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PubMed1998

Sequence-dependent dynamics of TATA-Box binding sites.

We have carried out two nanosecond-length molecular dynamics simulations on a DNA oligomer, d(GCGTAAAAAAAACGC)2, which contains a weak binding site for the TATA-box binding protein. An analysis of the resulting trajectories shows that this oligomer behaves differently from a related oligomer [d(GCGTATATAAAACGC)2] studied earlier using the same protocol (Flatters, D., M. Young, D. L. Beveridge, and R. Lavery. 1997. Conformational properties of the TATA-box binding sequence of DNA. J. Biomol. Struct. & Dyn. 14:757-765), and which contains a strong binding site for the same protein. The two basepair mutations that relate these oligomers lead to significant changes in time-averaged structure and in dynamic behavior, which extend over entire length of the oligomer and appear to be compatible with the experimentally observed decrease of binding and functional activity. These results suggest that molecular dynamics simulations, taking into account explicit solvent and counterions, and avoiding the truncation of electrostatic interactions, are a powerful tool for investigating the indirect aspects of protein-nucleic acid recognition.

Base Sequence↗

PubMed1999

A study of vibrational relaxation of B-state carbon monoxide in the heme pocket of photolyzed carboxymyoglobin.

The vibrational energy relaxation of dissociated carbon monoxide in the heme pocket of sperm whale myoglobin has been studied using equilibrium molecular dynamics simulation and normal mode analysis methods. Molecular dynamics trajectories of solvated myoglobin were run at 300 K for both the delta- and epsilon-tautomers of the distal histidine, His64. Vibrational population relaxation times were estimated using the Landau-Teller model. For carbon monoxide (CO) in the myoglobin epsilon-tautomer, for a frequency of omega0 = 2131 cm-1 corresponding to the B1 state, T1epsilon(B1) = 640 +/- 185 ps, and for a frequency of omega0 = 2119 cm-1 corresponding to the B2 state, T1epsilon(B2) = 590 +/- 175 ps. Although the CO relaxation rates in both the epsilon- and delta-tautomers are similar in magnitude, the simulations predict that the vibrational relaxation of the CO is faster in the delta-tautomer. For CO in the myoglobin delta-tautomer, it was found that the relaxation times were identical within error for the two CO substate frequencies, T1delta(B1) = 335 +/- 115 ps and T1delta(B2) = 330 +/- 145 ps. These simulation results are in reasonable agreement with experimental results of Anfinrud and coworkers (unpublished results). Normal mode calculations were used to identify the dominant coupling between the protein and CO molecules. The calculations suggest that the residues of the myoglobin pocket, acting as a first solvation shell to the CO molecule, contribute the primary "doorway" modes in the vibrational relaxation of the oscillator.

Animals↗

PubMed1998

Static versus dynamic predictions of protective stepping following waist-pull perturbations in young and older adults.

The purposes of this study were: (1) to determine the frequency of protective stepping for balance recovery in subjects of different ages and fall-status, and (2) to compare predicted stepping based on a dynamic model (Pai and Patton, 1997. Journal of Biomechanics 30, 347 354) involving displacement and velocity combinations of the center of mass (COM) versus a static model based on displacement alone against experimentally induced stepping. Responses to three different magnitudes of forward waist pulls were recorded for 13 young, 18 older-non-fallers and 18 older-fallers. The COM phase plane trajectories derived from motion analysis were compared with the model-predicted threshold values for stepping. We found that the older fallers had the highest percentage of stepping trials (52%), followed by older-non-fallers (17.3%), and young (2.7%) at the lowest perturbation level. Younger subjects stepped less often than the elderly at the middle level. Everyone consistently stepped at the highest level of perturbation. Overall, the dynamic model showed better predictive capacity (65%) than the static model (5%) for estimating the initiation of stepping. Furthermore, the threshold for step initiation derived from the dynamic model could consistently predict when a step must occur. However, it was limited, especially among older fallers at the low perturbation level, in that it considered some steps 'unnecessary' that were presumably triggered by fear of falling or other factors.

Accidental Falls↗

PubMed2003

Observing membrane protein diffusion at subnanometer resolution.

Single sodium-driven rotors from a bacterial ATP synthase were embedded into a lipid membrane and observed in buffer solution at subnanometer resolution using atomic force microscopy (AFM). Time-lapse AFM topographs show the movement of single proteins within the membrane. Subsequent analysis of their individual trajectories, in consideration of the environment surrounding the moving protein, allow principal modes of the protein motion to be distinguished. Within one trajectory, individual proteins can undergo movements assigned to free as well as to obstacled diffusion. The diffusion constants of these two modes of motion are considerably different. Without the structural information about the membrane environment restricting the moving proteins, it would not be possible to reveal insight into these mechanisms. The high-resolution AFM topographs suggest that, in future studies, such data revealed under various physiological conditions will provide novel insights into molecular mechanisms that drive membrane protein assembly and supply excellent boundary conditions to model protein-protein arrangements.

Diffusion↗

PubMed2000

Transitions from alpha to pi helix observed in molecular dynamics simulations of synthetic peptides.

Molecular dynamics simulations were carried out for three 13-residue peptides of the form AcNH-A-A-E-X-A-E-A-H-A-A-E-K-A-CONH(2) with X = A, F, and W. All three peptides exhibited unexpected dynamical behavior, undergoing a transition from an alpha-helical to a pi-helical structure in the course of 5-ns trajectories in aqueous solution. Analysis of peptide length, accessible surface, interaction energies, hydrogen bonding, and dihedral angles was consistent with alpha --> pi transitions at 2800, 500, and 800 ps for X = A, F and W, respectively. The transitions occurred sequentially and cooperatively, propagating from the C- to the N-terminus for X = A and W and from the center toward both termini for X = F. The time scale of the overall transition ranged from 300 to 500 ps. For all three peptides the backbone structural transition was accompanied by a concerted rearrangement of the charged side chains, including a 3 A increase in the distance between carboxylate groups of Glu-3 and Glu-6. During the transition the peptide backbone hydrogen-bonding patterns were disrupted at the interface between the alpha-helical and nascent pi-helical regions, with peptide groups forming water-bridged hydrogen bonds. The peptide structures exhibited significant fluidity, with individual residues sampling alpha-, pi-, and 3(10)-helical conformations, as well as a "coil" state, without any intramolecular hydrogen bonds. The studied peptides have been designed to form alpha-helices when incorporated in novel hemoprotein model compounds, peptide-sandwiched mesohemes, which consist of two identical peptides covalently attached to an Fe(III) mesoporphyrin [Liu, D., Williamson, D. A., Kennedy, M. L., Williams, T. D., Morton, M. M., and Benson, D. R. (1999) J. Am. Chem. Soc. 121, 11798-11812]. The possibility of adopting pi-helical structures by the constituent peptides may influence the properties of the hemoprotein models.

Computer Simulation↗

PubMedDate not supplied

Molecular dynamic and free energy studies of primary resistance mutations in HIV-1 protease-ritonavir complexes.

To understand the basis of drug resistance of the HIV-1 protease, molecular dynamic (MD) and free energy calculations of the wild-type and three primary resistance mutants, V82F, I84V, and V82F/I84V, of HIV-1 protease complexed with ritonavir were carried out. Analysis of the MD trajectories revealed overall structures of the protein and the hydrogen bonding of the catalytic residues to ritonavir were similar in all four complexes. Substantial differences were also found near the catalytic binding domain, of which the double mutant complex has the greatest impact on conformational changes of the protein and the inhibitor. The tip of the HIV-1 protease flap of the double mutant has the greater degree of opening with respect to that of the others. Additionally, the phenyl ring of Phe82 moves away from the binding pocket S1', and the conformational change of ritonavir subsite P1' consequently affects the cavity size of the protein and the conformational energy of the inhibitor. Calculations of binding free energy using the solvent continuum model were able to reproduce the same trend of the experimental inhibition constant. The results show that the resistance mutants require hydrophobic residues to maintain the interactions in the binding pocket. Changes of the cavity volume correlate well with free energy penalties due to the mutation and are responsible for the loss of drug susceptibility.

Catalytic Domain↗

PubMed2003

Fluorescence quenching of dyes by tryptophan: interactions at atomic detail from combination of experiment and computer simulation.

Fluorescence spectroscopy and molecular dynamics (MD) simulation are combined to characterize the interaction of two organic fluorescent dyes, rhodamine 6G (R6G) and an oxazine derivative (MR121), with the amino acid tryptophan in aqueous solution. Steady-state and time-resolved fluorescence quenching experiments reveal the formation of essentially nonfluorescent ground-state dye/Trp complexes. The MD simulations are used to elucidate the molecular interaction geometries involved. The MD-derived probability distribution of the distance r between the centers of geometry of the dye and quencher ring systems, P(r), extends to higher distances for R6G than for MR121 due to population in the R6G/Trp system of fluorescent interaction geometries between Trp and the phenyl ring and ester group of the dye. The consequence of this is the experimental finding that under the conditions used in the simulations about 25% of the R6G dye is fluorescent in comparison with 10% of the MR121. Combining the above findings allows determination of the "quenching distance", r, above which no quenching occurs. r is found to be very similar (approximately 5.5 A) for both dye/Trp systems, corresponding to close to van der Waals contact. Both experimental dynamic Stern-Volmer analysis and the MD trajectories demonstrate that the main determinant of the fluorescence intensity is static quenching. The approach presented is likely to be useful in the structural interpretation of data obtained from fluorescent conjugates commonly used for monitoring the binding and dynamics of biomolecular systems.

Computer Simulation↗

PubMed2002

Azapeptides structurally based upon inhibitory sites of cystatins as potent and selective inhibitors of cysteine proteases.

A series of azapeptides as potential inhibitors of cysteine proteases were synthesized. Their structures, based on the binding center of cystatins, contain an azaglycine residue (Agly) in place of the evolutionarily conserved glycine residue in the N-terminal part of the enzyme binding region of cystatins. Incorporation of Agly should lead to deactivation of the acyl-enzyme complex formed against nucleophilic attack by water molecules in the final step of peptide bond hydrolysis. The majority of synthesized azapeptides shows high inhibitory potency toward the investigated cysteine proteases, papain, cathepsin B, and cathepsin K. One of them, Z-Arg-Leu-Val-Agly-Ile-Val-OMe (compound 17), which contains in its sequence the amino acid residues from the N-terminal binding segment as well as the hydrophobic residues from the first binding loop of human cystatin C, proved to be a highly potent and selective inhibitor of cathepsin B. It inhibits cathepsin B with a K(i) value of 0.088 nM. To investigate the influence of the structure of compound 17 for its inhibitory properties, we determined its conformation by means of NMR studies and theoretical calculations. The Z-Arg-Leu-Val-Agly fragment, covalently linked to Cys29 of cathepsin B, was also developed and modeled, in the catalytic pocket of the enzyme, through a molecular dynamics approach, to analyze ligand-protein interactions in detail. Analysis of the simulation trajectories generated using the AMBER force field provided us with atomic-level understanding of the conformational variability of this inhibitor, which is discussed in the context of other experimental and theoretical data.

Aza Compounds↗

PubMed2006

Microscopic and thermodynamic properties of the HFA134a-water interface: atomistic computer simulations and tensiometry under pressure.

A combined computational and experimental approach is used to determine the interfacial thermodynamic and structural properties of the liquid 1,1,1,2-tetrafluoroethane (HFA134a)-vapor and liquid HFA134a-water (HFA134a|W) interfaces at 298 K and saturation pressure. Molecular dynamics (MD) computer simulations reveal a stable interface between HFA134a and water. The "10-90" interfacial thickness is comparable with those typically reported for organic-water systems. The interfacial tension of the HFA134a|W interface obtained from the pressure tensor analysis of the MD trajectory is in good agreement with the experimental value determined using in situ high-pressure tensiometry. These results indicate that the potential models utilized are capable of describing the intermolecular interactions between these two fluids. The tension of the HFA134a|W interface is significantly lower than those typically observed for conventional oil-water interfaces and similar to that of the compressed CO(2)-water interface, observed at moderate CO(2) pressures. The MD and tensiometric results are also compared and contrasted with the HFA134a|W and chlorofluorocarbon-water tension values estimated from a parametric relationship. This represents the first report of the interfacial and microscopic properties of the (propellant) hydrofluoroalkanes (HFA)|W interface. The results presented here are of relevance in the design of surfactants capable of forming and stabilizing water-in-HFA microemulsions. Reverse aqueous microemulsions in HFA-based pressurized metered-dose inhalers are candidate formulations for the systemic delivery of biomolecules to and through the lungs.

Computer Simulation↗

PubMed1998

Computer-assisted rational design of immunosuppressive compounds.

We describe the rational design of immunosuppressive peptides without relying on information regarding their receptors or mechanisms of action. The design strategy uses a variety of topological and shape descriptors in combination with an analysis of molecular dynamics trajectories for the identification of potential drug candidates. This strategy was applied to the development of immunosuppressive peptides with enhanced potency. The lead compounds were peptides, derived from the heavy chain of HLA class I, that modulate immune responses in vitro and in vivo. In particular, a peptide derived from HLA-B2702, amino acids 75-84 (2702.75-84) prolonged skin and heart allograft survival in mice. The biological activity of the rationally designed peptides was tested in a heterotopic mouse heart allograft model. The molecule predicted to be most potent displayed an immunosuppressive activity approximately 100 times higher than the lead compound.

Animals↗

PubMed2006

The inherent structure landscape of a protein.

Using the Gō model of a real protein, we explore the landscape of its metastable structures. First, we show how the inherent structure energy density can be obtained from the probability density determined by sampling molecular dynamics trajectories and quenching. The analysis of the inherent structure landscape can characterize the folding transition. Then we show how thermodynamics of the inherent states can be established to study the equilibrium properties of proteins. Our work brings some elements into the current discussion about the protein dynamical transition. The study uses a simplified model to illustrate the ideas, but, as the inherent structure landscape is much simpler than the free energy surface of the protein, it appears to be accessible for an all-atom model of a small protein, at the expense of much longer calculations.

Protein Conformation↗

PubMed2002

Energetics of glycerol conduction through aquaglyceroporin GlpF.

Aquaglyceroporin GlpF selectively conducts water and linear polyalcohols, such as glycerol, across the inner membrane of Escherichia coli. We report steered molecular dynamics simulations of glycerol conduction through GlpF, in which external forces accelerate the transchannel conduction in a manner that preserves the intrinsic conduction mechanism. The simulations reveal channel-glycerol hydrogen bonding interactions and the stereoselectivity of the channel. Employing Jarzynski's identity between free energy and irreversible work, we reconstruct the potential of mean force along the conduction pathway through a time series analysis of molecular dynamics trajectories. This potential locates binding sites and barriers inside the channel; it also reveals a low energy periplasmic vestibule suited for efficient uptake of glycerol from the environment.

Aquaporins↗

PubMed1982

Correlation of movement patterns via pattern recognition.

A structural pattern recognition method for the quantitative determination of equivalence or similarity between movement patterns was examined. A chain encoding technique was implemented for the analysis of lower limb trajectories during walking and running. Conjoint angular displacement or angular velocity patterns provided kinematic data which were cross-correlated to determine geometric congruity of within and between subject motor patterns. The correlations of the movement patterns during different speeds of locomotion revealed numerical coefficients which consistently and quantitatively discriminated the similarity or dissimilarity of limb movement patterns.

Journal Article↗

PubMed1998

Brownian and essential dynamics studies of the HIV-1 integrase catalytic domain.

The three-dimensional structure of the active site region of the enzyme HIV-1 integrase is not unambiguously known. This region includes a flexible peptide loop that cannot be well resolved in crystallographic determinations. Here we present two different computational approaches with different levels of resolution and on different time-scales to understand this flexibility and to analyze the dynamics of this part of the protein. We have used molecular dynamics simulations with an atomic model to simulate the region in a realistic and reliable way for 1 ns. It is found that parts of the loop wind up after 300 ps to extend an existing helix. This indicates that the helix is longer than in the earlier crystal structures that were used as basis for this study. Very recent crystal data confirms this finding, underlining the predictive value of accurate MD simulations. Essential dynamics analysis of the MD trajectory yields an anharmonic motion of this loop. We have supplemented the MD data with a much lower resolution Brownian dynamics simulation of 600 ns length. It provides ideas about the slow-motion dynamics of the loop. It is found that the loop explores a conformational space much larger than in the MD trajectory, leading to a "gating"-like motion with respect to the active site.

Catalytic Domain↗

PubMed1999

Computer simulation of the interaction of non-steroidal anti-inflammatory drugs: indoprofen and NS398 with cyclooxygenase.

We have applied computer simulation technique to study interaction of two anti-inflammatory drugs (NSAIDs) indoprofen and NS398 with cyclooxygenase (COX-1 and COX-2) enzymes. We have also investigated conformational flexibility of the two drugs by systematic search and simulated annealing molecular dynamics (SAMD) methods. Both the drugs were docked in the cyclooxygenase channel using in house docking program IMF1. The complexes were energy minimised by molecular mechanics (MM) method. These were heated for 30 picoseconds (ps), equilibrated for 110 ps at 300K and subjected to 'production simulation' for 110 ps by molecular dynamics (MD) method using Sanderís module of AMBER 5.0 package and united atom force field mostly from PARM96.DAT. Integration was carried out with time step of 0.001 ps, distance dependent di-electric constant with scaling factor 2.0 for 1-4 interaction and cut-off distance for non-bonded pair-list equal to 8A. The non-bonded pair-list was upgraded after every 20 cycles. The coordinate output from MD trajectories is analysed using analysis package of AMBER 5.0, MOLMOL, P-CURVES 3.0 and in house packages: ANALMD, ANALP1. We have observed perturbative changes in COX-1 and COX-2 structures due to indoprofen and NS398. In case of indoprofen specific changes between COX-1 and COX-2 were noted in helix D, H6, S6 and helix H8 in the cyclooxygenase cavity. In case of NS398 these were in helix B in membrane binding domain, helix H6, S8 and S10 in cyclooxygenase cavity and helices H14-H16 in small lobe close to haem binding region. Implications of these results in enzyme selectivity by NSAIDs is discussed here.

Anti-Inflammatory Agents, Non-Steroidal↗

PubMed2002

Identification of sources contributing to Mid-Atlantic regional aerosol.

Source types or source regions contributing to the concentration of atmospheric fine particles measured at Brigantine National Wildlife Refuge, NJ, were identified using a factor analysis model called Positive Matrix Factorization (PMF). Cluster analysis of backward air trajectories on days of high- and low-factor concentrations was used to link factors to potential source regions. Brigantine is a Class I visibility area with few local sources in the center of the eastern urban corridor and is therefore a good location to study Mid-Atlantic regional aerosol. Sulfate (expressed as ammonium sulfate) was the most abundant species, accounting for 49% of annual average fine mass. Organic compounds (22%; expressed as 1.4 x organic carbon) and ammonium nitrate (10%) were the next abundant species. Some evidence herein suggests that secondary organic aerosol formation is an important contributor to summertime regional aerosol. Nine factors were identified that contributed to PM2.5 mass concentrations: coal combustion factors (66%, summer and winter), sea salt factors (9%, fresh and aged), motor vehicle/mixed combustion (8%), diesel/Zn-Pb (6%), incinerator/industrial (5%), oil combustion (4%), and soil (2%). The aged sea salt concentrations were highest in springtime, when the land breeze-sea breeze cycle is strongest. Comparison of backward air trajectories of high- and low-concentration days suggests that Brigantine is surrounded by sources of oil combustion, motor vehicle/mixed combustion, and waste incinerator/industrial emissions that together account for 17% of PM2.5 mass. The diesel/Zn-Pb factor was associated with sources north and west of Brigantine. Coal combustion factors were associated with coal-fired power plants west and southwest of the site. Particulate carbon was associated not only with oil combustion, motor vehicle/mixed combustion, waste incinerator/industrial, and diesel/Pb-Zn, but also with the coal combustion factors, perhaps through common transport.

Aerosols↗

PubMed2005

Trace gases and particulate matter emissions from wildfires and agricultural burning in Northeastern Mexico during the 2000 fire season.

An inventory of air pollutants emitted from forest and agricultural fires in Northeastern Mexico for the period of January to August of 2000 is presented. The emissions estimates were calculated using an emissions factor methodology. The inventory accounts for the emission of carbon monoxide (CO), methane, nonmethane hydrocarbons, ammonia, nitrogen oxides, and particulate matter (PM). Particulate matter emissions include estimates for fine PM and coarse PM. A total of 2479 wildfires were identified in the domain for the period of interest, which represented approximately 810,000 acres burned and 621,130 short tons emitted (81% being CO). The main source of information used to locate and estimate the extent of the fires came from satellite imagery. A geographic information system was used to determine the type of vegetation burned by each fire. More than 54% of the total area burned during the period of study was land on the State of Tamaulipas. However, >58% of the estimated emissions came from the State of Coahuila. This was because of the mix of vegetation types burned in each state. With respect to the temporal distribution, 76.9% of the fires occurred during the months of April and May consuming almost 78% of the total area burned during the period of study. Analysis of wind forward trajectories of air masses passing through the burned areas and 850-mb wind reanalyses indicate possible transboundary transport of the emissions from Mexico to the United States during the occurrence of the major wildfires identified.

Agriculture↗

PubMedDate not supplied

Theoretical comparison between structural and dynamical features of Dolastatins 11 and 12 antineoplastic depsipeptides.

Molecular mechanics (MM) and dynamics (MD) calculations in vacuo and in water have been performed for the natural cyclodepsipeptides Dolastatins 11 and 12 isolated from the sea hare Dolabella auricularia. The analysis of the MD trajectories for the two systems can give useful insight on the backbone structural features, side-chain and peptide-water interactions as well as on the inter- and intra-molecular hydrogen bonds. A comparison between the selected and analysed lowest energy isomers shows the different conformational behaviour of the compounds. Finally, with the aim to ascertain a structure-activity relationship for the two peptides, the interactions of both Dolastatins with water, generic hydrophobic environment, magnesium and calcium ions have been investigated by means of the GRID program.

Depsipeptides↗