Krzysztof Kuczera

Structure and function of S-adenosylhomocysteine hydrolase.

In mammals, S-adenosylhomocysteine hydrolase (AdoHcyase) is the only known enzyme to catalyze the breakdown of S-adenosylhomocysteine (AdoHcy) to homocysteine and adenosine. AdoHcy is the product of all adenosylmethionine (AdoMet)-dependent biological transmethylations. These reactions have a wide range of products, and are common in all facets of biometabolism. As a product inhibitor, elevated levels of AdoHcy suppress AdoMet-dependent transmethylations. Thus, AdoHcyase is a regulator of biological transmethylation in general. The three-dimensional structure of AdoHcyase complexed with reduced nicotinamide adenine dinucleotide phosphate (NADH) and the inhibitor (1′R, 2′S, 3′R)-9-(2′,3′-dihyroxycyclopenten-1-yl)adenine (DHCeA) was solved by a combination of the crystallographic direct methods program, SnB, to determine the selenium atom substructure and by treating the multiwavelength anomalous diffraction data as a special case of multiple isomorphous replacement. The enzyme architecture resembles that observed for NAD-dependent dehydrogenases, with the catalytic domain and the cofactor binding domain each containing a modified Rossmann fold. The two domains form a deep active site cleft containing the cofactor and bound inhibitor molecule. A comparison of the inhibitor complex of the human enzyme and the structure of the rat enzyme, solved without inhibitor, suggests that a 17° rigid body movement of the catalytic domain occurs upon inhibitor/substrate binding.

Algorithms for constrained molecular dynamics

In molecular dynamics simulations, the fastest components of the potential field impose severe restrictions on the stability and hence the speed of computational methods. One possibility for treating this problem is to replace the fastest components with algebraic length constraints. In this article the resulting systems of mixed differential and algebraic equations are studied. Commonly used discretization schemes for constrained Hamiltonian systems are discussed. The form of the nonlinear equations is examined in detail and used to give convergence results for the traditional nonlinear solution technique SHAKE iteration and for a modification based on successive overrelaxation (SOR). A simple adaptive algorithm for finding the optimal relaxation parameter is presented. Alternative direct methods using sparse matrix techniques are discussed. Numerical results are given for the new techniques, which have been implemented in the molecular modeling software package CHARMM and show as much as twofold improvement over SHAKE iteration.

Ab initio calculations of S1 excited state vibrational spectra of benzene, naphthalene and anthracene

Abstract Normal-mode calculations are presented for the lowest singlet excited states S 1 of benzene, naphthalene and anthracene. Optimized geometries and Cartesian harmonic force constants of the excited states are obtained from ab initio calculations at the CIS/6-31G, CIS/6-31G ∗ , CIS/6-311G and CIS/6-311G ∗ levels for benzene, and at CIS/6-31G and CIS/6-31G ∗ levels for naphthalene and anthracene. Normal-mode analysis is performed in internal coordinates, yielding vibrational frequencies and forms of normal modes for the parent molecules and their perdeuterated derivatives. The results are compared with corresponding properties of the ground state S 0 calculated at the Hartree-Fock level and with available experimental data. The overall changes in molecular geometry and vibrational spectra upon S 0 → S 1 excitation are small. For benzene we find excellent agreement of the entire calculated S 1 vibrational spectrum with experimental results. For naphthalene and anthracene the calculated vibrational frequencies are in good agreement with the limited available experimental data. Our calculations provide predictions of frequencies and types of normal modes for the complete S 1 vibrational spectra of these molecules, and suggest reassignments of several normal-mode frequencies compared to the limited experimental results that are currently available.

Influence of temperature and viscosity on anthracene rotational diffusion in organic solvents: Molecular dynamics simulations and fluorescence anisotropy study

Molecular dynamics simulations and fluorescence anisotropy decay measurements are used to investigate the rotational diffusion of anthracene in two organic solvents—cyclohexane and 2-propanol—at several temperatures. Molecular dynamics simulations of 1 ns length were performed for anthracene in cyclohexane (at 280, 296, and 310 K) and in 2-propanol (at 296 K). The calculated time constants for reorientation of the short in-plane axis were 7–9 and 11–16 ps at 296 K in cyclohexane and 2-propanol, respectively, in excellent agreement with corresponding fluorescence depolarization measurements of 8 and 14 ps. The measured rotational reorientation times and the calculated average rotational diffusion coefficients varied in accord with Debye–Stokes–Einstein theory. Their magnitudes were close to values predicted for an ellipsoid of shape and size equivalent to an anthracene molecule, and exhibited predictable variation with external conditions—increasing with temperature and decreasing with solvent viscosity. H...

Unassisted Transport of N-acetyl-L-tryptophanamide through Membrane: Experiment and Simulation of Kinetics

Cellular transport machinery, such as channels and pumps, is working against the background of unassisted material transport through membranes. The permeation of a blocked tryptophan through a 1,2-dioleoyl-sn-glycero-3-phosphocholine (DOPC) membrane is investigated to probe unassisted or physical transport. The transport rate is measured experimentally and modeled computationally. The time scale measured by parallel artificial membrane permeation assay (PAMPA) experiments is ~8 h. Simulations with the milestoning algorithm suggest mean first passage time (MFPT) of ~4 h and the presence of a large barrier at the center of the bilayer. A similar calculation with the solubility-diffusion model yields a MFPT of ~15 min. This permeation rate is 9 orders of magnitude slower than the permeation rate of only a tryptophan side chain (computed by us and others). This difference suggests critical dependence of transport time on permeant size and hydrophilicity. Analysis of the simulation results suggests that the permeant partially preserves hydrogen bonding of the peptide backbone to water and lipid molecules even when it is moving closer to the bilayer center. As a consequence, defects of the membrane structure are developed to assist permeation.

Structure and Dynamics of Calcium-activated Calmodulin in Solution

Abstract Two 4-ns molecular dynamics simulations of calcium loaded calmodulin in solution have been performed, using both standard nonbonded cutoffs and Ewald summation to treat electrostatic interactions. Our simulation results are generally consistent with solution experimental studies of calmodulin structure and dynamics, including NMR, cross-linking, fluorescence and x-ray scattering. The most interesting result of the molecular dynamics simulations is the detection of large-scale structural fluctuations of calmodulin in solution. The globular N- and C-terminal domains tend to move approximately like rigid bodies, with fluctuations of interdomain distances within a 7 Å range and of interdomain angles by up to 60 deg. Essential dynamics analysis indicates that the three dominant types of motion involve bending of the central helix in two perpendicular planes and a twist in which the domains rotate in opposite directions around the central helix. In the more realistic Ewald trajectory the protein backbone remains mostly within a 2–3 Å root-mean-square distance from the crystal structure, the secondary structure within the domains is conserved and middle part of the central helix becomes disordered. The central helix itself exhibits limited fluctuations, with its bend angle exploring the 0–50° range and the end-to-end distance falling in 39–43 Å. The results of the two simulations were similar in many respects. However, the cutoff trajectory exhibited a larger deviation from the crystal, loss of several helical hydrogen bonds in the N-terminal domain and lack of structural disorder in the central helix.

Helix Formation in a Pentapeptide: Experiment and Force-field Dependent Dynamics

We used a combined approach of experiment and simulation to determine the helical population and folding pathway of a small helix forming blocked pentapeptide, Ac-(Ala)(5)-NH(2). Experimental structural characterization of this blocked peptide was carried out with far UV circular dichroism spectroscopy, FTIR, and NMR measurements. These measurements confirm the presence of the α-helical state in a buffer solution. Direct molecular dynamics and replica-exchange simulations of the pentapeptide were performed using several popular force fields with explicit solvent. The simulations yielded statistically reliable estimates of helix populations, melting curves, folding, and nucleation times. The distributions of conformer populations are used to measure folding cooperativity. Finally, a statistical analysis of the sample of helix-coil transition paths was performed. The details of the calculated helix populations, folding kinetics and pathways vary with the employed force field. Interestingly, the helix populations, folding, and unfolding times obtained from most of the studied force fields are in qualitative agreement with each other and with available experimental data, with the deviations corresponding to several kcal/mol in energy at 300 K. Most of the force fields also predict qualitatively similar transition paths, with unfolding initiated at the C-terminus. Accuracy of potential energy parameters, rather than conformational sampling may be the limiting factor in current molecular simulations.

Orientation of fluorescent lipid analogue BODIPY-PC to probe lipid membrane properties: insights from molecular dynamics simulations.

Single-molecule fluorescence measurements have been used to characterize membrane properties, and recently showed a linear evolution of the fluorescent lipid analogue BODIPY-PC toward small tilt angles in Langmuir-Blodgett monolayers as the lateral surface pressure is increased. In this work, we have performed comparative molecular dynamics (MD) simulations of BODIPY-PC in DPPC (dipalmitoylphosphatidylcholine) monolayers and bilayers at three surface pressures (3, 10, and 40 mN/m) to explore (1) the microscopic correspondence between monolayer and bilayer structures, (2) the fluorophores position within the membrane, and (3) the microscopic driving forces governing the fluorophores tilting. The MD simulations reveal very close agreement between the monolayer and bilayer systems in terms of the fluorophores orientation and lipid chain order, suggesting that monolayer experiments can be used to approximate bilayer systems. The simulations capture the trend of reduced tilt angle of the fluorophore with increasing surface pressure, as seen in the experimental results, and provide detailed insights into fluorophore location and orientation, not obtainable in the experiments. The simulations also reveal that the enthalpic contribution is dominant at 40 mN/m, resulting in smaller tilt angles of the fluorophore, and the entropy contribution is dominant at lower pressures, resulting in larger tilt angles.

Experiments and comprehensive simulations of the formation of a helical turn

We investigate the kinetics and thermodynamics of a helical turn formation in the peptide Ac-WAAAH-NH(2). NMR measurements indicate that this peptide has significant tendency to form a structure of a helical turn, while temperature dependent CD establishes the helix fraction at different temperatures. Molecular dynamics and milestoning simulations agree with experimental observables and suggest an atomically detailed picture for the turn formation. Using a network representation, two alternative mechanisms of folding are identified: (i) a direct co-operative mechanism from the unfolded to the folded state without intermediate formation of hydrogen bonds and (ii) an indirect mechanism with structural intermediates with two residues in a helical conformation. This picture is consistent with kinetic measurements that reveal two experimental time scales of sub-nanosecond and several nanoseconds.

Prediction of phase equilibria and transport properties in carbon-dioxide expanded solvents by molecular simulation

We review our recent work on the calculations of the phase equilibrium and transport properties in carbon-dioxide (CO2) expanded liquids (CXLs) via Monte Carlo and molecular dynamics (MD) simulations. Gibbs ensemble Monte Carlo simulations were performed to determine the volume expansion, the pressure–composition and pressure–density phase diagrams for CO2 expanded acetonitrile, acetone, methanol, ethanol, acetic acid, toluene and 1-octene. MD simulations were conducted to compute the translational diffusion coefficients, rotational correlation times and shear viscosities in CO2 expanded acetonitrile. Potential parameters for the pure component together with standard mixing rules were used to describe the interactions between the mixture components. A good agreement between simulation results and available experimental data is achieved. The simulation results for the volume expansion, the pressure–composition and pressure–density phase diagrams were in some cases superior to the Peng–Robinson (PR) equation of state correlations, showing the ability of molecular simulation to predict CXL properties for their use as solvent media in engineering processes.