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At least 1,639 records · Page 91Linked to original sources
PubMed2003

Cooperative fluctuations of unliganded and substrate-bound HIV-1 protease: a structure-based analysis on a variety of conformations from crystallography and molecular dynamics simulations.

The dynamics of HIV-1 protease, both in unliganded and substrate-bound forms have been analyzed by using an analytical method, Gaussian network model (GNM). The method is applied to different conformations accessible to the protein backbone in the native state, observed in crystal structures and snapshots from fully atomistic molecular dynamics (MD) simulation trajectories. The modes of motion obtained from GNM on different conformations of HIV-1 protease are conserved throughout the MD simulations. The flaps and 40's loop of the unliganded HIV-1 protease structure are identified as the most mobile regions. However, in the liganded structure these flaps lose mobility, and terminal regions of the monomers become more flexible. Analysis of the fast modes shows that residues important for stability are in the same regions of all the structures examined. Among these, Gly86 appears to be a key residue for stability. The contribution of residues in the active site region and flaps to the stability is more pronounced in the substrate-bound form than in the unliganded form. The convergence of modes in GNM to similar regions of HIV-1 protease, regardless of the conformation of the protein, supports the robustness of GNM as a potentially useful and predictive tool.

Binding Sites↗
PubMed2006

Combining docking and molecular dynamic simulations in drug design.

A rational approach is needed to maximize the chances of finding new drugs, and to exploit the opportunities of potential new drug targets emerging from genomic and proteomic initiatives, and from the large libraries of small compounds now readily available through combinatorial chemistry. Despite a shaky early history, computer-aided drug design techniques can now be effective in reducing costs and speeding up drug discovery. This happy outcome results from development of more accurate and reliable algorithms, use of more thoughtfully planned strategies to apply them, and greatly increased computer power to allow studies with the necessary reliability to be performed. Our review focuses on applications and protocols, with the main emphasis on critical analysis of recent studies where docking calculations and molecular dynamics (MD) simulations were combined to dock small molecules into protein receptors. We highlight successes to demonstrate what is possible now, but also point out drawbacks and future directions. The review is structured to lead the reader from the simpler to more compute-intensive methods. Thus, while inexpensive and fast docking algorithms can be used to scan large compound libraries and reduce their size, more accurate but expensive MD simulations can be applied when a few selected ligand candidates remain. MD simulations can be used: during the preparation of the protein receptor before docking, to optimize its structure and account for protein flexibility; for the refinement of docked complexes, to include solvent effects and account for induced fit; to calculate binding free energies, to provide an accurate ranking of the potential ligands; and in the latest developments, during the docking process itself to find the binding site and correctly dock the ligand a priori.

Computer Simulation↗
PubMed1996

Molecular dynamics simulations of apocytochrome b562--the highly ordered limit of molten globules.

BACKGROUND: Cytochrome B562 is a heme-containing, four-helix bundle. It has been proposed that the apo form of the protein is a molten globule. We present a molecular dynamics study of apocytochrome b562 to investigate its structural and dynamic properties. RESULTS: Our simulations suggest that all four helices are essentially intact and confirm that the experimental difficulties of assigning helical NOEs in the C-terminal helix are not due to structural disorder. The increased 'moltenness' of the apoprotein is due to an increased mobility of the sidechains. The small observed increase in compressibility for the apoprotein is proposed to be the result of an increase in the intrinsic protein compressibility, which is opposed by the increase in the size of the protein hydration shell. CONCLUSIONS: Apocytochrome b562 is postulated to be near the highly ordered limit of the molten globule state, a structure whose molten character is due primarily to increased sidechain mobility with concurrent loss in tertiary contacts between the helices, rather than changes in the folding topology or substantially increased disorder of the secondary structure.

Animals↗
PubMed2001

Forces and energetics of hapten-antibody dissociation: a biased molecular dynamics simulation study.

The unbinding of fluorescein from the single-chain Fv fragment of the 4D5Flu antibody is investigated by biased molecular dynamics with an implicit solvation model. To obtain statistically meaningful results, a large number of unbinding trajectories are calculated; they involve a total simulation time of more than 200 ns. Simulations are carried out with a time-dependent perturbation and in the presence of a constant force. The two techniques, which provide complementary information, induce unbinding by favoring an increase in the distance between the ligand and the antibody. This distance is an appropriate progress variable for the dissociation reaction and permits direct comparison of the unbinding forces in the simulations with data from atomic force microscopy (AFM). The time-dependent perturbation generates unfolding pathways that are close to equilibrium and can be used to reconstruct the mean force; i.e. the derivative of the potential of mean force, along the reaction coordinate. This is supported by an analysis of the overall unbinding profile and the magnitude of the mean force, which are similar to those of the unbinding force (i.e. the external force due to the time-dependent perturbation) averaged over several unbinding events. The multiple simulations show that unbinding proceeds along a rather well-defined pathway for a broad range of effective pulling speeds. Initially, there is a distortion of the protein localized in the C-terminal region followed by the fluorescein exit from the binding site. This occurs in steps that involve breaking of specific electrostatic and van der Waals interactions. It appears that the simulations do not explore the same barriers as those measured in the AFM experiments because of the much higher unfolding speed in the former. The dependence of the force on the logarithm of the loading rate is linear and the slope is higher than in the AFM, in agreement with experiment in other systems, where different slopes were observed for different regimes. Based on the unbinding events, mutations in the 4D5Flu antigen binding site are predicted to result in significant changes in the unbinding force.

Animals↗
PubMed2006

Molecular dynamics simulations of interaction between protein-tyrosine phosphatase 1B and a bidentate inhibitor.

AIM: To investigate the dynamic properties of protein-tyrosine phosphatase (PTP) 1B and reveal the structural factors responsible for the high inhibitory potency and selectivity of the inhibitor SNA for PTP1B. METHODS: We performed molecular dynamics (MD) simulations using a long time-scale for both PTP1B and PTP1B complexed with the inhibitor SNA, the most potent and selective PTP1B inhibitor reported to date. The trajectories were analyzed by using principal component analysis. RESULTS: Trajectory analyses showed that upon binding the ligand, the flexibility of the entire PTP1B molecule decreases. The most notable change is the movement of the WPD-loop. Our simulation results also indicated that electrostatic interactions contribute more to PTP1B-SNA complex conformation than the van der Waals interactions, and that Lys41, Arg47, and Asp48 play important roles in determining the conformation of the inhibitor SNA and in the potency and selectivity of the inhibitor. Of these, Arg47 contributed most. These results were in agreement with previous experimental results. CONCLUSION: The information presented here suggests that potent and selective PTP1B inhibitors can be designed by targeting the surface residues, for example the region containing Lys41, Arg47, and Asp48, instead of the second phosphate binding site (besides the active phosphate binding site).

Binding Sites↗
PubMed2007

Computational diagnosis of protein conformational diseases: short molecular dynamics simulations reveal a fast unfolding of r-LDL mutants that cause familial hypercholesterolemia.

The molecular basis of conformational diseases frequently resides in mutant proteins constituting a subset of the vast mutational space. While the subtleties of protein structure point to molecular dynamics (MD) techniques as promising tools for an efficient exploration of such a space, the average size of proteins and the time scale of unfolding events make this goal difficult with present computational capabilities. We show here, nevertheless, that an efficient approach is already feasible for modular proteins. Familial hypercholesterolemia (FH) is a conformational disease linked to mutations in the gene encoding the low density lipoprotein receptor. A high percentage of these mutations has been found in the seven small modular binding repeats of the receptor. Taking advantage of its small size, we have performed an in depth MD study of the fifth binding repeat. Fast unfolding dynamics have been observed in the absence of a structural bound calcium ion, which agrees with its reported essential role in the stability of the module. In addition, several mutations detected in FH patients have been analyzed, starting from the native conformation. Our results indicate that in contrast with the wild type protein and an innocuous control mutant, disease-related mutants experience, in short simulation times (2-8 ns), gross departures from the native state that lead to unfolded conformations and, in some cases, to binding site desorganization deriving in calcium release. Computational diagnosis of mutations leading to conformational diseases seems thus feasible, at least for small or modular pathogenic proteins.

Calcium↗
PubMed2005

Conformational determinants of tandem GU mismatches in RNA: insights from molecular dynamics simulations and quantum mechanical calculations.

Structure and energetic properties of base pair mismatches in duplex RNA have been the focus of numerous investigations due to their role in many important biological functions. Such efforts have contributed to the development of models for secondary structure prediction of RNA, including the nearest-neighbor model. In RNA duplexes containing GU mismatches, 5'-GU-3' tandem mismatches have a different thermodynamic stability than 5'-UG-3' mismatches. In addition, 5'-GU-3' mismatches in some sequence contexts do not follow the nearest-neighbor model for stability. To characterize the underlying atomic forces that determine the structural and thermodynamic properties of GU tandem mismatches, molecular dynamics (MD) simulations were performed on a series of 5'-GU-3' and 5'-UG-3' duplexes in different sequence contexts. Overall, the MD-derived structural models agree well with experimental data, including local deviations in base step helicoidal parameters in the region of the GU mismatches and the model where duplex stability is associated with the pattern of GU hydrogen bonding. Further analysis of the simulations, validated by data from quantum mechanical calculations, suggests that the experimentally observed differences in thermodynamic stability are dominated by GG interstrand followed by GU intrastrand base stacking interactions that dictate the one versus two hydrogen bonding scenarios for the GU pairs. In addition, the inability of 5'-GU-3' mismatches in different sequence contexts to all fit into the nearest-neighbor model is indicated to be associated with interactions of the central four base pairs with the surrounding base pairs. The results emphasize the role of GG and GU stacking interactions on the structure and thermodynamics of GU mismatches in RNA.

Base Pair Mismatch↗
PubMed2006

A study of collective atomic fluctuations and cooperativity in the U1A-RNA complex based on molecular dynamics simulations.

Cooperative interactions play an important role in recognition and binding in macromolecular systems. In this study, we find that cross-correlated atomic fluctuations can be used to identify cooperative networks in a protein-RNA system. The dynamics of the RRM-containing protein U1A-stem loop 2 RNA complex have been calculated theoretically from a 10 ns molecular dynamics (MD) simulation. The simulation was analyzed by calculating the covariance matrix of all atomic fluctuations. These matrix elements are then presented in the form of a two-dimensional grid, which displays fluctuations on a per residue basis. The results indicate the presence of strong, selective cross-correlated fluctuations throughout the RRM in U1A-RNA. The atomic fluctuations correspond well with previous biophysical studies in which a multiplicity of cooperative networks have been reported and indicate that the various networks identified in separate individual experiments are fluctuationally correlated into a hyper-network encompassing most of the RRM. The calculated results also correspond well with independent results from a statistical covariance analysis of 330 aligned RRM sequences. This method has significant implications as a predictive tool regarding cooperativity in the protein-nucleic acid recognition process.

Amino Acid Sequence↗
PubMed2007

Thermal denaturation of polyalanine peptide in water by molecular dynamics simulations and theoretical prediction of infrared spectra: helix-coil transition kinetics.

Perspectives in the helix-coil transition kinetics of secondary structures are examined by temperature-jump molecular dynamics (T-jump MD) simulations and theoretically calculated infrared (IR) spectra. Homopolymeric polyalanine, Ac-(A)(21)-NHMe (A21), is unfolded in water by T-jumps from 273 to 300 K approximately 450 K using AMBER ff99 and ff03 force fields. MD simulation results provide in silico evidence that 3(10)-helix and type I beta-turn motifs are highly probable in both ff99 and ff03 results. Temperature-dependent difference IR spectra of A21 do not possess an isosbestic point in both results, and isotope-labeled difference IR spectra in ff03 results predict characteristic profiles observed in experiments. Unfolding rates obtained from simulated time-resoled IR spectra are in good agreement with those estimated by helical contents, but they are still an order of magnitude smaller than experimental values. We demonstrate that the conventional criteria such as single-exponential fit of transient amide I absorbance, sigmoidal fit of temperature-dependent amide I absorbance, and Arrhenius plot of relaxation rates cannot guarantee the validity of assuming a two-state mechanism. We suggest a way of determining T(m) by the temperature dependence of center frequency and full width at half-maximum of amide I band. Overall, both ff99 and ff03 force fields give consistent results in reproducing key aspects concerned experimentally, but are not predominantly satisfactory in quantitative aspects.

Algorithms↗
PubMed2001

Dielectric relaxation in an enzyme active site: molecular dynamics simulations interpreted with a macroscopic continuum model.

Dielectric relaxation plays an important role in many chemical processes in proteins, including acid-base titration, ligand binding, and charge transfer reactions. Its complexity makes experimental characterization difficult, and so, theoretical approaches are valuable. The comparison of molecular dynamics free energy simulations with simpler models such as a dielectric continuum model is especially useful for obtaining qualitative insights. We have analyzed a charge insertion process that models deprotonation or mutation of an important side chain in the active site of the enzyme aspartyl-tRNA synthetase. Complexes with the substrate aspartate and the analogue asparagine were studied. The resulting dielectric relaxation was found to involve both ligand and side chain rearrangements in the active site and to account for a large part of the overall charging free energy. With the continuum model, charge insertion is performed along a two-step pathway: insertion into a static environment, followed by relaxation of the environment. These correspond to different physical processes and require different protein dielectric constants. A low value of approximately 1 is needed for the static step, consistent with the parametrization of the molecular mechanics charge set used. A value of 3-6 (depending on the exact insertion site and the nature of the ligand) is needed to describe the dielectric relaxation step. This moderate value indicates that, for this system, the local protein polarizability in the active site is within at most a factor of 2 of that expected at nonspecific positions in a protein interior.

Aspartate-tRNA Ligase↗
PubMed2005

Molecular dynamics simulations of complexes between wild-type and mutant anthrax protective antigen variants and a model anthrax toxin receptor.

Bacillus anthracis, a spore-forming infectious bacterium, produces a toxin consisting of three proteins: lethal factor (LF), edema factor (EF), and protective antigen (PA). LF and EF possess intracellular enzymatic functions, the net effect of which is to severely compromise host innate immunity. During an anthrax infection PA plays the critical role of facilitating entry of both EF and LF toxins into host cell cytoplasm. Crystal structures of all three of the anthrax toxins have been determined, as well as the crystal structure of the (human) von Willebrand factor A (integrin VWA/I domain) -- an anthrax toxin receptor. A theoretical structure of the complex between VWA/I and PA has also been reported. Here we report on the results of 1,000 psec molecular dynamics (MD) simulations carried out on complexes between the Anthrax Protective Antigen Domain 4 (PA-D4) and the von Willebrand Factor A (VWA/I). MD simulations (using Insight II software) were carried out for complexes containing wild-type (WT) PA-D4, as well as for complexes containing three different mutants of PA-D4, one containing three substitutions in the PA-D4 "small loop" (residues 679-693) (D683A/L685E/Y688C), one containing a single substitution at a key site at the PA-D4 -- receptor interface (K679A) and another containing a deletion of eleven residues at the C-terminus of PA (Delta724-735). All three sets of PA mutations have been shown experimentally to result in serious deficiencies in PA function. Our MD results are consistent with these findings. Major disruptions in interactions were observed between the mutant PA-D4 domains and the anthrax receptor during the MD simulations. Many secondary structural features in PA-D4 are also severely compromised when VWA complexes with mutant variants of PA-D4 are subjected to MD simulations. These MD simulation results clearly indicate the importance of the mutated PA-D4 residues in both the "small loop" and at the carboxyl terminus in maintaining a PA conformation that is capable of effective interaction with the anthrax toxin receptor.

Antigens, Bacterial↗
PubMed2007

Energetics and dynamics in MbCN: CN--vibrational relaxation from molecular dynamics simulations.

The dynamics of the cyanide anion bound to sperm-whale myoglobin is investigated using atomistic simulations. With density-functional theory, a 2D potential energy surface for the cyanide-heme complex is calculated. Two deep minima with a stabilization energy of approximately 50 kcal/mol corresponding to two different binding orientations (Fe-CN and Fe-NC) of the ligand are found. The Fe-CN conformation is favored over Fe-NC by several kcal/mol. Mixed quantum mechanics/molecular mechanics calculations show that the binding orientation affects the bond strength of the ligand, with a significantly different bond length and a 25 cm-1 shift in the fundamental CN-frequency. For the molecular dynamics (MD) simulations, a 3-center fluctuating charge model for the Fe-CN unit is developed that captures polarization and ligand-metal charge transfer. Stability arguments based on the energetics around the active site and the CN- frequency shifts suggest that the Fe-CN conformation with epsilon-protonation of His epsilon 64 are most likely, which is in agreement with experiment. Both equilibrium and nonequilibrium MD simulations are carried out to investigate the relaxation time scale and possible relaxation pathways in bound MbCN. The nonequilibrium MD simulations with a vibrationally excited ligand reveal that vibrational relaxation takes place on a time scale of hundreds of picoseconds within the active site. This finding supports the hypothesis that the experimentally observed relaxation rate (3.6 ps) reflects the repopulation of the electronic ground state.

Animals↗
PubMed2001

Mobility of the active site bound paraoxon and sarin in zinc-phosphotriesterase by molecular dynamics simulation and quantum chemical calculation.

The kinetic data published on phosphotriesterase (PTE), with various complexed metals, clearly indicates that the P=O and P=S bonds of phosphotriester and thiophosphotriester substrates, respectively, are strongly polarized by one or both of the active site complexed metal ions. However, this observation is not consistent with the three-dimensional X-ray crystal structure of zinc-substituted PTE with active site bound substrate analogue diethyl 4-methylbenzylphosphonate. In this structure, the distance between the phosphoryl oxygen and the nearest zinc is 3.4 A, a distance too large to afford strong polarization. In the present paper, the geometry and mobility of various PTE active site-substrate complexes are examined by performing both molecular dynamics (MD) simulations and quantum mechanical calculations. Two known substrates are considered, paraoxon and sarin, although their turnover rates vary about 100-fold. The results indicate that PTE forms a complex with either substrate in which the phosphoryl oxygen becomes strongly coordinated with the less buried zinc atom. It is shown that the geometry of the active site is changed when the protein is immersed in a water bath and relaxed by MD. The most substantial conformational change is the opening of the gateway in a pocket where the location of the leaving group is expected. The opening is observed for the pure enzyme as well as for the enzyme/substrate complexes and it ranges from 11 to 18 A. It is also shown that the pockets, in which the substrate substituents are localized, exhibit different flexibility and interact with the substrate with coordinated conformational adjustments.

Aryldialkylphosphatase↗
PubMed2005

Density-functional-based molecular-dynamics simulations of molten salts.

The physicochemical properties of two molten salts, namely, KCl and NaCl, have been studied with a molecular-dynamics approach using a density-functional-based tight-binding (DFTB) model. The obtained results have been compared with a number of previously reported simulations, carried out on smaller systems and using classical force-field techniques. A good agreement has been found for both structural parameters and macroscopic properties, such as self-diffusion coefficients. Furthermore, our DFTB results are very close to the available experimental data. From a more general point of view, our results demonstrate the applicability of DFTB as an efficient tool in the modeling of melts. At the same time, the quality of the obtained results supports the use of this as a reliable alternative to the more expensive ab initio dynamics approaches, if accurate parameters are provided.

Journal Article↗
PubMed2005

Binding of 5'-GMP to the GluR2 AMPA receptor: insight from targeted molecular dynamics simulations.

Guanine nucleotides behave as competitive antagonists at ionotropic glutamate receptors and show neuroprotective activity in different experimental excitotoxicity paradigms, both in vivo and in cultured cell preparations. Taking 5'-GMP as the reference nucleotide, we have tried to understand how these molecules interact with the agonist-binding site of the GluR2 alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionate (AMPA) receptor. Using a crystallographic model of the ligand-binding core of the GluR2 receptor in complex with kainate, we have previously analyzed the structural changes associated to the binding of agonists to the receptor and suggested a mechanism for the coupling of agonist binding to channel gating. In the present investigation we used the structure of the apo form of the receptor to probe the primary interactions between GMP and GluR2 by means of an automated docking program. A targeted molecular dynamics (TMD) simulation procedure was subsequently used to force the closing of the protein and to study the rearrangement of the ligand and surrounding amino acids. The resulting structure provides a plausible model of the nucleotide-receptor complex. Indirect support for the validity of our approach was obtained when the same methodology was shown to yield structures of the kainate-GluR2 and 6,7-dinitroquinoxaline-2,3-dione (DNQX)-GluR2 complexes that were in very good agreement with the published crystallographic structures. Both the stacking interaction between the phenyl ring of Tyr73 and the purine ring of GMP and a salt bridge between the phosphate group of GMP and Arg108 in the S1 domain, together with several hydrogen bonds, are proposed to secure the anchoring of GMP to the agonist-binding site. Unlike conventional competitive antagonists, such as DNQX, occupancy of the site by GMP still allows receptor segments S1 and S2 to close tightly around GMP without interacting with the critical residue Glu209 that triggers channel opening. Thus, GMP appears to be rather a false agonist than a competitive antagonist. This fact and the nature of the energy barriers that stabilize GMP bound to the closed form of the receptor provide an explanation for the unusual behavior of some guanine nucleotides in ligand-displacement experiments.

Animals↗
PubMed2003

Computational study of ketosteroid isomerase: insights from molecular dynamics simulation of enzyme bound substrate and intermediate.

Delta(5)-3-Ketosteroid Isomerase (KSI) catalyzes the isomerization of 5,6-unsaturated ketosteroids to their 4,5-unsaturated isomers at a rate approaching the diffusion limit. The isomerization reaction follows a two-step general acid-base mechanism starting with Asp38-CO(2)(-) mediated proton abstraction from a sp(3)-hybridized carbon atom, alpha to carbonyl group, providing a dienolate intermediate. In the second step, Asp38-CO(2)H protonates the C6 of the intermediate providing a 4,5-unsaturated ketosteroid. The details of the mechanism have been highly controversial despite several experimental and computational studies of this enzyme. The general acid-base catalysis has been proposed to involve either a catalytic diad or a cooperative hydrogen bond mechanism. In this paper, we report our results from the 1.5 nanosecond molecular dynamics (MD) simulation of enzyme bound natural substrate (E.S) and enzyme bound intermediate (E. In) solvated in a TIP3P water box. The final coordinates from our MD simulation strongly support the cooperative hydrogen bond mechanism. The MD simulation of E.S and E. In shows that both Tyr14 and Asp99 are hydrogen bonded to the O3 of the substrate or intermediate. The average hydrogen bonding distance between Tyr14-OH and O3 becomes shorter and exhibits less fluctuation on E.S --> E. In. We also observe dynamic motions of water moving in and out of the active site in the E.S structures. This free movement of water disappears in the E. In structures. The active site is shielded by hydrophobic residues, which come together and squeeze out the waters from the active site in the E. In complex.

Catalysis↗
PubMed2005

Short-time Fourier transform analysis of ab initio molecular dynamics simulation: collision reaction between CN and C4H6.

Collision reactions between cyano radical (CN) and dimethylacetylene (C4H6) are thought to occur in the atmosphere of Saturn's moon Titan. However, it is difficult to reproduce reactions occurring in unique environments to study their dynamical processes. In this study, collision reactions between CN and C4H6 were investigated using ab initio molecular dynamics (AIMD) simulations. The simulation results were categorized into three kinds: nonreactive collision, incorporation, and substitution. Short-time Fourier transform analysis of velocity autocorrelation functions obtained by the AIMD simulations, which has been recently developed by our research group, was performed to examine the nonequilibrium condition of the vibrational states. Spectrograms, which correspond to the time evolution of power spectra, clarify the relationship between the three reaction channels and the dynamical changes of the vibrational states.

Journal Article↗
PubMed2006

Characterization of de novo four-helix bundles by molecular dynamics simulations.

We have investigated the structure and dynamics of three cavitand-based four-helix bundles (caviteins) by computer simulation. In these systems, designed de novo, each of the four helices contain the identical basis sequence EELLKKLEELLKKG (N1). Each cavitein consists of a rigid macrocycle (cavitand) with four aryl linkages, to each of which is connected an N1 peptide by means of a linker peptide. The three caviteins studied here differ only in the linker peptide, which consist of one, two, or three glycine residues. Previous experimental work has shown that these systems exhibit very different behavior in terms of stability and oligomerization states despite the small differences in the linker peptide. Given that to date no three-dimensional structure is available for these caviteins, we have undertaken a series of molecular dynamics (MD) simulations in explicit water to try to rationalize the large differences in the experimentally observed behavior of these systems. Our results provide insight, for the first time, into why and how the cavitein with a single glycine linker forms dimers. In addition, our results indicate why although the two- and three-glycine-linked caviteins have similar stabilities, they have different native-like characteristics: the cavitein with three glycines can form a supercoiled helix, whereas the one with two glycines cannot. These findings may provide a useful guide in the rational de novo design of novel proteins with finely tunable structures and functions in the future.

Amino Acid Sequence↗