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PubMed2006

Docking studies on glycoside hydrolase Family 47 endoplasmic reticulum alpha-(1-->2)-mannosidase I to elucidate the pathway to the substrate transition state.

Alpha-(1-->2)-mannosidase I from the endoplasmic reticulum (ERManI), a Family 47 glycoside hydrolase, is a key enzyme in the N-glycan synthesis pathway. Catalytic-domain crystal structures of yeast and human ERMan1s have been determined, the former with a hydrolytic product and the latter without ligands, with the inhibitors 1-deoxymannojirimycin and kifunensine, and with a thiodisaccharide substrate analog. Both inhibitors were bound at the base of the funnel-shaped active site as the unusual 1C4 conformer, while the substrate analog glycon is a 3S1 conformer. In the current study, AutoDock was used to dock alpha-D-mannopyranosyl-(1-->2)-alpha-D-mannopyranose with its glycon in chair (1C4,4C1), half-chair (3H2,3H4,4H3), skew-boat (OS2,3S1,5S1), boat (2,5B,3,OB,B1,4,B2,5), and envelope (3E,4E,E3,E4) conformations into the yeast ERManI active site. Both docked energies and forces on docked ligand atoms were calculated to determine how the ligand distorts to the transition state. From these, we can conclude that (1) both 1C4 and OS2 can be the starting conformers; (2) the most likely binding pathway is 1C4-->3H2-->OS2-->3,OB-->3S1-->3E; (3) the transition state is likely to be close to a 3E conformation.

Binding Sites↗

PubMed2004

Is it possible docking and scoring new ligands with few experimental data? Preliminary results on estrogen receptor as a case study.

Estrogens are steroid hormones playing critical roles in several physiological processes, which bind the estrogen receptors ERalpha and ERbeta. Aim of this work is to analyze, by different docking experiments, the behavior of a set of compounds, mimicking estrogens activity, in order to understand the relationship between ERalpha and such new ligands. Main goal is to verify, using a widely tested scoring software procedure applied on a set of 10 compounds, the possibility to produce new lead candidate molecules in lack of, or with few experimental data. Our preliminary results reveal the significance of HINT software as a scoring function in docking methodology and specifically, as a mean for assessing the consistency of docking solutions.

Estrogen Receptor alpha↗

PubMedDate not supplied

Synthesis and anti-tyrosine kinase activity of 3-(substituted-benzylidene)-1, 3-dihydro-indolin derivatives: investigation of their role against p60c-Src receptor tyrosine kinase with the application of receptor docking studies.

A series of 3-(substituted-benzylidene)-1, 3-dihydro-indolin-2-thione derivatives were synthesized as modified congeners of 3-(substituted-benzylidene)-1, 3-dihydro-indolin-2-one series. All the synthesized compounds were examined for their in vitro anti-tyrosine kinase activity against p60c-Src. The activity results revealed that compounds (Z)-3-(4'-Dimethylamino-benzylidene)-1, 3-dihydro-indolin-2-thione (12) (E)-3-(2', 6'-Dichloro-benzylidene)-1, 3-dihydro-indolin-2-thione (13) and (E)-3-(3'-Hydroxy-4'-methoxy-benzylidene)-1, 3-dihydro-indolin-2-thione (19) exhibited anti-tyrosine kinase activity with IC50 value of 21.91, 21.20 and 30.92 microM, respectively. These results are comparable to PP1 [1-tert-Butyl-3-p-tolyl-1H-pyrazolo[3, 4-d]pyrimidine-4-yl-amine] (IC50=0.17 microM), which is reported as a potent and selective p60c-Src tyrosine kinase inhibitor. Some thio congeners are found to be more potent than oxo derivatives; however, no significant correlation was observed between the activity profiles of these two series. Docking program was used to investigate the docking mode of each compound at the active site. Among all of the compounds, only (Z)-3-(2'-Chloro-benzylidene)-1, 3-dihydro-indolin-2-one (8) and (E)-3-(3'-Nitro-benzylidene)-1, 3-dihydro-indolin-2-thione (16) were docked at the active site where the PP1 was embedded.

Amino Acid Sequence↗

PubMed2005

Synechocystis ferredoxin/ferredoxin-NADP(+)-reductase/NADP+ complex: Structural model obtained by NMR-restrained docking.

Ferredoxin (Fd) and ferredoxin-NADP(+)-reductase (FNR) are two terminal physiological partners of the photosynthetic electron transport chain. Based on a nuclear magnetic resonance (NMR)-restrained-docking approach, two alternative structural models of the Fd-FNR complex in the presence of NADP+ are proposed. The protein docking simulations were performed with the software BiGGER. NMR titration revealed a 1:1 stoichiometry for the complex and allowed the mapping of the interacting residues at the surface of Fd. The NMR chemical shifts were encoded into distance constraints and used with theoretically calculated electronic coupling between the redox cofactors to propose experimentally validated docked complexes.

Amino Acid Sequence↗

PubMed2006

Docking of a single phage lambda to its membrane receptor maltoporin as a time-resolved event.

We have been able to observe the first step in bacteriophage infection, the docking of phage lambda to its membrane receptor maltoporin, at the single-particle level. High-resolution conductance recording from a single trimeric maltoporin channel reconstituted into a planar lipid bilayer has allowed detection of the simultaneous and irreversible interaction of the phage tail with all three monomers of the receptor. The formation of a phage-maltoporin complex affects the channel transport properties. Our analysis demonstrates that phage attaches symmetrically to all three receptor monomers. The statistics of sugar binding to the phage-receptor complex on the side opposite to phage docking show that the monomers of maltoporin still bind sugar independently, with the kinetic constants expected from those of the phage-free receptor. This finding suggests that phage docking does not distort the structure of the receptor, and that the phage-binding regions are close to, but do not overlap with, the sugar-binding domains of the maltoporin monomers. However, ion fluxes through the pores of maltoporin in the phage-receptor complex share a new common pathway. We expect that the present study contributes to the current needs for structural information on the functional complexes involved in intercellular recognition.

Bacterial Outer Membrane Proteins↗

PubMed2005

Interplay between SRPK and Clk/Sty kinases in phosphorylation of the splicing factor ASF/SF2 is regulated by a docking motif in ASF/SF2.

The arginine-serine (RS)-rich domain of the SR protein ASF/SF2 is phosphorylated by SR protein kinases (SRPKs) and Clk/Sty kinases. However, the mode of phosphorylation by these kinases and their coordination in the biological regulation of ASF/SF2 is unknown. Here, we report the crystal structure of an active fragment of human SRPK1 bound to a peptide derived from an SR protein. This structure led us to identify a docking motif in ASF/SF2. We find that this docking motif restricts phosphorylation of ASF/SF2 by SRPK1 to the N-terminal part of the RS domain - a property essential for its assembly into nuclear speckles. We further show that Clk/Sty causes release of ASF/SF2 from speckles by phosphorylating the C-terminal part of its RS domain. These results suggest that the docking motif of ASF/SF2 is a key regulatory element for sequential phosphorylation by SRPK1 and Clk/Sty and, thus, is essential for its subcellular localization.

Amino Acid Motifs↗

PubMed2005

Molecular modeling and docking simulations of scorpion toxins and related analogs on human SKCa2 and SKCa3 channels.

The small-conductance Ca2+-activated K+ (SKCa) channels modulate cytosolic Ca2+ concentration in excitable and non-excitable tissues by regulating the membrane potential and are responsible of slow action potential after hyperpolarization that inhibits cell firing. Among these, human SKCa2 and SKCa3 channels differ in the pore region by only two residues: Ala331 and Asn367 (human small-conductance calcium-activated potassium channel, hSKCa2) instead of Val485 and His521 (hSKCa3). To design highly selective blockers of hSKCa channels, a number of known hSKCa2 and/or hSKCa3-active peptides (i.e. scorpion toxins and analogs thereof) were analyzed for their interactions and selectivities toward these channels. Molecular models of hSKCa2 and hSKCa3 channels (S5-H5-S6 portion) were generated, and scorpion toxins/peptides of unsolved three-dimensional (3D) structures were modeled. Models of toxin-channel complexes were generated by the bimolecular complex generation with global evaluation, and ranking (BiGGER) docking software and selected by using a screening method of the docking solutions. A high degree of correlation was found to exist between docking energies and experimental Kd values of peptides that blocked hSKCa2 and/or hSKCa3 channels, suggesting it could be appropriate to predict Kd values of other bioactive peptides. The best scoring complexes were also used to identify key residues of both interacting partners, indicating that such an approach should help the design of more active and/or selective peptide blockers of targeted ion channels.

Amino Acid Motifs↗

PubMed2006

High-resolution protein-protein docking.

The high-resolution prediction of protein-protein docking can now create structures with atomic-level accuracy. This progress arises from both improvements in the rapid sampling of conformations and increased accuracy of binding free energy calculations. Consequently, the quality of models submitted to the blind prediction challenge CAPRI (Critical Assessment of PRedicted Interactions) has steadily increased, including complexes predicted from homology structures of one binding partner and complexes with atomic accuracy at the interface. By exploiting experimental information, docking has created model structures for real applications, even when confronted with challenges such as moving backbones and uncertain monomer structures. Work remains to be done in docking large or flexible proteins, ranking models consistently, and producing models accurate enough to allow computational design of higher affinities or specificities.

Animals↗

PubMed2002

Vacuole fusion at a ring of vertex docking sites leaves membrane fragments within the organelle.

Three membrane microdomains can be identified on docked vacuoles: "outside" membrane, not in contact with other vacuoles, "boundary" membrane that contacts adjacent vacuoles, and "vertices," where boundary and outside membrane meet. In living cells and in vitro, vacuole fusion occurs at vertices rather than from a central pore expanding radially. Vertex fusion leaves boundary membrane within the fused organelle and is an unexpected pathway for the formation of intralumenal membranes. Proteins that regulate docking and fusion (Vac8p, the GTPase Ypt7p, its HOPS/Vps-C effector complex, the t-SNARE Vam3p, and protein phosphatase 1) accumulate at these vertices during docking. Their vertex enrichment requires cis-SNARE complex disassembly and is thus part of the normal fusion pathway.

Biological Transport↗

PubMed2001

Munc18-1 promotes large dense-core vesicle docking.

Secretory vesicles dock at the plasma membrane before Ca(2+) triggers their exocytosis. Exocytosis requires the assembly of SNARE complexes formed by the vesicle protein Synaptobrevin and the membrane proteins Syntaxin-1 and SNAP-25. We analyzed the role of Munc18-1, a cytosolic binding partner of Syntaxin-1, in large dense-core vesicle (LDCV) secretion. Calcium-dependent LDCV exocytosis was reduced 10-fold in mouse chromaffin cells lacking Munc18-1, but the kinetic properties of the remaining release, including single fusion events, were not different from controls. Concomitantly, mutant cells displayed a 10-fold reduction in morphologically docked LDCVs. Moreover, acute overexpression of Munc18-1 in bovine chromaffin cells increased the amount of releasable vesicles and accelerated vesicle supply. We conclude that Munc18-1 functions upstream of SNARE complex formation and promotes LDCV docking.

Animals↗

PubMed1998

Docking and fusion in neurosecretion.

A central issue in neurobiology concerns the mechanisms of membrane fusion that are essential for the rapid regulated delivery of neurotransmitters into the synapse. While many gene products are required for neurosecretion, recent research has focused on defining the core exocytotic machinery that is responsible for the docking of synaptic vesicles (SVs) and their fusion with the plasma membrane. N-ethylmaleimide-sensitive factor (NSF), soluble NSF attachment protein (SNAP) and SNAP receptor (SNARE) proteins are essential for fusion but may not be critical for SV docking. Current evidence suggests that NSF functions during an ATP-dependent step after docking but before fusion. NSF may function to liberate SNARE proteins from complexes so that the proteins on apposed membranes align in a parallel fashion to bring SVs into close contact with the plasma membrane for fusion.

Animals↗

PubMed2002

Prediction of protein-protein interactions by docking methods.

Recently, developments have been made in predicting the structure of docked complexes when the coordinates of the components are known. The process generally consists of a stage during which the components are combined rigidly and then a refinement stage. Several rapid new algorithms have been introduced in the rigid docking problem and promising refinement techniques have been developed, based on modified molecular mechanics force fields and empirical measures of desolvation, combined with minimisations that switch on the short-range interactions gradually. There has also been progress in developing a benchmark set of targets for docking and a blind trial, similar to the trials of protein structure prediction, has taken place.

Algorithms↗

PubMed2002

Protein-protein association kinetics and protein docking.

Rigid body protein docking methods frequently yield false positive structures that have good surface complementarity, but are far from the native complex. The main reason for this is the uncertainty of the protein structures to be docked, including the positions of solvent-exposed sidechains. Substantial efforts have been devoted to finding near-native structures by rescoring the docked conformations and employing various filters. An alternative approach emulates the process of protein-protein association, that is, first finding the region in which binding is likely to occur and then refining the complex while allowing for flexibility.

Binding Sites↗

PubMed1997

Effects of four analgesic treatments on the behavioural and cortisol responses of 3-week-old lambs to tail docking.

The behavioural and cortisol responses of groups of seven or eight lambs were used to determine which of three methods of tail docking (rubber ring, Burdizzo and rubber ring combined, or heated docking iron) produced the least signs of pain in the first 3 h after use and which of four analgesic treatments (1.0 ml bupivacaine subcutaneously, 0.5 ml bupivacaine epidurally, a topical cold analgesic spray or diclofenac 1.5 mg kg-1) was most effective in reducing these signs. Amputation with a heated docking iron produced levels of behaviour and cortisol responses which did not differ markedly from those of handled controls. The rubber ring method produced the greatest increase in all parameters (total active behaviour 110 +/- 91 counts; 51 +/- 23 min spent in abnormal postures; peak cortisol 93 +/- 51 nmol l-1). Subcutaneous bupivacaine, administered immediately prior to application of the ring, appeared to be the analgesic treatment most effective at reducing these responses (23 +/- 15 counts; 24 +/- 22 min.; 44 +/- 20 nmol l-1).

Administration, Topical↗

PubMed1998

Comparison of methods for the reduction of acute pain produced by rubber ring castration or tail docking of week-old lambs.

Behavioural and plasma cortisol changes were recorded for groups of eight Suffolk x Greyface lambs subjected to castration or tail docking using rubber rings with and without local anaesthetic treatment. Immediately after application of the rubber ring, local anaesthetic (2 x 0.2 ml 2% lignocaine) was administered either by needle and syringe or by high-pressure needleless injection into each side of the neck of the scrotum or tail at the site of the ring, or by high pressure needleless injection into the testes before ring application. In other groups, the innervation to the scrotum or tail was disabled by crushing with a powered bloodless castrator just proximal to the ring. Measurements were recorded in groups of control (handled) lambs, with and without local anaesthetic treatment. Application of local anaesthetic by high pressure needleless injection had little effect on either plasma cortisol values or behaviour of control lambs. For castration, application of the bloodless castrator and/or local anaesthetic at the ring site reduced the peak plasma cortisol concentration by 50% (P < or = 0.01), the incidence of active behavioural responses by 80 and 64% (P < or = 0.01) respectively, and the time spent in abnormal postures by 68 and 59% (P < or = 0.01) respectively. Both methods were effective in reducing pain for tail docking [active behavioural responses reduced by more than 80% (P < or = 0.01) and abnormal postures by 56% (P < or = 0.01)], although local anaesthetic was more effective, reducing the peak cortisol by 60% (P < or = 0.01) [crushing by 44% (P > 0.05)]. Injection of local anaesthetic into the testes was less effective than injection into the neck of the scrotum at the site of the ring [reduction in abnormal lying postures (P < or = 0.05), 45 vs 71%, respectively]. The rapid action, effectiveness, and ease of application of these experimental methods may provide the basis for commercially viable methods for reducing the acute pain produced by rubber ring castration and tail docking of lambs.

Anesthetics, Local↗

PubMed1998

Development of filter functions for protein-ligand docking.

Current docking methods can generate bound conformations of a ligand close to the experimentally observed structure of a protein-ligand complex. However, the scoring functions used to evaluate the potential solutions are not yet reliable enough at giving the highest ranks to the best structure predictions. One approach to this problem is the use of filter functions that are applied to all docked conformations to remove structures with certain energetically unfavorable properties. We present a computationally efficient scheme for such a postprocessing of docking results. For each of the conformations generated for a given protein-ligand complex, four properties are calculated: the fraction of the ligand volume buried inside the binding pocket, the size of lipophilic cavities along the protein-ligand interface, the solvent-accessible surface (SAS) of nonpolar parts of the ligand, and the number of close contacts between nonhydrogen-bonded polar atoms of the ligand and the protein. These four terms were used to filter out the majority of the calculated solutions and to rescore the remaining ones. On a test set of 32 protein-ligand complexes, this protocol significantly improves the accuracy of the structure predictions.

Crystallography, X-Ray↗

PubMed2001

A conformational change in the "loop E-like" motif of the hairpin ribozyme is coincidental with domain docking and is essential for catalysis.

The catalysis of site-specific RNA cleavage and ligation by the hairpin ribozyme requires the formation of a tertiary interaction between two independently folded internal loop domains, A and B. Within the B domain, a tertiary structure has been identified, known as the loop E motif, that has been observed in many naturally occurring RNAs. One characteristic of this motif is a partial cross-strand stack of a G residue on a U residue. In a few cases, including loop B of the hairpin ribozyme, this unusual arrangement gives rise to photoreactivity. In the hairpin, G21 and U42 can be UV cross-linked. Here we show that docking of the two domains correlates very strongly with a loss of UV reactivity of these bases. The rate of the loss of photoreactivity during folding is in close agreement with the kinetics of interdomain docking as determined by hydroxyl-radical footprinting and fluorescence resonance energy transfer (FRET). Fixing the structure of the complex in the cross-linked form results in an inability of the two domains to dock and catalyze the cleavage reaction, suggesting that the conformational change is essential for catalysis.

Catalysis↗

PubMed2002

Human topoisomerase I inhibition: docking camptothecin and derivatives into a structure-based active site model.

Human topoisomerase I (top1) is an important target for anti-cancer drugs, which include camptothecin (CPT) and its derivatives. To elucidate top1 inhibition in vitro, we made a series of duplex DNA substrates containing a deoxyadenosine stereospecifically modified by a covalent adduct of benzo[a]pyrene (BaP) diol epoxide [Pommier, Y., et al. (2000) Proc. Natl. Acad. Sci. U.S.A. 97, 10739-10744]. The known orientation of the hydrocarbon adduct in the DNA duplex relative to the top1 cleavage site, in combination with a top1/DNA crystal structure [Redinbo, M. R., et al. (1998) Science 279, 1504-1513], was used to construct a structure-based model to explain the in vitro top1 inhibition results obtained with adducted DNA duplexes. Here we experimentally determined that the lactone form of CPT was stabilized by an irreversible top1/DNA covalent complex. We removed the BaP moiety from the DNA in the published model, and docked the lactone forms of CPT and derivatives into the top1/DNA active site cavity. The docked ligands were minimized, and interaction energy scores between the ligands and the top1/DNA complex were determined. CPT docks perpendicular to the DNA backbone, projects outward from the major groove, and makes a network of potential H-bonds with the active site DNA and top1 residues, including Arg364, Lys532, and Asn722. The results are consistent with the known structure-activity relationships of CPT and derivatives. In addition, the model proposed a novel top1/N352A "resistance" mutation for 10-OH derivatives of CPT. The in vitro biochemical characterization of the top1/N352A mutant supported the model.

Binding Sites↗