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PubMed1994

Monte Carlo docking of protein-DNA complexes: incorporation of DNA flexibility and experimental data.

A Monte Carlo simulation program (MONTY) has been developed to dock proteins onto DNA. Protein and DNA interact via square-well potentials for hydrogen bond and van der Waals interactions. The effect of the inclusion of DNA flexibility and experimentally derived restraints has been tested on members of the helix-turn-helix family of DNA binding proteins. Unwinding and bending the DNA double helix improves the number of correctly retrieved hydrogen bonds in simulations starting from the 434 cro protein monomer complexed with a standard B-DNA OR1 half-site. Agreement with phosphate ethylation interference and mutagenesis data is rewarded with energy bonuses. This protocol was tested on protein-DNA complexes of 434 cro, lac headpiece and a mutant lac headpiece resembling the gal repressor headpiece with the recognition helices in correct and reversed orientations in the DNA major groove. The inclusion of experimental data gives an improved convergence of the correctly oriented structures and allows for an easier discrimination between correctly and incorrectly docked complexes.

Algorithms↗
PubMed2003

Molecular docking of substrates and inhibitors in the catalytic site of CYP6B1, an insect cytochrome p450 monooxygenase.

Furanocoumarins represent plant toxins that are used in the treatment of a variety of skin diseases and are metabolized by cytochrome p450 monooxygenases (p450s) existing in insects such as Papilio polyxenes (the black swallowtail). To elucidate the active site in the CYP6B1 protein that is the principal p450 existing in this species, we have constructed a homology model of it based on sequence and structure alignments with the bacterial CYP102 protein whose crystal structure has been defined and with the insect CYP6B4 protein that also metabolizes furanocoumarins. In the derived CYP6B1 model, Phe116 and His117 in SRS1, Phe371 in SRS5 and Phe484 in SRS6 contribute to the formation of a resonant network that stabilizes the p450's catalytic site and allows for interactions with its furanocoumarin substrates. The first two of these residues are absolutely conserved in all members of the insect CYP6B subfamily and the last two are variable in different members of the CYP6B subfamily. A combination of theoretical and experimental docking analyses of two substrates (xanthotoxin and bergapten) and two inhibitors (coumarin and pilocarpine) of this p450 provide significant information on the positioning of furanocoumarins within this catalytic pocket. Molecular replacement models based on the results of variations at two of these critical amino acids provide support for our furanocoumarin-docked model and begin to rationalize the altered substrate reactivities observed in experimental analyses.

5-Methoxypsoralen↗
PubMed2005

Inhibitory mode of N-phenyl-4-pyrazolo[1,5-b] pyridazin-3-ylpyrimidin-2-amine series derivatives against GSK-3: molecular docking and 3D-QSAR analyses.

Glycogen synthase kinase 3 (GSK-3) inhibition is an important research topic because of its wide range of associated health implications. The interaction mode of a series of N-phenyl-4-pyrazolo[1,5-b]pyridazin-3-ylpyrimidin-2-amine compounds with human GSK-3 has been studied using molecular docking and 3D-QSAR approaches. In the 3D-QSAR studies, the molecular alignment and conformation determination are so important that they affect the success of a model. Flexible docking (AutoDock3.0.5) was used for the determination of 'active' conformation and molecular alignment. Comparative molecular field analysis (CoMFA) and comparative molecular similarity indices analysis (CoMSIA) were used to develop 3D-QSAR models of 80 N-phenyl-4-pyrazolo[1,5-b]pyridazin-3-ylpyrimidin-2-amine compounds. The r(2) values were 0.870 and 0.861 for CoMFA and CoMSIA models, respectively. The predictive ability of these models was validated by 10 compounds of the test set. Mapping these models back to the topology of the active site of GSK-3 led to a better understanding of the vital N-phenyl-4-pyrazolo[1,5-b]pyridazin-3-ylpyrimidin-2-amines-GSK-3 interactions. The results demonstrate that combination of ligand-based and receptor-based modeling is a powerful approach to build 3D-QSAR models. The interaction mode from this study may be helpful for the design of a novel inhibitor and guide the selection of candidate sites for further experimental studies on site-directed mutagenesis.

Catalytic Domain↗
PubMed2002

Calcineurin-dependent regulation of Crz1p nuclear export requires Msn5p and a conserved calcineurin docking site.

Calcineurin, a conserved Ca(2+)/calmodulin-regulated protein phosphatase, plays a crucial role in Ca(2+) signaling in a wide variety of cell types. In Saccharomyces cerevisiae, calcineurin positively regulates transcription in response to stress by dephosphorylating the transcription factor Crz1p/Tcn1p. Dephosphorylation promotes Crz1p nuclear localization in part by increasing the efficiency of its nuclear import. In this work, we show that calcineurin-dependent dephosphorylation of Crz1p also down-regulates its nuclear export. Using a genetic approach, we identify Msn5p as the exportin for Crz1p. In addition, we define the Crz1p nuclear export signal (NES) and show that it interacts with Msn5p in a phosphorylation-dependent manner. This indicates that calcineurin regulates Crz1p nuclear export by dephosphorylating and inactivating its NES. Finally, we define a motif in Crz1p, PIISIQ, similar to the PxIxIT docking site for calcineurin on the mammalian transcription factor NFAT, that mediates the in vivo interaction between calcineurin and Crz1p and is required for calcineurin-dependent regulation of Crz1p nuclear export and activity. Therefore, in yeast as in mammals, a docking site is required to target calcineurin to its substrate such that it can dephosphorylate it efficiently.

Active Transport, Cell Nucleus↗
PubMed2000

A family competition evolutionary algorithm for automated docking of flexible ligands to proteins.

In this paper, we study an evolutionary algorithm for flexible ligand docking. Based on family competition and adaptive rules, the proposed approach consists of global and local strategies by integrating decreasing mutations and self-adaptive mutations. To demonstrate the robustness of the proposed approach, we apply it to the problems of the first international contests on evolutionary optimization. Following the description of function optimization, our approach is applied to a dihydrofolate reductase enzyme with the anti-cancer drug methotrexate and with two analogs of the antibacterial drug trimethoprim. Our numerical results indicate that the proposed approach is robust. The docked lowest energy structures have rms derivations ranging from 0.72 A to 1.98 A with respect to the corresponding crystal structure.

Algorithms↗
PubMed2003

Probing the structure of falcipain-3, a cysteine protease from Plasmodium falciparum: comparative protein modeling and docking studies.

Increasing resistance of malaria parasites to conventional antimalarial drugs is an important factor contributing to the persistence of the disease as a major health threat. The ongoing search for novel targets has resulted in identification and expression of several enzymes including cysteine proteases that are implicated in hemoglobin degradation. Falcipain-2 and falcipain-3 are considered to be the two principal cysteine proteases in this degradation, and hence, are potential drug targets. A homology model of falcipain-3 was built and validated by various structure/geometry verification tools as well as docking studies of known substrates. The correlation coefficient of 0.975 between interaction energies and K(m) values of these substrates provided additional support for the model. On comparison with the previously reported falcipain-2 homology model, the currently constructed falcipain-3 structure showed important differences between the S2 pockets that might explain the variations in the K(m) values of various substrates for these enzymes. Further, docking studies also provided insight into possible binding modes and interactions of ligands with falcipain-3. Results of the current study could be employed in de novo drug design leading to development of new antimalarial agents.

Amino Acid Sequence↗
PubMed2003

The role of geometric complementarity in secondary structure packing: a systematic docking study.

A strong similarity between the major aspects of protein folding and protein recognition is one of the emerging fundamental principles in protein science. A crucial importance of steric complementarity in protein recognition is a well-established fact. The goal of this study was to assess the importance of the steric complementarity in protein folding, namely, in the packing of the secondary structure elements. Although the tight packing of protein structures, in general, is a well-known fact, a systematic study of the role of geometric complementarity in the packing of secondary structure elements has been lacking. To assess the role of the steric complementarity, we used a docking procedure to recreate the crystallographically determined packing of secondary structure elements in known protein structures by using the geometric match only. The docking results revealed a significant percentage of correctly predicted packing configurations. Different types of pairs of secondary structure elements showed different degrees of steric complementarity (from high to low: beta-beta, loop-loop, alpha-alpha, and alpha-beta). Interestingly, the relative contribution of the steric match in different types of pairs was correlated with the number of such pairs in known protein structures. This effect may indicate an evolutionary pressure to select tightly packed elements of secondary structure to maximize the packing of the entire structure. The overall conclusion is that the steric match plays an essential role in the packing of secondary structure elements. The results are important for better understanding of principles of protein structure and may facilitate development of better methods for protein structure prediction.

Binding Sites↗
PubMed2003

Asymmetric mutation rates at enzyme-inhibitor interfaces: implications for the protein-protein docking problem.

We have carried out a thorough and systematic sequence-structure study on how the pattern of conservation at the interface differs from the noninteracting surface in seven proteases and their inhibitors. As expected, the interface of a protease could be easily distinguished from the noninteracting surface by a concentrated area of conservation. In contrast, there was less distinction to be made between the interface and the noninteracting surface of inhibitors, and in five of the seven cases, a higher proportion of the interface area was variable compared to the rest of the surface. This is likely to cause a problem for binding-site prediction methods that assume the largest cluster of highly conserved residues on the surface of a protein corresponds to the interface. We conclude that such methods would succeed when applied to our protease test cases, but complications could arise with the inhibitors. These results also impact on methods to solve the protein-protein docking problem that use conservation at the interface to provide the location of the two protein binding sites prior to application of the docking algorithm.

Algorithms↗
PubMed2006

CIRSE: a solvation energy estimator compatible with flexible protein docking and design applications.

We present the Coordinate Internal Representation of Solvation Energy (CIRSE) for computing the solvation energy of protein configurations in terms of pairwise interactions between their atoms with analytic derivatives. Currently, CIRSE is trained to a Poisson/surface-area benchmark, but CIRSE is not meant to fit this benchmark exclusively. CIRSE predicts the overall solvation energy of protein structures from 331 NMR ensembles with 0.951+/-0.047 correlation and predicts relative solvation energy changes between members of individual ensembles with an accuracy of 15.8+/-9.6 kcal/mol. The energy of individual atoms in any of CIRSE's 17 types is predicted with at least 0.98 correlation. We apply the model in energy minimization, rotamer optimization, protein design, and protein docking applications. The CIRSE model shows some propensity to accumulate errors in energy minimization as well as rotamer optimization, but these errors are consistent enough that CIRSE correctly identifies the relative solvation energies of designed sequences as well as putative docked complexes. We analyze the errors accumulated by the CIRSE model during each type of simulation and suggest means of improving the model to be generally useful for all-atom simulations.

Models, Molecular↗
PubMed2001

Modeling of the bacterial luciferase-flavin mononucleotide complex combining flexible docking with structure-activity data.

Although the crystal structure of Vibrio harveyi luciferase has been elucidated, the binding sites for the flavin mononucleotide and fatty aldehyde substrates are still unknown. The determined location of the phosphate-binding site close to Arg 107 on the alpha subunit of luciferase is supported here by point mutagenesis. This information, together with previous structure-activity data for the length of the linker connecting the phosphate group to the isoalloxazine ring represent important characteristics of the luciferase-bound conformation of the flavin mononucleotide. A model of the luciferase-flavin complex is developed here using flexible docking supplemented by these structural constraints. The location of the phosphate moiety was used as the anchor in a flexible docking procedure performed by conformation search by using the Monte Carlo minimization approach. The resulting databases of energy-ranked feasible conformations of the luciferase complexes with flavin mononucleotide, omega-phosphopentylflavin, omega-phosphobutylflavin, and omega-phosphopropylflavin were filtered according to the structure-activity profile of these analogs. A unique model was sought not only on energetic criteria but also on the geometric requirement that the isoalloxazine ring of the active flavin analogs must assume a common orientation in the luciferase-binding site, an orientation that is also inaccessible to the inactive flavin analog. The resulting model of the bacterial luciferase-flavin mononucleotide complex is consistent with the experimental data available in the literature. Specifically, the isoalloxazine ring of the flavin mononucleotide interacts with the Ala 74-Ala 75 cis-peptide bond as well as with the Cys 106 side chain in the alpha subunit of luciferase. The model of the binary complex reveals a distinct cavity suitable for aldehyde binding adjacent to the isoalloxazine ring and flanked by other key residues (His 44 and Trp 250) implicated in the active site.

Binding Sites↗
PubMed1999

Macromolecular docking of a three-body system: the recognition of human growth hormone by its receptor.

Human growth hormone (hGH) binds to its receptor (hGHr) in a three-body interaction: one molecule of the hormone and two identical monomers of the receptor form a trimer. Curiously, the hormone-receptor interactions in the trimer are not equivalent and the formation of the complex occurs in a specific kinetic order (Cunningham BC, Ultsch M, De Vos AM, Mulkerrin MG, Clauser KR, Wells JA, 1991, Science 254:821-825). In this paper, we model the recognition of hGH to the hGHr using shape complementarity of the three-dimensional structures and macromolecular docking to explore possible binding modes between the receptor and hormone. The method, reported previously (Hendrix DK, Kuntz ID, 1998, Pacific symposium on biocomputing 1998, pp 1234-1244), is based upon matching complementary-shaped strategic sites on the molecular surface. We modify the procedure to examine three-body systems. We find that the order of binding seen experimentally is also essential to our model. We explore the use of mutational data available for hGH to guide our model. In addition to docking hGH to the hGHr, we further test our methodology by successfully reproducing 16 macromolecular complexes from X-ray crystal structures, including enzyme-inhibitor, antibody-antigen, protein dimer, and protein-DNA complexes.

Algorithms↗
PubMed1993

Docking the mitochondrial inhibitor protein IF1 to a membrane receptor different from the F1-ATPase beta subunit.

Monoclonal antibodies reacting with the inhibitor protein (IF1) of the mitochondrial ATPase/ATP synthase complex did not modify the IF1-induced inhibition of soluble F1 ATPase activity. On the contrary, they increased the ATPase activity of inverted electron-transport particles without inducing a significant release of IF1 from these particles. This suggested that IF1 could be linked to a membrane protein when it was not inhibiting the ATPase activity. IF1 antibodies have been used to show that IF1 can bind not only to the beta subunit of F1-ATPase [Klein, G., Satre, M., Dianoux, A. C. & Vignais, P. V. (1981) Biochemistry 20, 1339-1344] but also to a protein present in the inner-mitochondrial membrane. The cross-linking of IF1 to this membrane protein gave a product of M(r) 15000-16000 that migrated differently from IF1 and from the dimer of IF1 using SDS/PAGE. When the cross-linked product was obtained by using a cleavable cross-linking reagent, the complex between IF1 and the docking protein was partly dissociated and free IF1 was recovered. Considering the molecular mass of IF1, this docking protein for IF1 has apparent M(r) 5000-6000. The complex between IF1 and this receptor protein can be detected in low amounts by antibodies against IF1 in the absence of cross-linking reagent. Since this complex remained in the pellet after treatment of the membrane with Triton X-100, it should be a membrane protein. Therefore, IF1 can bind not only to its inhibitory-binding site at the beta subunit of F1, but also to a non inhibitory site which is a membrane protein of approximate M(r) 5000-6000.

Animals↗
PubMed2005

Data-driven docking for the study of biomolecular complexes.

With the amount of genetic information available, a lot of attention has focused on systems biology, in particular biomolecular interactions. Considering the huge number of such interactions, and their often weak and transient nature, conventional experimental methods such as X-ray crystallography and NMR spectroscopy are not sufficient to gain structural insight into these. A wealth of biochemical and/or biophysical data can, however, readily be obtained for biomolecular complexes. Combining these data with docking (the process of modeling the 3D structure of a complex from its known constituents) should provide valuable structural information and complement the classical structural methods. In this review we discuss and illustrate the various sources of data that can be used to map interactions and their combination with docking methods to generate structural models of the complexes. Finally a perspective on the future of this kind of approach is given.

Mass Spectrometry↗
PubMed2005

Structure, epitope mapping, and docking simulation of a gibberellin mimic peptide as a peptidyl mimotope for a hydrophobic ligand.

Using NMR spectroscopy and simulated annealing calculations, we determined the solution structure of the disulfide-linked cyclized decapeptide ACLPWSDGPC (SD), which is bound to an anti-(gibberellin A(4)) mAb 4-B8(8)/E9 and was found to be the first peptidyl mimotope for a hydrophobic ligand. The resulting structure of the peptide showed a beta-turn-like conformation in residues three to seven and the region converges well (average rmsd 0.54 A). The binding activity and the epitopes of the peptide to the antibody were assessed using saturation transfer difference (STD)-NMR experiments. We also conducted docking simulations between the peptide and the mAb to determine how the peptide is bound to the mAb. Resonances around the beta-turn-like conformation of peptide SD (residues 3-5) showed strong STD enhancement, which agreed well with results from docking simulation between peptide SD and the mAb. Together with the commonality of amino acid residues of the mAb involved in interactions with gibberellin A(4) (GA(4)) and peptide SD, we concluded that peptide SD is bound to the antigen-binding site of mAb 4-B8(8)/E9 as a GA(4) mimic, confirming evidence for the existence of peptide mimics even for hydrophobic ligands.

Amino Acid Sequence↗
PubMed2004

Measurement of intermolecular distances for the natural agonist Peptide docked at the cholecystokinin receptor expressed in situ using fluorescence resonance energy transfer.

Fluorescence resonance energy transfer is a powerful biophysical technique used to analyze the structure of membrane proteins. Here, we used this tool to determine the distances between a distinct position within a docked agonist and a series of distinct sites within the intramembranous confluence of helices and extracellular loops of the cholecystokinin (CCK) receptor. Pseudo-wild-type CCK receptor constructs having single reactive cysteine residues inserted into each of these sites were developed. The experimental strategy included the use of the full agonist, Alexa488-CCK, bound to these receptors as donor, with Alexa568 covalently bound to the specific sites within the CCK receptor as acceptor. Site-labeling was achieved by derivatization of intact cells with a novel fluorescent methanethiosulfonate reagent. A high degree of spectral overlap was observed between receptor-bound donor and receptor-derivatized acceptors, with no transfer observed for a series of controls representing saturation of the receptor binding site with nonfluorescent ligand and use of a null-reactive CCK receptor construct. The measured distances between the fluorophore within the docked agonist and the sites within the first (residue 102) and third (residue 341) extracellular loops of the receptor were shorter than those directed to the second loop (residue 204) or to intramembranous helix two (residue 94). These distances were accommodated well within a refined molecular model of the CCK-occupied receptor that is fully consistent with all existing structure-activity and photoaffinity-labeling studies. This approach provides the initial insights into the conformation of extracellular loop regions of this receptor and establishes clear differences from analogous loops in the rhodopsin crystal structure.

Amino Acid Sequence↗
PubMed2005

Nitrogenase complexes: multiple docking sites for a nucleotide switch protein.

Adenosine triphosphate (ATP) hydrolysis in the nitrogenase complex controls the cycle of association and dissociation between the electron donor adenosine triphosphatase (ATPase) (Fe-protein) and its target catalytic protein (MoFe-protein), driving the reduction of dinitrogen into ammonia. Crystal structures in different nucleotide states have been determined that identify conformational changes in the nitrogenase complex during ATP turnover. These structures reveal distinct and mutually exclusive interaction sites on the MoFe-protein surface that are selectively populated, depending on the Fe-protein nucleotide state. A consequence of these different docking geometries is that the distance between redox cofactors, a critical determinant of the intermolecular electron transfer rate, is coupled to the nucleotide state. More generally, stabilization of distinct docking geometries by different nucleotide states, as seen for nitrogenase, could enable nucleotide hydrolysis to drive the relative motion of protein partners in molecular motors and other systems.

Adenosine Diphosphate↗
PubMed1999

Activation of PPARgamma coactivator-1 through transcription factor docking.

Transcriptional coactivators have been viewed as constitutively active components, using transcription factors mainly to localize their functions. Here, it is shown that PPARgamma coactivator-1 (PGC-1) promotes transcription through the assembly of a complex that includes the histone acetyltransferases steroid receptor coactivator-1 (SRC-1) and CREB binding protein (CBP)/p300. PGC-1 has a low inherent transcriptional activity when it is not bound to a transcription factor. The docking of PGC-1 to peroxisome proliferator-activated receptor gamma (PPARgamma) stimulates an apparent conformational change in PGC-1 that permits binding of SRC-1 and CBP/p300, resulting in a large increase in transcriptional activity. Thus, transcription factor docking switches on the activity of a coactivator protein.

Animals↗
PubMed1993

Attempts to mimic docking processes of the immune system: recognition-induced formation of protein multilayers.

The assemblage of protein multilayers induced by molecular recognition, as seen, for example, in the immune cascade, has been mimicked by using streptavidin as a docking matrix. For these experiments, this protein matrix was organized on liposomes, monolayers at the air-water interface, and self-assembled layers on gold, all three containing biotin lipids. The docking of streptavidin to biotin at liposomal surfaces was confirmed by circular dichroism. Mixed double and triple layers of streptavidin, concanavalin A, antibody Fab fragments, and hormones are prepared at the air-water interface and on gold surfaces and were characterized by fluorescence microscopy and plasmon spectroscopy. With the use of biotin analogs that have lower binding constants it has been possible to achieve multiple formation and competitive replacement of the oriented protein assemblages.

Bacterial Proteins↗