rank of the near-native conformation in a list of candidate docking solutions was <20 in 85% of complexes with no major backbone motion on binding. Among them, as many as 7 out of 11 (64%) protease-inhibitor complexes can be successfully predicted as the highest rank conformations. The presented method can be further refined to include the binding site predictions and applied to the structures generated by the structural proteomics projects. All scripts are available on the Web.

Algorithms↗
PubMed1985

Immunochemical analysis of rough and smooth microsomes from rat liver. Segregation of docking protein in rough membranes.

Docking protein (or signal recognition particle receptor) is an integral membrane protein essential for translocation of nascent polypeptides across the membrane of the endoplasmic reticulum. It serves as the receptor for the signal recognition particle, and represents the site of interaction between the translation and the translocation systems. Results presented here demonstrate that this protein is localized exclusively in rough microsomal membranes. Rough and smooth microsomes were prepared and their content of various marker proteins was determined by immunochemical techniques. Whereas a number of proteins, including cytochromes b5 and P-450 and their reductases were evenly distributed between rough and smooth microsomes, docking protein was found at 20-fold higher levels in the rough fraction. On the basis of these results it is concluded that docking protein is a functionally characterized integral protein specifically restricted to rough microsomal membranes.

Animals↗
PubMed1995

Binding of CO to myoglobin from a heme pocket docking site to form nearly linear Fe-C-O.

The relative orientations of carbon monoxide (CO) bound to and photodissociated from myoglobin in solution have been determined with time-resolved infrared polarization spectroscopy. The bound CO is oriented < or = 7 degrees from the heme normal, corresponding to nearly linear FE-C-O. Upon dissociation from the Fe, CO becomes trapped in a docking site that orientationally constrains it to lie approximately in the plane of the heme. Because the bound and "docked" CO are oriented in nearly orthogonal directions CO binding from the docking site is suppressed. These solutions results help to establish how myoglobin discriminates against CO, a controversial issue dominated by the misconception that Fe-C-O is bent.

Binding Sites↗
PubMed1996

The full oncogenic activity of Ret/ptc2 depends on tyrosine 539, a docking site for phospholipase Cgamma.

RET/PTC oncogenes, generated by chromosomal rearrangements in papillary thyroid carcinomas, are constitutively activated versions of proto-RET, a gene coding for a receptor-type tyrosine kinase (TK) whose ligand is still unknown. RET/PTCs encode fusion proteins in which proto-RET TK and C-terminal domains are fused to different donor genes. The respective Ret/ptc oncoproteins display constitutive TK activity and tyrosine phosphorylation. We found that Ret/ptcs associate with and phosphorylate the SH2-containing transducer phospholipase Cgamma (PLCgamma). Two putative PLCgamma docking sites, Tyr-505 and Tyr-539, have been identified on Ret/ptc2 by competition experiments using phosphorylated peptides modelled on Ret sequence. Transfection experiments and biochemical analysis using Tyr-->Phe mutants of Ret/ptc2 allowed us to rule out Tyr-505 and to identify Tyr-539 as a functional PLCgamma docking site in vivo. Moreover, kinetic measurements showed that Tyr-539 is able to mediate high-affinity interaction with PLCgamma. Mutation of Tyr-539 resulted in a drastically reduced oncogenic activity of Ret/ptc2 on NIH 3T3 cells (75 to 90% reduction) both in vitro and in vivo, which correlates with impaired ability of Ret/ptc2 to activate PLCgamma. In conclusion, this paper demonstrates that Tyr-539 of Ret/ptc2 (Tyr-761 on the proto-RET product) is an essential docking site for the full transforming potential of the oncogene. In addition, the present data identify PLCgamma as a downstream effector of Ret/ptcs and suggest that this transducing molecule could play a crucial role in neoplastic signalling triggered by Ret/ptc oncoproteins.

3T3 Cells↗
PubMed2002

Interactions of Pex7p and Pex18p/Pex21p with the peroxisomal docking machinery: implications for the first steps in PTS2 protein import.

Peroxisomal PTS2-dependent matrix protein import starts with the recognition of the PTS2 targeting signal by the import receptor Pex7p. Subsequently, the formed Pex7p/cargo complex is transported from the cytosol to the peroxisomal docking complex, consisting of Pex13p and Pex14p. In Saccharomyces cerevisiae, the latter event is thought to require the redundant Pex18p and Pex21p. Here we mapped the Pex7p interaction domain of Pex13p to its N-terminal 100 amino acids. Pex18p and Pex21p also interacted with this region, albeit only in the presence of Pex7p. Expression of an N-terminally deleted version of Pex13p in a pex13delta mutant failed to restore growth on fatty acids due to a specific defect in the import of PTS2-containing proteins. We further show by yeast two-hybrid analysis, coimmunoprecipitation, and in vitro binding assays that Pex7p can bind Pex13p and Pex14p in the absence of Pex18p/Pex21p. The PTS2 protein thiolase was shown to interact with Pex14p but not with Pex13p in a Pex7p- and Pex18p/Pex21p-dependent manner, suggesting that only Pex14p binds cargo-loaded PTS2 receptor. We also found that the cytosolic Pex7p/thiolase-containing complex includes Pex18p. This complex accumulated in docking mutants but was absent in cells lacking Pex18p/Pex21p, indicating that Pex18p/Pex21p are required already before the docking event.

Acetyl-CoA C-Acyltransferase↗
PubMed2003

Phosphorylation of p90 ribosomal S6 kinase (RSK) regulates extracellular signal-regulated kinase docking and RSK activity.

Stimulation of the Ras/extracellular signal-regulated kinase (ERK) pathway can modulate cell growth, proliferation, survival, and motility. The p90 ribosomal S6 kinases (RSKs) comprise a family of serine/threonine kinases that lie at the terminus of the ERK pathway. Efficient RSK activation by ERK requires its interaction through a docking site located near the C terminus of RSK, but the regulation of this interaction remains unknown. In this report we show that RSK1 and ERK1/2 form a complex in quiescent HEK293 cells that transiently dissociates upon mitogen stimulation. Complex dissociation requires phosphorylation of RSK1 serine 749, which is a mitogen-regulated phosphorylation site located near the ERK docking site. Using recombinant RSK1 proteins, we find that serine 749 is phosphorylated by the N-terminal kinase domain of RSK1 in vitro, suggesting that ERK1/2 dissociation is mediated through RSK1 autophosphorylation of this residue. Consistent with this hypothesis, we find that inactivating mutations in the RSK1 kinase domains disrupted the mitogen-regulated dissociation of ERK1/2 in vivo. Analysis of different RSK isoforms revealed that RSK1 and RSK2 readily dissociate from ERK1/2 following mitogen stimulation but that RSK3 remains associated with active ERK1/2. RSK activity assays revealed that RSK3 also remains active longer than RSK1 and RSK2, suggesting that prolonged ERK association increased the duration of RSK3 activation. These results provide new evidence for the regulated nature of ERK docking interactions and reveal important differences among the closely related RSK family members.

Amino Acid Sequence↗