Biomedical subjects

Jeremy C Smith

Publications and source records attributed to Jeremy C Smith.

At least 19 recordsLinked to original sources

PubMed2007

Protein dynamics from X-ray crystallography: anisotropic, global motion in diffuse scattering patterns.

Understanding X-ray crystallographic diffuse scattering is likely to improve our comprehension of equilibrium collective protein dynamics. Here, using molecular dynamics (MD) simulation, a detailed analysis is performed of the origins of diffuse scattering in crystalline Staphylococcal nuclease, for which the complete diffuse scattering pattern has been determined experimentally. The hydrogen-atom contribution and the scattering range over which the scattering can be considered to be a sum of solvent and protein scattering are determined. Two models of correlated protein motion are investigated by calculating the model-derived diffuse scattering and comparing with the scattering calculated directly from MD trajectories. In one model, previously used in diffuse scattering interpretation, the atomic displacement correlations decay isotropically with increasing separation. Model correlation lengths are obtained by refining the model scattering against the simulation-derived scattering pattern, and are found to be significantly different from those correlation lengths derived directly from the MD trajectories. Furthermore, the convergence between the model-derived and MD-derived scattering is poor. The second model, in which the displacement correlations are calculated from the principal components of the MD trajectories, is capable of fully reproducing the MD-derived diffuse scattering if the approximately 50% lowest-frequency modes are included. However, a small number ( approximately 10) of lowest-frequency and largest-amplitude modes dominates the diffuse scattering and thus the correlated protein motions. A detailed analysis of the principal components is performed. In particular, the effective free energy profile associated with each principle mode is analyzed and the eigenfrequency and damping coefficient computed using a model of Brownian dynamics. Those collective modes with effective frequencies below approximately 0.5 THz, including those that determine the diffuse scattering, are overdamped.

Anisotropy↗

PubMed2006

Conformational heterogeneity and low-frequency vibrational modes of proteins.

Molecular dynamics simulation and normal mode analysis are used to calculate the vibrational density of states of dihydrofolate reductase complexed with nicotinamide adenine dinucleotide phosphate at 120 K and the results are compared with the experimental spectrum derived from inelastic neutron scattering. The simulation results indicate that the experimental spectrum arises from an average over proteins trapped in different conformations with structural differences mainly in the loop regions, and that these conformations have significantly different low-frequency (<20 cm(-1)) spectra. Thus, the experimentally measured spectrum is an average over the vibrational modes of different protein conformations and is thus inhomogeneously broadened. The implications of this broadening for future neutron scattering experiments and ligand binding calculations are discussed.

Computer Simulation↗

PubMed2006

Orientation preferences of backbone secondary amide functional groups in peptide nucleic acid complexes: quantum chemical calculations reveal an intrinsic preference of cationic D-amino acid-based chiral PNA analogues for the P-form.

Geometric descriptions of nonideal interresidue hydrogen bonding and backbone-base water bridging in the minor groove are established in terms of polyamide backbone carbonyl group orientation from analyses of residue junction conformers in experimentally determined peptide nucleic acid (PNA) complexes. Two types of interresidue hydrogen bonding are identified in PNA conformers in heteroduplexes with nucleic acids that adopt A-like basepair stacking. Quantum chemical calculations on the binding of a water molecule to an O2 base atom in glycine-based PNA thymine dimers indicate that junctions modeled with P-form backbone conformations are lower in energy than a dimer comprising the predominant conformation observed in A-like helices. It is further shown in model systems that PNA analogs based on D-lysine are better able to preorganize in a conformation exclusive to P-form helices than is glycine-based PNA. An intrinsic preference for this conformation is also exhibited by positively charged chiral PNA dimers carrying 3-amino-D-alanine or 4-aza-D-leucine residue units that provide for additional rigidity by side-chain hydrogen bonding to the backbone carbonyl oxygen. Structural modifications stabilizing P-form helices may obviate the need for large heterocycles to target DNA pyrimidine bases via PNA.DNA-PNA triplex formation. Quantum chemical modeling methods are used to propose candidate PNA Hoogsteen strand designs.

Amides↗

PubMed2006

Analyzing large-scale structural change in proteins: comparison of principal component projection and Sammon mapping.

Effective analysis of large-scale conformational transitions in macromolecules requires transforming them into a lower dimensional representation that captures the dominant motions. Herein, we apply and compare two different dimensionality reduction techniques, namely, principal component analysis (PCA), a linear method, and Sammon mapping, which is nonlinear. The two methods are used to analyze four different protein transition pathways of varying complexity, obtained by using either the conjugate peak refinement method or constrained molecular dynamics. For the return-stroke in myosin, both Sammon mapping and PCA show that the conformational change is dominated by a simple rotation of a rigid body. Also, in the case of the T-->R transition in hemoglobin, both methods are able to identify the two main quaternary transition events. In contrast, in the cases of the unfolding transition of staphylococcal nuclease or the signaling switch of Ras p21, which are both more complex conformational transitions, only Sammon mapping is able to identify the distinct phases of motion.

Amino Acid Substitution↗

PubMed2006

Simulations of the myosin II motor reveal a nucleotide-state sensing element that controls the recovery stroke.

During the recovery stroke, the myosin motor is primed for the next power stroke by a 60 degree rotation of its lever arm. This reversible motion is coupled to the activation of the ATPase function of myosin through conformational changes along the relay helix, which runs from the Switch-2 loop near the ATP to the converter domain carrying the lever arm. Via a hydrogen bond between the side-chain of Asn475 on the relay helix and the Gly457/Ser456 peptide group on the Switch-2, the rotation of the converter domain is coupled to the formation of a hydrogen bond between Gly457 and gamma-phosphate that is essential for ATP hydrolysis. Here, molecular dynamics simulations of Dictyostelium discoideum myosin II in the two end conformations of the recovery stroke with different nucleotide states (ATP, ADP x Pi, ADP) reveal that the side-chain of Asn475 breaks away from Switch-2 upon ATP hydrolysis to make a hydrogen bond with Tyr573. This sensing of the nucleotide state is achieved by a small displacement of the cleaved gamma-phosphate towards Gly457 which in turn pushes Asn475 away. The sensing plays a dual role by (i) preventing the wasteful reversal of the recovery stroke while the nucleotide is in the ADP x Pi state, and (ii) decoupling the relay helix from Switch-2, thus allowing the power stroke to start upon initial binding to actin while Gly457 of Switch-2 keeps interacting with the Pi (known to be released only later after tight actin binding). A catalytically important salt bridge between Arg238 (on Switch-1) and Glu459 (on Switch-2), which covers the hydrolysis site, is seen to form rapidly when ATP is added to the pre-recovery stroke conformer and remains stable after the recovery stroke, indicating that it has a role in shaping the ATP binding site by induced fit.

Adenosine Diphosphate↗

PubMed2006

Insights into the chemomechanical coupling of the myosin motor from simulation of its ATP hydrolysis mechanism.

The molecular motor myosin converts chemical energy from ATP hydrolysis into mechanical work, thus driving a variety of essential motility processes. Although myosin function has been studied extensively, the catalytic mechanism of ATP hydrolysis and its chemomechanical coupling to the motor cycle are not completely understood. Here, the catalysis mechanism in myosin II is examined using quantum mechanical/molecular mechanical reaction path calculations. The resulting reaction pathways, found in the catalytically competent closed/closed conformation of the Switch-1/Switch-2 loops of myosin, are all associative with a pentavalent bipyramidal oxyphosphorane transition state but can vary in the activation mechanism of the attacking water molecule and in the way the hydrogens are transferred between the heavy atoms. The coordination bond between the Mg2+ metal cofactor and Ser237 in the Switch-1 loop is broken in the product state, thereby facilitating the opening of the Switch-1 loop after hydrolysis is completed, which is required for subsequent strong rebinding to actin. This reveals a key element of the chemomechanical coupling that underlies the motor cycle, namely, the modulation of actin unbinding or binding in response to the ATP or ADP x P(i) state of nucleotide-bound myosin.

Adenosine Triphosphate↗

PubMed2006

Structural and energetic determinants of primary proton transfer in bacteriorhodopsin.

In the light-driven bacteriorhodopsin proton pump, the first proton transfer step is from the retinal Schiff base to a nearby carboxylate group. The mechanism of this transfer step is highly controversial, in particular whether a direct proton jump is allowed. Here, we review the structural and energetic determinants of the direct proton transfer path computed by using a combined quantum mechanical/molecular mechanical approach. Both protein flexibility and electrostatic interactions play an important role in shaping the proton transfer energy profile. Detailed analysis of the energetics of putative transitions in the first half of the photocycle focuses on two elements that determine the likelihood that a given configuration of the active site is populated during the proton-pumping cycle. First, the rate-limiting barrier for proton transfer must be consistent with the kinetics of the photocycle. Second, the active-site configuration must be compatible with a productive overall pumping cycle.

Bacteriorhodopsins↗

PubMed2006

Temperature-dependent protein dynamics: a simulation-based probabilistic diffusion-vibration Langevin description.

An enduring challenge in the understanding of internal protein motions is the effective separation and characterization of diffusive and vibrational dynamical components. To address this problem, here nanosecond molecular dynamics trajectories of myoglobin in aqueous solution, performed over a range of temperatures between 120 and 300 K, are subjected to principal component analysis, and the coordinate autocorrelation functions of the resulting principal modes are interpreted using a model combining damped Langevin vibration within potential wells and barrier-crossing diffusion between them. Both the vibrational frequency and the fraction of the mean-square fluctuation arising from vibrational motion undergo transitions with temperature at about 180 K. In contrast, the vibrational friction remains linear with temperature. The diffusional component of the mean-square fluctuation increases dramatically at the dynamical transition. The heights of the energy barriers between the potential wells are estimated, and the associated diffusion constants are calculated using Kramers' rate theory. Model functions of the frequency dependence of the frictional and diffusional quantities are obtained. The dynamic structure factor from the full molecular dynamics trajectory is well reproduced by the model. Overall, the results indicate that a global description of nanosecond temperature-dependent diffusion and vibrational internal protein dynamics can be obtained by applying the results of the present diffusion-vibration model to the vibrational motions obtained from a normal-mode analysis.

Algorithms↗

PubMed2006

Low-temperature protein dynamics: a simulation analysis of interprotein vibrations and the boson peak at 150 k.

An understanding of low-frequency, collective protein dynamics at low temperatures can furnish valuable information on functional protein energy landscapes, on the origins of the protein glass transition and on protein-protein interactions. Here, molecular dynamics (MD) simulations and normal-mode analyses are performed on various models of crystalline myoglobin in order to characterize intra- and interprotein vibrations at 150 K. Principal component analysis of the MD trajectories indicates that the Boson peak, a broad peak in the dynamic structure factor centered at about approximately 2-2.5 meV, originates from approximately 10(2) collective, harmonic vibrations. An accurate description of the environment is found to be essential in reproducing the experimental Boson peak form and position. At lower energies other strong peaks are found in the calculated dynamic structure factor. Characterization of these peaks shows that they arise from harmonic vibrations of proteins relative to each other. These vibrations are likely to furnish valuable information on the physical nature of protein-protein interactions.

Cold Temperature↗

PubMed2006

Tight in titin.

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Computer Simulation↗

PubMed2005

Pressure-dependent transition in protein dynamics at about revealed by molecular dynamics simulation.

Molecular dynamics simulations of a crystalline protein, Staphylococcal nuclease, over the pressure range 1 bar to 15 kbar reveal a qualitative change in the internal protein motions at approximately 4 kbar. This change involves the existence of two linear regimes in the mean-square displacement for internal protein motion, (P) with a twofold decrease in the slope for P>4 kbar. The major effect of pressure on the dynamics is a loss, with increasing pressure of large amplitude, collective protein modes below 2 THz effective frequency, accompanied by restriction of large-scale solvent translational motion.

Computer Simulation↗

PubMed2005

Correlated dynamics determining x-ray diffuse scattering from a crystalline protein revealed by molecular dynamics simulation.

The dynamical origin of the x-ray diffuse scattering by crystals of a protein, Staphylococcal nuclease, is determined using molecular dynamics simulation. A smooth, nearly isotropic scattering shell at originates from equal contributions from correlations in nearest-neighbor water molecule dynamics and from internal protein motions, the latter consisting of -helix pitch and inter--strand fluctuations. Superposed on the shell are intense, three-dimensional scattering features that originate from a very small number of slowly varying (>10 ns) collective motions. The individual three-dimensional features are assigned to specific collective motions in the protein, and some of these explicitly involve potentially functional active-site deformations.

Computer Simulation↗

PubMed2005

Can proteins and crystals self-catalyze methyl rotations?

The chi (C(alpha)-C(beta)) torsional barrier in the dipeptide alanine (N-methyl-l-alanyl-N-methylamide) crystal was investigated using ab initio calculations at various levels of theory, molecular mechanics, and molecular dynamics. For one of the two molecules in the asymmetric unit the calculations suggest that rotation around the chi dihedral angle is catalyzed by the crystal environment, reducing by up to approximately 2kT the torsional barrier in the crystal with respect to that in the gas phase. This catalytic effect is present at both low and room temperature and originates from a van der Waals destabilization of the minima in the methyl dihedral potential coming from the nonbonded environment of the side chain. Screening of a subset of the Protein Data Bank with a pharmacophore model reproducing the crystal environment around this side chain methyl identified a protein containing an alanine residue with an environment similar to that in the crystal. Calculations indicate that this chi torsional barrier is also reduced in the protein at low temperature but not at room temperature. This suggests that environment-catalyzed rotation of methyl groups can occur both in the solid phase and in native biological structures, though this effect might be temperature-dependent. The relevance of this catalytic effect is discussed in terms of its natural occurrence and its possible contribution to the low-frequency vibrational modes of molecules.

Catalysis↗

PubMed2005

Catalytic transesterification of dialkyl phosphates by a bioinspired dicopper(II) macrocyclic complex.

For a number of phosphoryltransfer enzymes, including the exonuclease subunit of DNA polymerase I, a mechanism involving two-metal ions and double Lewis-acid activation of the substrate, combined with leaving group stabilization, has been proposed. Inspired by the active site structure of this enzyme, we have designed as a synthetic phosphoryl transfer catalyst the dicopper(II) macrocyclic complex LCu(2). Crystal structures of complexes [(L)Cu(2)(mu-NO(3))(NO(3))](NO(3))(2) (1), [(L)Cu(2)(mu-CO(3))(CH(3)OH)](BF(4))(2) (2), and [(L)Cu(2)(mu-O(2)P(OCH(3))(2))(NO(3))](NO(3))(2) (3) illustrate various possibilities for the interaction of oxoanions with the dicopper(II) site. 1 efficiently promotes the transesterification of dimethyl phosphate (DMP) in CD(3)OD, k(cat) = 2 x 10(-)(4) s(-)(1) at 55 degrees C. 1 is the only available catalyst for the smooth transesterification of highly inert simple dialkyl phosphates. From photometric titrations and the pH dependence of reactivity, we conclude that a complex [(L)Cu(2)(DMP)(OCH(3))](2+) is the reactive species. Steric bulk at the -OR substituents of phosphodiester substrates O(2)P(OR)(2)(-) drastically reduces the reactivity of 1. This is explained with -OR leaving group stabilization by Cu coordination, an interaction which is sensitive to steric crowding at the alpha-C-atom of substituent R. A proposed reaction mechanism related to that of the exonuclease unit of DNA polymerase I is supported by DFT calculations on reaction intermediates. The complex [(L)Cu(3)(mu(3)-OH)(mu-CH(3)O)(2)(CH(3)CN)(2)](ClO(4))(3) (4) incorporates a [Cu(OH)(OCH(3))(2)(CH(3)CN)(2)](-) complex anion, which might be considered as an analogue of the [PO(2)(OCH(3))(2)(OCD(3))](2)(-) transition state (or intermediate) of DMP transesterification catalyzed by LCu(2).

Journal Article↗

PubMed2005

Structural basis of cellulosome efficiency explored by small angle X-ray scattering.

Cellulose, the main structural component of plant cell walls, is the most abundant carbohydrate polymer in nature. To break down plant cell walls, anaerobic microorganisms have evolved a large extracellular enzyme complex termed cellulosome. This megadalton catalytic machinery organizes an enzymatic assembly, tenaciously bound to a scaffolding protein via specialized intermodular "cohesin-dockerin" interactions that serve to enhance synergistic activity among the different catalytic subunits. Here, we report the solution structure properties of cellulosome-like assemblies analyzed by small angle x-ray scattering and molecular dynamics. The atomic models, generated by our strategy for the free chimeric scaffoldin and for binary and ternary complexes, reveal the existence of various conformations due to intrinsic structural flexibility with no, or only coincidental, inter-cohesin interactions. These results provide primary evidence concerning the mechanisms by which these protein assemblies attain their remarkable synergy. The data suggest that the motional freedom of the scaffoldin allows precise positioning of the complexed enzymes according to the topography of the substrate, whereas short-scale motions permitted by residual flexibility of the enzyme linkers allow "fine-tuning" of individual catalytic domains.

Biophysics↗

PubMed2005

Tuning of retinal twisting in bacteriorhodopsin controls the directionality of the early photocycle steps.

Productive proton pumping by bacteriorhodopsin requires that, after the all-trans to 13-cis photoisomerization of the retinal chromophore, the photocycle proceeds with proton transfer and not with thermal back-isomerization. The question of how the protein controls these events in the active site is addressed here using quantum mechanical/molecular mechanical reaction-path calculations. The results indicate that, while retinal twisting significantly contributes to lowering the barrier for the thermal cis-trans back-isomerization, the rate-limiting barrier for this isomerization is still 5-6 kcal/mol larger than that for the first proton-transfer step. In this way, the retinal twisting is finely tuned so as to store energy to drive the subsequent photocycle while preventing wasteful back-isomerization.

Bacteriorhodopsins↗

PubMed2005

Langevin model of the temperature and hydration dependence of protein vibrational dynamics.

The modification of internal vibrational modes in a protein due to intraprotein anharmonicity and solvation effects is determined by performing molecular dynamics (MD) simulations of myoglobin, analyzing them using a Langevin model of the vibrational dynamics and comparing the Langevin results to a harmonic, normal mode model of the protein in vacuum. The diagonal and off-diagonal Langevin friction matrix elements, which model the roughness of the vibrational potential energy surfaces, are determined together with the vibrational potentials of mean force from the MD trajectories at 120 K and 300 K in vacuum and in solution. The frictional properties are found to be describable using simple phenomenological functions of the mode frequency, the accessible surface area, and the intraprotein interaction (the displacement vector overlap of any given mode with the other modes in the protein). The frictional damping of a vibrational mode in vacuum is found to be directly proportional to the intraprotein interaction of the mode, whereas in solution, the friction is proportional to the accessible surface area of the mode. In vacuum, the MD frequencies are lower than those of the normal modes, indicating intramolecular anharmonic broadening of the associated potential energy surfaces. Solvation has the opposite effect, increasing the large-amplitude vibrational frequencies relative to in vacuum and thus vibrationally confining the protein atoms. Frictional damping of the low-frequency modes is highly frequency dependent. In contrast to the damping effect of the solvent, the vibrational frequency increase due to solvation is relatively temperature independent, indicating that it is primarily a structural effect. The MD-derived vibrational dynamic structure factor and density of states are well reproduced by a model in which the Langevin friction and potential of mean force parameters are applied to the harmonic normal modes.

Computer Simulation↗

PubMed2005

Protein/ligand binding free energies calculated with quantum mechanics/molecular mechanics.

The calculation of binding affinities for flexible ligands has hitherto required the availability of reliable molecular mechanics parameters for the ligands, a restriction that can in principle be lifted by using a mixed quantum mechanics/molecular mechanics (QM/MM) representation in which the ligand is treated quantum mechanically. The feasibility of this approach is evaluated here, combining QM/MM with the Poisson-Boltzmann/surface area model of continuum solvation and testing the method on a set of 47 benzamidine derivatives binding to trypsin. The experimental range of the absolute binding energy (DeltaG = -3.9 to -7.6 kcal/mol) is reproduced well, with a root-mean-square (RMS) error of 1.2 kcal/mol. When QM/MM is applied without reoptimization to the very different ligands of FK506 binding protein the RMS error is only 0.7 kcal/mol. The results show that QM/MM is a promising new avenue for automated docking and scoring of flexible ligands. Suggestions are made for further improvements in accuracy.

Ligands↗