Efficient docking of peptides to proteins without prior knowledge of the binding site

Reliability in docking of ligand molecules to proteins or other targets is an important challenge for molecular modeling. Applications of the docking technique include not only prediction of the binding mode of novel drugs, but also other problems like the study of protein-protein interactions. Here we present a study on the reliability of the results obtained with the popular AutoDock program. We have performed systematical studies to test the ability of AutoDock to reproduce eight different protein/ligand complexes for which the structure was known, without prior knowledge of the binding site. More specifically, we look at factors influencing the accuracy of the final structure, such as the number of torsional degrees of freedom in the ligand. We conclude that the Autodock program package is able to select the correct complexes based on the energy without prior knowledge of the binding site. We named this application blind docking, as the docking algorithm is not able to "see" the binding site but can still find it. The success of blind docking represents an important finding in the era of structural genomics.     

Inhibition of nitric oxide synthase isoforms by tris-malonyl-C(60)-fullerene adducts

C(3)-tris-malonyl-C(60)-fullerene and D(3)-tris-malonyl-C(60)-fullerene derivatives inhibit citrulline and NO formation by all three nitric oxide synthase isoforms in a manner fully reversible by dilution. The inhibition of citrulline formation by C(3)-tris-malonyl-C(60)-fullerene occurs with IC(50) values of 24, 17, and 123 microM for the neuronal, endothelial, and inducible nitric oxide synthase (NOS) isoforms, respectively. As measured at 100 microM l-arginine, neuronal NOS-catalyzed nitric oxide formation was inhibited 50% at a concentration of 25 microM C(3)-tris-malonyl-C(60)-fullerene. This inhibition was a multisite, positively cooperative inhibition with a Hill coefficient of 2.0. C(3)-tris-malonyl-C(60)-fullerene inhibited the arginine-independent NADPH-oxidase activity of nNOS with an IC(50) value of 22 microM but had no effects on its cytochrome c reductase activity at concentrations as high as 300 microM. The inhibition of nNOS activity by C(3)-tris-malonyl-C(60)-fullerene reduced the maximal velocity of product formation but did not alter the EC(50) value for activation by calmodulin. C(3)-tris-malonyl-C(60)-fullerene reduced the maximal velocity of citrulline formation by inducible NOS without altering the K(m) for l-arginine substrate or the EC(50) value for tetrahydrobiopterin cofactor. As measured by sucrose density gradient centrifugation, fully inhibitory concentrations of C(3)-tris-malonyl-C(60)-fullerene did not produce a dissociation of nNOS dimers into monomers. These observations are consistent with the proposal that C(3)-tris-malonyl-C(60)-fullerene inhibits the inter-subunit transfer of electrons, presumably by a reversible distortion of the dimer interface.     

Interaction of cytochrome c with cytochrome oxidase: two different docking scenarios

Cytochrome c is the specific and efficient electron transfer mediator between the two last redox complexes of the mitochondrial respiratory chain. Its interaction with both partner proteins, namely cytochrome c(1) (of complex III) and the hydrophilic Cu(A) domain (of subunit II of oxidase), is transient, and known to be guided mainly by electrostatic interactions, with a set of acidic residues on the presumed docking site on the Cu(A) domain surface and a complementary region of opposite charges exposed on cytochrome c. Information from recent structure determinations of oxidases from both mitochondria and bacteria, site-directed mutagenesis approaches, kinetic data obtained from the analysis of isolated soluble modules of interacting redox partners, and computational approaches have yielded new insights into the docking and electron transfer mechanisms. Here, we summarize and discuss recent results obtained from bacterial cytochrome c oxidases from both Paracoccus denitrificans, in which the primary electrostatic encounter most closely matches the mitochondrial situation, and the Thermus thermophilus ba(3) oxidase in which docking and electron transfer is predominantly based on hydrophobic interactions.     

Ligand binding: functional site location,similarity and docking

Computational methods for the detection and characterisation of protein ligand-binding sites have increasingly become an area of interest now that large amounts of protein structural information are becoming available prior to any knowledge of protein function. There have been particularly interesting recent developments in the following areas: first, functional site detection, whereby protein evolutionary information has been used to locate binding sites on the protein surface; second, functional site similarity, whereby structural similarity and three-dimensional templates can be used to compare and classify and potentially locate new binding sites; and third, ligand docking, which is being used to find and validate functional sites, in addition to having more conventional uses in small-molecule lead discovery.     

Interaction of the dibutylchloromethyltin chloride binding site with the carbodiimide binding site in mitochondria

An examination of the effect of dibutylchloromethyltin/chloride on the carbodiimide binding proteolipid of mitrochondrial ATPase has revealed that in the presence of the alkyltin, (1) binding of dicyclohexycarbodiimide is decreased (2) the electron spin resonance spectrum of a nitroxide analogue of dicyclohexylcarbodiimide exhibits line broadening characteristic of either an increase of polarity or a decrease in viscosity of the carbodiimide binding site (3) the rate of reduction of the nitroxide probe by ascorbate is increased threefold. These phenomena suggest a possible mode of action for the inhibition of ATP synthesis by alkyltins.     

Interaction of cytochrome c with mitochondrial proteins and cybacrone-dextran

Interaction of cytochrome c with electron carriers in intact and damaged (with destroyed outer membrane) rat liver mitochondria was studied. It was shown that the increase in ionic strength causes changes in the respiration rate of damaged mitochondria due to the reduction of the cytochrome c affinity for its binding sites in the organelles. This suggests that cytochrome c concentration in the intermembrane space of intact mitochondria is increased by salts, whereas the increase in ionic strength has a slight influence on the rates of succinate oxidase and external rotenone-insensitive NADH-oxidase of intact mitochondria. At low ionic strength values, the Michaelis constant (KM) value of external NADH-oxidase for cytochrome c exceeds by one order of magnitude that for succinate oxidase, while the maximal activity of these two systems is nearly the same. The increase in ionic strength causes an increase in the KM value for both oxidases. Interaction of cytochrome c with mitochondrial proteins was modelled by cytochrome c interaction with cibacron-dextran anions. It was concluded that the ionic strength-sensitive electrostatic interactions play a decisive role in cytochrome c binding to electron carriers in mitochondrial membranes. However, cytochrome c content and its binding parameters in intact-mitochondrial membranes prevent the latent activity of external NADH oxidase to be revealed in intact mitochondria after the increase in the ionic strength of the surrounding medium.     

Interaction of uncouplers with the mitochondrial membrane: a high-affinity binding site

2-Nitro-4-azidocarbonylcyanide phenylhydrazone (N₃CCP), a potent water-soluble uncoupler at pH 6–8, was used to determine the nature of binding of the uncoupler to the mitochondrial membrane. Equilibrium binding studies with N₃CCP showed that isolated pigeon heart mitochondria contain 1.6 ± 0.3 high-affinity binding sites per cytochrome a. Several different types of chemical uncouplers were also found to bind to the same high-affinity site as evidenced by their observed competition with N₃CCP. The potassium ionophore valinomycin and the respiratory inhibitor antimycin A did not affect uncoupler binding to the high-affinity sites nor did active respiration of the mitochondria. The number of high-affinity binding sites was essentially unchanged by extraction of 80% of the mitochondrial phospholipids. The ability of the uncouplers to bind to the high-affinity binding sites is proportional to the uncoupler activities. These data support the idea that the high-affinity binding sites of mitochondria are protein(s) which are involved in the coupling reactions of oxidative phosphorylation and that uncoupler bound at these sites is responsible for the uncoupling activity.     

Interaction of mammalian end binding proteins with CAP-Gly domains of CLIP-170 and p150(glued)

End binding proteins (EBs) track growing microtubule ends and play a master role in organizing dynamic protein networks. Mammalian cells express up to three different EBs (EB1, EB2, and EB3). Besides forming homodimers, EB1 and EB3 also assemble into heterodimers. One group of EB-binding partners encompasses proteins that harbor CAP-Gly domains. The binding properties of the different EBs towards CAP-Gly proteins have not been systematically investigated. This information is, however, important to compare and contrast functional differences. Here we analyzed the interactions between CLIP-170 and p150(glued) CAP-Gly domains with the three EB homodimers and the EB1-EB3 heterodimer. Using isothermal titration calorimetry we observed that some EBs bind to the individual CAP-Gly domains with similar affinities while others interact with their targets with pronounced differences. We further found that the two types of CAP-Gly domains use alternative mechanisms to target the C-terminal domains of EBs. We succeeded to solve the crystal structure of a complex composed of a heterodimer of EB1 and EB3 C-termini together with the CAP-Gly domain of p150(glued). Together, our results provide mechanistic insights into the interaction properties of EBs and offer a molecular framework for the systematic investigation of their functional differences in cells.     

Interaction of ADP-ribosylated actin with actin binding proteins.

Actin ADP-ribosylated at Arg177 was previously shown not to polymerise after increasing the ionic strength, but to cap the barbed ends of filaments. Here we confirm that the polymerisation of ADP-ribosylated actin is inhibited, however, under specific conditions the modified actin copolymerises with native actin, indicating that its ability to take part in normal subunit interactions within filaments is not fully eliminated. We also show that ADP-ribosylated actin forms antiparallel but not parallel dimers: the former are not able to form filaments. ADP-ribosylated actin interacts with deoxyribonuclease I, vitamin D binding protein, thymosin beta(4), cofilin and gelsolin segment 1 like native actin. Interaction with myosin subfragment 1 revealed that the potential of the modified actin to aggregate into oligomers or short filaments is not fully eliminated.     

Interaction between stretch of residues 633-642 (actin binding site) and nucleotide binding site on skeletal myosin subfragment 1 heavy chain

Using a complementary sequence or antipeptide to selectively neutralize the stretch of residues 633-642 of skeletal myosin heavy chain, we recently demonstrated that this segment is an actin binding site operating in the absence as in the presence of nucleotide and that this stretch 633-642 is not part of the nucleotide binding site [Chaussepied & Morales (1988) Proc. Natl. Acad. Sci. U.S.A. 85, 7471-7475]. In the present study, we determined that the covalent cross-linking of the antipeptide to the stretch 633-642 [induced by 1-ethyl-3-[3-(dimethylamino)propyl]carbodiimide] does not alter the overall polypeptide conformation since no changes were observed on the far-ultraviolet CD spectra and thiol reactivity measurements. The presence of the antipeptide did not influence significantly the enhancement of tryptophan fluorescence induced by ATP.Mg2+ or ADP.Mg2+ binding to the myosin head (S1) nor did it on the ATP.Mg2+-induced tryptic proteolysis of S1 heavy chain. Moreover, fluorescence quenching studies, using acrylamide and the analogue, 1,N6-ethenoadenosine 5'-triphosphate, indicated that the nucleotide bound to antipeptide-S1 complex has an accessibility to the solute quencher close to that observed when it is bound to native S1. Additionally, neutralization of the stretch 633-642 of the S1 heavy chain by the antipeptide did not influence the stabilization of the Mg2+.ADP.sodium vanadate-S1 complex. On the other hand, experiments using antipeptide-induced protection against the cleavage of the S1 heavy chain by Arg-C protease demonstrated that the presence of Mg2+.ADP.sodium vanadate in the S1 nucleotide site did not affect the interaction of the antipeptide with the stretch of residues 633-642.(ABSTRACT TRUNCATED AT 250 WORDS)     

The inhibitory binding site(s) of Zn2+ in cytochrome c oxidase

EXAFS analysis of Zn binding site(s) in bovine-heart cytochrome c oxidase and characterization of the inhibitory effect of internal zinc on respiratory activity and proton pumping of the liposome reconstituted oxidase are presented. EXAFS identifies tetrahedral coordination site(s) for Zn(2+) with two N-histidine imidazoles, one N-histidine imidazol or N-lysine and one O-COOH (glutamate or aspartate), possibly located at the entry site of the proton conducting D pathway in the oxidase and involved in inhibition of the oxygen reduction catalysis and proton pumping by internally trapped zinc.     

Interaction of echinomycin with An.Tn. and (AT)n regions flanking its CG binding site.

We have prepared DNA fragments containing the sequences A15CGT15, T15CGA15 and T(AT)8CG(AT)15 cloned within the SmaI site of the pUC19 polylinker. These have been used as substrates in footprinting experiments with DNase I and diethylpyrocarbonate probing the effects of echinomycin, binding to the central CG, on the structure of the surrounding sequences. No clear DNase I footprints are seen with T15CGA15 though alterations in the nuclease susceptibility of surrounding regions suggest that the ligand is binding, albeit weakly at this site. All the other fragments show the expected footprints around the CG site. Regions of An and Tn are rendered much more reactive to DNase I and adenines on the 3'-side of the CG become hyperreactive to diethylpyrocarbonate. Regions of alternating AT show unusual changes in the presence of the ligand. At low concentrations (5 microM) cleavage of TpA is enhanced, whereas at higher concentrations a cleavage pattern with a four base pair repeat is evident. A similar pattern is seen with micrococcal nuclease. Modification by diethylpyrocarbonate is strongest at alternate adenines which are staggered in the 5'-direction across the two strands. We interpret these changes by suggesting secondary drug binding within regions of alternating AT, possibly to the dinucleotide ApT. DNase I footprinting experiments performed at 4 degrees C revealed neither enhancements nor footprints for flanking regions of homopolymeric A and T suggesting that the conformational changes are necessary consequence of drug binding.     

Scoring optimisation of unbound protein-protein docking including protein binding site predictions

The prediction of the structure of the protein-protein complex is of great importance to better understand molecular recognition processes. During systematic protein-protein docking, the surface of a protein molecule is scanned for putative binding sites of a partner protein. The possibility to include external data based on either experiments or bioinformatic predictions on putative binding sites during docking has been systematically explored. The external data were included during docking with a coarse-grained protein model and on the basis of force field weights to bias the docking search towards a predicted or known binding region. The approach was tested on a large set of protein partners in unbound conformations. The significant improvement of the docking performance was found if reliable data on the native binding sites were available. This was possible even if data for single key amino acids at a binding interface are included. In case of binding site predictions with limited accuracy, only modest improvement compared with unbiased docking was found. The optimisation of the protocol to bias the search towards predicted binding sites was found to further improve the docking performance resulting in approximately 40% acceptable solutions within the top 10 docking predictions compared with 22% in case of unbiased docking of unbound protein structures.     

Interaction of cytochrome c with reaction centers of Rhodopseudomonas sphaeroides R-26: localization of the binding site by chemical cross-linking and immunochemical studies

The location of the cytochrome binding site on the reaction center of Rhodopseudomonas sphaeroides was studied by two different approaches. In one, cross-linking agents, principally dithiobis(propionimidate) and dimethyl suberimidate, were used to link cytochrome c and cytochrome c2 to reaction centers; in the other, the inhibition of electron transfer by antibodies against the subunits was investigated. Cytochrome c (horse) cross-linked to the L and M subunits, whereas cytochrome c2 (R. sphaeroides) cross-linked only to the L subunit. The cross-linked reaction center-cytochrome complexes were isolated by affinity chromatography. The rate of electron transfer in the cross-linked cytochrome c2 complex was the same as that in the un-cross-linked complex. However, when cytochrome c was used, the rate in the cross-linked complex was about 15 times slower than that in the un-cross-linked complex. Fab fragments of antibodies specific against the L and M subunits blocked electron transfer from both cytochrome c (horse) and cytochrome c2 (R. sphaeroides). Antibodies specific for the H subunit did not block either reaction. We conclude that the cytochrome binding site on the reaction center is close (approximately 10 A) to both the L and M subunits, possibly in a cleft between them.     

Interaction of triiodothyronine-biotin conjugate with binding proteins in immunoassay systems

The study presents a new design of a test system for the detection of a thyroid hormone, free 3,3??,5-triiodo-L-thyronine (free T₃), by enzyme-linked immunosorbent assay (ELISA) and immunoradiometric assay (IRMA) in human blood serum. For this purpose, a low-molecular-weight bifunctional conjugate of T₃ with biotin (Bt) was synthesized. The conjugate T₃-Bt can be bound to biotin-binding proteins on a solid support via its biotin residue, and T₃ portion of the conjugate can interact with a monoclonal antibody against T₃ (anti-T₃-MAb) that is labeled with horseradish peroxidase or iodine-125 in ELISA and IRMA, respectively. The immunochemical interaction is hindered if the T₃ residue is involved in a preformed complex of T₃-Bt with avidin in a solid phase. Computer simulations revealed that the iodothyronine residue is shielded by a glycan component of avidin in such a complex. Binding of T₃-Bt to both T₃-free sites of anti-T₃-MAb and to avidin on a solid support was achieved by delayed introduction of T₃-Bt into avidin-coated plates that were preliminarily co-incubated with labeled anti-T₃-MAb and the analyzed T₃ sample.     

Inhibitor binding studies of Mycobacterium tuberculosis MraY (Rv2156c): Insights from molecular modeling,docking, and simulation studies

Abstract

Tuberculosis (TB) is a contagious disease caused by Mycobacterium tuberculosis (M.tb) or tubercule bacillus, and H37Rv is the most studied clinical strain. The recent development of resistance to existing drugs is a global health-care challenge to control and cure TB. Hence, there is a critical need to discover new drug targets in M.tb. The members of peptidoglycan biosynthesis pathway are attractive target proteins for antibacterial drug development. We have performed in silico analysis of M.tb MraY (Rv2156c) integral membrane protein and constructed the three-dimensional (3D) structure model of M.tb MraY based on homology modeling method. The validated model was complexed with antibiotic muraymycin D2 (MD2) and was used to generate structure-based pharmacophore model (e-pharmacophore). High-throughput virtual screening (HTVS) of Asinex database and molecular docking of hits was performed to identify the potential inhibitors based on their mode of interactions with the key residues involved in M.tb MraY–MD2 binding. The validation of these molecules was performed using molecular dynamics (MD) simulations for two best identified hit molecules complexed with M.tb MraY in the lipid bilayer, dipalmitoylphosphatidyl-choline (DPPC) membrane. The results indicated the stability of the complexes formed and retained non-bonding interactions similar to MD2. These findings may help in the design of new inhibitors to M.tb MraY involved in peptidoglycan biosynthesis.     

The binding of cytochrome c to neuroglobin: a docking and surface plasmon resonance study

It has recently been proposed that the role of neuroglobin in the protection of neurons from ischaemia induced cell death requires the formation of a transient complex with cytochrome c. No such complex has yet been isolated. Here, we present the results of soft docking calculations, which indicate one major binding site for cytochrome c to neuroglobin. The results yield a plausible structure for the most likely complex structure in which the hemes of each protein are in close contact. NMR analysis identifies the formation of a weak complex in which the heme group of cytochrome c is involved. surface plasmon resonance studies provide a value of 45muM for the equilibrium constant for cytochrome c binding to neuroglobin, which increases significantly as the ionic strength of the solution increases. The temperature dependence of the binding constant indicates that the complex formation is associated with a small unfavourable enthalpy change (1.9kcalmol(-1)) and a moderately large, favourable entropy change (14.8calmol(-1)deg(-1)). The sensitivity of the binding constant to the presence of salt suggests that the complex formation involves electrostatic interactions.     

Interaction of membrane-spanning proteins with peripheral and lipid-anchored membrane proteins: perspectives from protein-lipid interactions (Review)

Studies of lipid-protein interactions in double-reconstituted systems involving both integral and peripheral or lipid-anchored proteins are reviewed. Membranes of dimyristoyl phosphatidylglycerol containing either myelin proteolipid protein or cytochrome c oxidase were studied. The partner peripheral proteins bound to these membranes were myelin basic protein or cytochrome c, respectively. In addition, the interactions between the myelin proteolipid protein and avidin that was membrane-anchored by binding to N-biotinyl phosphatidylethanolamine were studied in dimyristoyl phosphatidylcholine membranes. Steric exclusion plays a significant role when sizes of the peripheral protein and transmembrane domain of the integral protein are comparable. Even so, the effects on avidin-linked lipids are different from those induced by myelin basic protein on freely diffusible lipids, both interacting with the myelin proteolipid protein. Both the former and the cytochrome c/cytochrome oxidase couple evidence a propagation of lipid perturbation out from the intramembrane protein interface that could be a basis for formation of microdomains.