Biomedical subjects

W A Goddard

Publications and source records attributed to W A Goddard.

At least 19 recordsLinked to original sources

PubMed2004

Hildebrand and Hansen solubility parameters from molecular dynamics with applications to electronic nose polymer sensors.

We introduce the Cohesive Energy Density (CED) method, a multiple sampling Molecular Dynamics computer simulation procedure that may offer higher consistency in the estimation of Hildebrand and Hansen solubility parameters. The use of a multiple sampling technique, combined with a simple but consistent molecular force field and quantum mechanically determined atomic charges, allows for the precise determination of solubility parameters in a systematic way (sigma = 0.4 hildebrands). The CED method yields first-principles Hildebrand parameter predictions in good agreement with experiment [root-mean-square (rms) = 1.1 hildebrands]. We apply the CED method to model the Caltech electronic nose, an array of 20 polymer sensors. Sensors are built with conducting leads connected through thin-film polymers loaded with carbon black. Odorant detection relies on a change in electric resistivity of the polymer film as function of the amount of swelling caused by the odorant compound. The amount of swelling depends upon the chemical composition of the polymer and the odorant molecule. The pattern is unique, and unambiguously identifies the compound. Experimentally determined changes in relative resistivity of seven polymer sensors upon exposure to 24 solvent vapors were modeled with the CED estimated Hansen solubility components. Predictions of polymer sensor responses result in Pearson R2 coefficients between 0.82 and 0.99.

Algorithms↗

PubMed2001

Antibody catalysis of the oxidation of water.

Recently we reported that antibodies can generate hydrogen peroxide (H2O2) from singlet molecular oxygen (1O2*). We now show that this process is catalytic, and we identify the electron source for a quasi-unlimited generation of H2O2. Antibodies produce up to 500 mole equivalents of H2O2 from 1O2*, without a reduction in rate, and we have excluded metals or Cl- as the electron source. On the basis of isotope incorporation experiments and kinetic data, we propose that antibodies use H2O as an electron source, facilitating its addition to 1O2* to form H2O3 as the first intermediate in a reaction cascade that eventually leads to H2O2. X-ray crystallographic studies with xenon point to putative conserved oxygen binding sites within the antibody fold where this chemistry could be initiated. Our findings suggest a protective function of immunoglobulins against 1O2* and raise the question of whether the need to detoxify 1O2* has played a decisive role in the evolution of the immunoglobulin fold.

Animals↗

PubMed2001

Chelators for radioimmunotherapy: I. NMR and ab initio calculation studies on 1,4,7,10-tetra(carboxyethyl)-1,4,7,10-tetraazacyclododecane (DO4Pr) and 1,4,7-tris(carboxymethyl)-10-(carboxyethyl)-1,4,7,10-tetraazacyclododecane (DO3A1Pr).

This work describes the modification of the chelating agent 1,4,7,10-tetraazacyclododecane-N,N',N' ',N' "-tetraacetic acid (DOTA) to improve the rate of metal loading for radioimmunotherapy applications. Previous ab initio calculations predicted that the compounds 1,4,7,10-tetra(carboxyethyl)-1,4,7,10-tetraazacyclododecane (DO4Pr) and 1,4,7-tris(carboxymethyl)-10-(carboxyethyl)-1,4,7,10-tetraazacyclododecane (DO3A1Pr) have a ca. 2000-fold improvement in yttrium metal loading rates compared to those of DOTA (Jang, Y. H.; Blanco, M.; Dasgupta, S.; Keire, D. A.; Shively, J. E.; Goddard, W. A., III. J. Am. Chem. Soc. 1999, 121, 6142-6151). In this study, we report the synthesis, purification, (1)H-NMR chemical shift assignments, pK(a) values, metal loading rate measurements, and additional ab initio calculations of these two compounds. The yttrium loading rates of DO3A1Pr are approximately twice those of DOTA, at pH 4.6 and 37 degrees C. The NMR data indicates that the DO4Pr analogue forms a stable type I complex but does not form a type II complex. The new ab initio calculations performed on DO4Pr and DO3A1Pr indicate that the rate-determining step is the deprotonation of the first macrocycle amine proton, not the second proton as assumed in the previous calculations. The new calculations predict an improvement in the rate of metal loading that more closely matches the experimentally observed change in the rate.

Acetates↗

PubMed2001

Catalysis research of relevance to carbon management: progress, challenges, and opportunities.

The goal of the "Opportunities for Catalysis Research in Carbon Management" workshop was to review within the context of greenhouse gas/carbon issues the current state of knowledge, barriers to further scientific and technological progress, and basic scientific research needs in the areas of H2 generation and utilization, light hydrocarbon activation and utilization, carbon dioxide activation, utilization, and sequestration, emerging techniques and research directions in relevant catalysis research, and in catalysis for more efficient transportation engines. Several overarching themes emerge from this review. First and foremost, there is a pressing need to better understand in detail the catalytic mechanisms involved in almost every process area mentioned above. This includes the structures, energetics, lifetimes, and reactivities of the species thought to be important in the key catalytic cycles. As much of this type of information as is possible to acquire would also greatly aid in better understanding perplexing, incomplete/inefficient catalytic cycles and in inventing new, efficient ones. The most productive way to attack such problems must include long-term, in-depth fundamental studies of both commercial and model processes, by conventional research techniques and, importantly, by applying various promising new physicochemical and computational approaches which would allow incisive, in situ elucidation of reaction pathways. There is also a consensus that more exploratory experiments, especially high-risk, unconventional catalytic and model studies, should be undertaken. Such an effort will likely require specialized equipment, instrumentation, and computational facilities. The most expeditious and cost-effective means to carry out this research would be by close coupling of academic, industrial, and national laboratory catalysis efforts worldwide. Completely new research approaches should be vigorously explored, ranging from novel compositions, fabrication techniques, reactors, and reaction conditions for heterogeneous catalysts, to novel ligands and ligation geometries (e.g., biomimetic), reaction media, and activation methods for homogeneous ones. The interplay between these two areas involving various hybrid and single-site supported catalyst systems should also be productive. Finally, new combinatorial and semicombinatorial means to rapidly create and screen catalyst systems are now available. As a complement to the approaches noted above, these techniques promise to greatly accelerate catalyst discovery, evaluation, and understanding. They should be incorporated in the vigorous international research effort needed in this field.

Journal Article↗

PubMed2000

Molecular mechanisms underlying differential odor responses of a mouse olfactory receptor.

The prevailing paradigm for G protein-coupled receptors is that each receptor is narrowly tuned to its ligand and closely related agonists. An outstanding problem is whether this paradigm applies to olfactory receptor (ORs), which is the largest gene family in the genome, in which each of 1,000 different G protein-coupled receptors is believed to interact with a range of different odor molecules from the many thousands that comprise "odor space." Insights into how these interactions occur are essential for understanding the sense of smell. Key questions are: (i) Is there a binding pocket? (ii) Which amino acid residues in the binding pocket contribute to peak affinities? (iii) How do affinities change with changes in agonist structure? To approach these questions, we have combined single-cell PCR results [Malnic, B., Hirono, J., Sato, T. & Buck, L. B. (1999) Cell 96, 713-723] and well-established molecular dynamics methods to model the structure of a specific OR (OR S25) and its interactions with 24 odor compounds. This receptor structure not only points to a likely odor-binding site but also independently predicts the two compounds that experimentally best activate OR S25. The results provide a mechanistic model for olfactory transduction at the molecular level and show how the basic G protein-coupled receptor template is adapted for encoding the enormous odor space. This combined approach can significantly enhance the identification of ligands for the many members of the OR family and also may shed light on other protein families that exhibit broad specificities, such as chemokine receptors and P450 oxidases.

Animals↗

PubMed2000

Conformation and proton configuration of pyrimidine deoxynucleoside oxidation damage products in water.

Emerging data strongly suggest that the oxidation of DNA bases can contribute to genomic instability. Structural changes to DNA, induced by base oxidation, may reduce the fidelity of DNA replication and interfere with sequence-specific DNA-protein interactions. We have examined the structures of a series of pyrimidine deoxynucleoside oxidation damage products in aqueous solution. The modified nucleosides studied include the deoxynucleoside derivatives of 5-hydroxyuracil, 5-hydroxycytosine, 5-(hydroxymethyl)uracil, 5-(hydroxymethyl)cytosine, 5-formyluracil, and 5-formylcytosine. The influence of base oxidation on ionization constants, sugar conformation, and tautomeric configuration has been determined on the basis of UV, proton, and nitrogen NMR spectra of the (15)N-enriched derivatives. The potential biological consequences of the structural perturbations resulting from base oxidation are discussed.

DNA Adducts↗

PubMed1999

First principles prediction of protein folding rates.

Experimental studies have demonstrated that many small, single-domain proteins fold via simple two-state kinetics. We present a first principles approach for predicting these experimentally determined folding rates. Our approach is based on a nucleation-condensation folding mechanism, where the rate-limiting step is a random, diffusive search for the native tertiary topology. To estimate the rates of folding for various proteins via this mechanism, we first determine the probability of randomly sampling a conformation with the native fold topology. Next, we convert these probabilities into folding rates by estimating the rate that a protein samples different topologies during diffusive folding. This topology-sampling rate is calculated using the Einstein diffusion equation in conjunction with an experimentally determined intra-protein diffusion constant. We have applied our prediction method to the 21 topologically distinct small proteins for which two-state rate data is available. For the 18 beta-sheet and mixed alpha-beta native proteins, we predict folding rates within an average factor of 4, even though the experimental rates vary by a factor of approximately 4 x 10(4). Interestingly, the experimental folding rates for the three four-helix bundle proteins are significantly underestimated by this approach, suggesting that proteins with significant helical content may fold by a faster, alternative mechanism. This method can be applied to any protein for which the structure is known and hence can be used to predict the folding rates of many proteins prior to experiment.

Animals↗

PubMed1999

The topomer-sampling model of protein folding.

Clearly, a protein cannot sample all of its conformations (e.g., approximately 3(100) approximately 10(48) for a 100 residue protein) on an in vivo folding timescale (<1 s). To investigate how the conformational dynamics of a protein can accommodate subsecond folding time scales, we introduce the concept of the native topomer, which is the set of all structures similar to the native structure (obtainable from the native structure through local backbone coordinate transformations that do not disrupt the covalent bonding of the peptide backbone). We have developed a computational procedure for estimating the number of distinct topomers required to span all conformations (compact and semicompact) for a polypeptide of a given length. For 100 residues, we find approximately 3 x 10(7) distinct topomers. Based on the distance calculated between different topomers, we estimate that a 100-residue polypeptide diffusively samples one topomer every approximately 3 ns. Hence, a 100-residue protein can find its native topomer by random sampling in just approximately 100 ms. These results suggest that subsecond folding of modest-sized, single-domain proteins can be accomplished by a two-stage process of (i) topomer diffusion: random, diffusive sampling of the 3 x 10(7) distinct topomers to find the native topomer ( approximately 0.1 s), followed by (ii) intratopomer ordering: nonrandom, local conformational rearrangements within the native topomer to settle into the precise native state.

Animals↗

PubMed1998

Kinetic steps for alpha-helix formation.

The kinetics of alpha-helix formation in polyalanine and polyglycine eicosamers (20-mers) were examined using torsional-coordinate molecular dynamics (MD). Of one hundred fifty-five MD experiments on extended (Ala)20 carried out for 0.5 ns each, 129 (83%) formed a persistent alpha-helix. In contrast, the extended state of (Gly)20 only formed a right-handed alpha-helix in two of the 20 MD experiments (10%), and these helices were not as long or as persistent as those of polyalanine. These simulations show helix formation to be a competition between the rates of (a) forming local hydrogen bonds (i.e. hydrogen bonds between any residue i and its i + 2, i + 3, i + 4, or i + 5th neighbor) and (b) forming nonlocal hydrogen bonds (HBs) between residues widely separated in sequence. Local HBs grow rapidly into an alpha-helix; but nonlocal HBs usually retard helix formation by "trapping" the polymer in irregular, "balled-up" structures. Most trajectories formed some nonlocal HBs, sometimes as many as eight. But, for (Ala)20, most of these eventually rearranged to form local HBs that lead to alpha-helices. A simple kinetic model describes the rate of converting nonlocal HBs into alpha-helices. Torsional-coordinate MD speeds folding by eliminating bond and angle degrees of freedom and reducing dynamical friction. Thus, the observed 210 ps half-life for helix formation is likely to be a lower bound on the real rate. However, we believe the sequential steps observed here mirror those of real systems.

Computer Simulation↗

PubMed1998

Substrate assistance in the mechanism of family 18 chitinases: theoretical studies of potential intermediates and inhibitors.

Based on first principles and molecular mechanics calculations, we conclude that the mechanism of hevamine (a family 18 chitinase) involves an oxazoline ion intermediate stabilized by the neighboring C2' acetamido group. In this intermediate, the acetamido carbonyl oxygen atom forms a covalent bond to C1' of N-acetyl-glucosamine and has a transferred positive charge from the pyranose ring onto the acetamido nitrogen atom, leading to an anchimeric stabilization of 38.1 kcal/mol when docked with hevamine. This double displacement mechanism involving an oxazoline intermediate distinguishes the family 18 chitinase (which have one acidic residue near the active site) from family 19 chitinase and from hen egg-white lysozyme, which have two acidic residues near the active site. The structural and electronic properties of the oxazoline intermediate are similar to the known chitinase inhibitor allosamidin, suggesting that allosamidins act as transition state analogs of an oxazoline intermediate. Structural and electronic features of the oxazoline ion likely to be important in the design of new chitinase inhibitors are discussed.

Acetylglucosamine↗

PubMed1998

The role of enzyme distortion in the single displacement mechanism of family 19 chitinases.

By using molecular dynamics simulations, we have examined the binding of a hexaNAG substrate and two potential hydrolysis intermediates (an oxazoline ion and an oxocarbenium ion) to a family 19 barley chitinase. We find the hexaNAG substrate binds with all sugars in a chair conformation, unlike the family 18 chitinase which causes substrate distortion. Glu 67 is in a position to protonate the anomeric oxygen linking sugar residues D and E whereas Asn 199 serves to hydrogen bond with the C2' N-acetyl group of sugar D, thus preventing the formation of an oxazoline ion intermediate. In addition, Glu 89 is part of a flexible loop region allowing a conformational change to occur within the active site to bring the oxocarbenium ion intermediate and Glu 89 closer by 4-5 A. A hydrolysis product with inversion of the anomeric configuration occurs because of nucleophilic attack by a water molecule that is coordinated by Glu 89 and Ser 120. Issues important for the design of inhibitors specific to family 19 chitinases over family 18 chitinases also are discussed.

Amino Acid Sequence↗

PubMed1998

Effects of pressure on the structure of metmyoglobin: molecular dynamics predictions for pressure unfolding through a molten globule intermediate.

We investigated the pathway for pressure unfolding of metmyoglobin using molecular dynamics (MD) for a range of pressures (0.1 MPa to 1.2 GPa) and a temperature of 300 K. We find that the unfolding of metmyoglobin proceeds via a two-step mechanism native --> molten globule intermediate --> unfolded, where the molten globule forms at 700 MPa. The simulation describes qualitatively the experimental behavior of metmyoglobin under pressure. We find that unfolding of the alpha-helices follows the sequence of migrating hydrogen bonds (i,i + 4) --> (i,i + 2).

Amino Acid Sequence↗

PubMed1997

The pentamer channel stiffening model for drug action on human rhinovirus HRV-1A.

Development of effective drugs against the rhinovirus (HRV) responsible for the common cold remains a challenge because there are over 100 serotypes. This process could be significantly aided by an understanding of the atomistic mechanism by which such drugs work. We suggest that the most effective drugs against HRV-1A act by stiffening the pentamer channel of the viral coat through which the RNA is released, preventing the steps leading to uncoating. Using molecular dynamics methods we tested this Pentamer Channel Stiffening Model (PCSM) by examining the changes in strain energy associated with opening the pentamer channel through which the RNA is released. We find that the PCSM strain correlates well with the effectiveness of the WIN (Sterling-Winthrop) drugs for HRV-1A. To illustrate the use of the PCSM to predict new drugs and to prioritize experimental tests, we tested three modifications of the WIN drugs that are predicted to be nearly as effective (for HRV-1A) as the best current drug.

Antiviral Agents↗

PubMed1995

De novo prediction of polypeptide conformations using dihedral probability grid Monte Carlo methodology.

We tested the dihedral probability grid Monte Carlo (DPG-MC) methodology to determine optimal conformations of polypeptides by applying it to predict the low energy ensemble for two peptides whose solution NMR structures are known: integrin receptor peptide (YGRGDSP, Type II beta-turn) and S3 alpha-helical peptide (YMSEDEL KAAEAAFKRHGPT). DPG-MC involves importance sampling, local random stepping in the vicinity of a current local minima, and Metropolis sampling criteria for acceptance or rejection of new structures. Internal coordinate values are based on side-chain-specific dihedral angle probability distributions (from analysis of high-resolution protein crystal structures). Important features of DPG-MC are: (1) Each DPG-MC step selects the torsion angles (phi, psi, chi) from a discrete grid that are then applied directly to the structure. The torsion angle increments can be taken as S = 60, 30, 15, 10, or 5 degrees, depending on the application. (2) DPG-MC utilizes a temperature-dependent probability function (P) in conjunction with Metropolis sampling to accept or reject new structures. For each peptide, we found close agreement with the known structure for the low energy conformational ensemble located with DPG-MC. This suggests that DPG-MC will be useful for predicting conformations of other polypeptides.

Amino Acid Sequence↗

PubMed1995

Building proteins from C alpha coordinates using the dihedral probability grid Monte Carlo method.

Dihedral probability grid Monte Carlo (DPG-MC) is a general-purpose method of conformational sampling that can be applied to many problems in peptide and protein modeling. Here we present the DPG-MC method and apply it to predicting complete protein structures from C alpha coordinates. This is useful in such endeavors as homology modeling, protein structure prediction from lattice simulations, or fitting protein structures to X-ray crystallographic data. It also serves as an example of how DPG-MC can be applied to systems with geometric constraints. The conformational propensities for individual residues are used to guide conformational searches as the protein is built from the amino-terminus to the carboxyl-terminus. Results for a number of proteins show that both the backbone and side chain can be accurately modeled using DPG-MC. Backbone atoms are generally predicted with RMS errors of about 0.5 A (compared to X-ray crystal structure coordinates) and all atoms are predicted to an RMS error of 1.7 A or better.

Amino Acids↗

PubMed1995

Prediction of polyelectrolyte polypeptide structures using Monte Carlo conformational search methods with implicit solvation modeling.

Many interesting proteins possess defined sequence stretches containing negatively charged amino acids. At present, experimental methods (X-ray crystallography, NMR) have failed to provide structural data for many of these sequence domains. We have applied the dihedral probability grid-Monte Carlo (DPG-MC) conformational search algorithm to a series of N- and C-capped polyelectrolyte peptides, (Glu)20, (Asp)20, (PSer)20, and (PSer-Asp)10, that represent polyanionic regions in a number of important proteins, such as parathymosin, calsequestrin, the sodium channel protein, and the acidic biomineralization proteins. The atomic charges were estimated from charge equilibration and the valence and van der Waals parameters are from DREIDING. Solvation of the carboxylate and phosphate groups was treated using sodium counterions for each charged side chain (one Na+ for COO-; two Na for CO(PO3)-2) plus a distance-dependent (shielded) dielectric constant, epsilon = epsilon 0 R, to simulate solvent water. The structures of these polyelectrolyte polypeptides were obtained by the DPG-MC conformational search with epsilon 0 = 10, followed by calculation of solvation energies for the lowest energy conformers using the protein dipole-Langevin dipole method of Warshel. These calculations predict a correlation between amino acid sequence and global folded conformational minima: 1. Poly-L-Glu20, our structural benchmark, exhibited a preference for right-handed alpha-helix (47% helicity), which approximates experimental observations of 55-60% helicity in solution. 2. For Asp- and PSer-containing sequences, all conformers exhibited a low preference for right-handed alpha-helix formation (< or = 10%), but a significant percentage (approximately 20% or greater) of beta-strand and beta-turn dihedrals were found in all three sequence cases: (1) Aspn forms supercoil conformers, with a 2:1:1 ratio of beta-turn:beta-strand:alpha-helix dihedral angles; (2) PSer20 features a nearly 1:1 ratio of beta-turn:beta-sheet dihedral preferences, with very little preference for alpha-helical structure, and possesses short regions of strand and turn combinations that give rise to a collapsed bend or hairpin structure; (3) (PSer-Asp)10 features a 3:2:1 ratio of beta-sheet:beta-turn:alpha-helix and gives rise to a superturn or C-shaped structure.

Algorithms↗

PubMed1994

Contributions of the thymine methyl group to the specific recognition of poly- and mononucleotides: an analysis of the relative free energies of solvation of thymine and uracil.

Experimental results indicate that interactions with the 5-methyl group of thymine often account for around 1 kcal/mol of the total selectivity at A.T base pairs in protein-DNA complexes. The limited ability of methyl groups to form noncovalent interactions of this magnitude has led to the hypothesis that the energy of solvation of this hydrophobic element is responsible for the observed contribution to selectivity; however, it has not been possible to test this experimentally. We report a molecular dynamics perturbation thermodynamics (MD/PT) analysis of the relative free energy of solvation of thymine and uracil, both as the free bases and in the context of double-stranded DNA. The use of MD/PT indicates that the effect of shielding the 5-methyl group from solvent accounts for 0.90 +/- 0.11 kcal/mol of the observed contribution to specificity in protein-DNA complexes. We suggest some implications of these results for the mechanism of sequence-specific DNA recognition, DNA structure, and the evolution of the deoxynucleotide synthesis pathways.

Adenine↗

PubMed1994

Protein simulations using techniques suitable for very large systems: the cell multipole method for nonbond interactions and the Newton-Euler inverse mass operator method for internal coordinate dynamics.

Two new methods developed for molecular dynamics simulations of very large proteins are applied to a series of proteins ranging up to the protein capsid of tomato bushy stunt virus (TBSV). For molecular dynamics of very large proteins and polymers, it is useful to carry out the dynamics using internal coordinates (say, torsions only) rather than Cartesian coordinates. This allows larger time steps, eliminates problems with the classical description of high energy modes, and focuses on the important degrees of freedom. The resulting equation of motion has the form. [formula: see text] where for T is the vector of generalized forces, M(theta) is the moments of inertia tensor, theta is the vector of torsions, and C is a vector containing Coriolis forces and nonbond forces. The problem is that to calculate the acceleration vector theta from M, C, and T requires inverting M(theta), an order N3 calculation. Since the number of degrees of freedom might be 300,000 for a million atom system, solving these equations every time step is impractical, restricting internal coordinate methods to small systems. The new method, Newton-Euler Inverse Mass Operator (NEIMO) dynamics, constructs the torsional accelerations vector theta = M-1 (T-C) directly by an order N process, allowing internal-coordinate dynamics to be solved for super larger (million atom) systems. The first use of the NEIMO method for molecular dynamics of proteins is presented here. A second serious difficulty for large proteins is calculation of the nonbond forces. We report here the first application to proteins of the new Cell Multipole Method (CMM) to evaluate the Coulomb and van der Waals interactions. The costs of CMM scales linearly with the number of particles while retaining an accuracy significantly better than standard nonbond methods (involving cutoffs). Results for NEIMO and CMM are given for simulations of a wide range of peptide and protein systems, including the protein capsid of TBSV with 488,000 atoms. The computational times for NEIMO and CMM are demonstrated to scale linearly with size. With NEIMO the dynamics time steps can be as large as 20 fs (for small peptides), much larger than possible with standard Cartesian coordinate dynamics. For TBSV we considered both the normal form and the high pH form, in which the Ca2+ ions are removed. These calculations lead to a contraction of the protein for both forms (probably because of ignoring the RNA core not observed in the X-ray).

Algorithms↗