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Biomedical subjects

K D Gibson

Publications and source records attributed to K D Gibson.

At least 19 recordsLinked to original sources

Applied reaction dynamics: efficient synthesis gas production via single collision partial oxidation of methane to CO on Rh111.

Supersonic molecular beams have been used to determine the yield of CO from the partial oxidation of CH4 on a Rh111 catalytic substrate, CH4+12O2-->CO+2H2, as a function of beam kinetic energy. These experiments were done under ultrahigh vacuum conditions with concurrent molecular beams of O2 and CH4, ensuring that there was only a single collision for the CH4 to react with the surface. The fraction of CH4 converted is strongly dependent on the normal component of the incident beam's translational energy, and approaches unity for energies greater than approximately 1.3 eV. Comparison with a simplified model of the methane-Rh111 reactive potential gives insight into the barrier for methane dissociation. These results demonstrate the efficient conversion of methane to synthesis gas, CO+2H2, are of interest in hydrogen generation, and have the optimal stoichiometry for subsequent utilization in synthetic fuel production (Fischer-Tropsch or methanol synthesis). Moreover, under the reaction conditions explored, no CO2 was detected, i.e., the reaction proceeded with the production of very little, if any, unwanted greenhouse gas by-products. These findings demonstrate the efficacy of overcoming the limitations of purely thermal reaction mechanisms by coupling nonthermal mechanistic steps, leading to efficient C-H bond activation with subsequent thermal heterogeneous reactions.

Journal Article↗

Experiments and simulations of hyperthermal Xe interacting with an ordered 1-decanethiol/Au(111) monolayer: penetration followed by high-energy, directed ejection.

A study of the interaction of hyperthermal Xe with a well-ordered standing-up phase of 1-decanethiol adsorbed on Au(111) is presented. Experimentally, double-differential measurements were made of the postcollision Xe kinetic energy as a function of incident and final angles. These experiments are compared to classical trajectory calculations. The results show the two expected channels: direct-inelastic scattering from the surface and accommodated Xe due to trapping-desorption. There is also evidence of a further interaction mechanism. This involves the penetration of the atom deep into the channels between the aligned chains of the monolayer. When the collision energy has been dissipated, the implanted Xe is expelled as the chains return to their equilibrium positions. The expelled Xe leaves the surface with an energy much higher than expected for trapping-desorption, and with an angular-intensity distribution peaked close to the direction of the 1-decanethiol chain orientation. For this reason, we call this new scattering mechanism directed ejection.

Journal Article↗

Physics-based protein-structure prediction using a hierarchical protocol based on the UNRES force field: assessment in two blind tests.

Recent improvements in the protein-structure prediction method developed in our laboratory, based on the thermodynamic hypothesis, are described. The conformational space is searched extensively at the united-residue level by using our physics-based UNRES energy function and the conformational space annealing method of global optimization. The lowest-energy coarse-grained structures are then converted to an all-atom representation and energy-minimized with the ECEPP/3 force field. The procedure was assessed in two recent blind tests of protein-structure prediction. During the first blind test, we predicted large fragments of alpha and alpha+beta proteins [60-70 residues with C(alpha) rms deviation (rmsd) <6 A]. However, for alpha+beta proteins, significant topological errors occurred despite low rmsd values. In the second exercise, we predicted whole structures of five proteins (two alpha and three alpha+beta, with sizes of 53-235 residues) with remarkably good accuracy. In particular, for the genomic target TM0487 (a 102-residue alpha+beta protein from Thermotoga maritima), we predicted the complete, topologically correct structure with 7.3-A C(alpha) rmsd. So far this protein is the largest alpha+beta protein predicted based solely on the amino acid sequence and a physics-based potential-energy function and search procedure. For target T0198, a phosphate transport system regulator PhoU from T. maritima (a 235-residue mainly alpha-helical protein), we predicted the topology of the whole six-helix bundle correctly within 8 A rmsd, except the 32 C-terminal residues, most of which form a beta-hairpin. These and other examples described in this work demonstrate significant progress in physics-based protein-structure prediction.

Amino Acid Sequence↗

Experimental and simulation study of neon collision dynamics with a 1-decanethiol monolayer.

A study of the energy accommodation of neon colliding with a crystalline self-assembled 1-decanethiol monolayer adsorbed on Au(111) is presented. The intensity and velocity dependencies of the scattered neon as a function of incident angle and energy were experimentally measured. Scattering calculations show good agreement with these results, which allows us to examine the detailed dynamics of the energy and momentum exchange at the surface. Simulation results show that interaction times are, at most, a few picoseconds. Even for these short times, energy exchange with the surface, both normal and in-plane, is very rapid. An important factor in determining the efficiency of energy exchange is the location at which the neon collides with the highly corrugated and structurally dynamic unit cell. Moreover, our combined experimental and theoretical results confirm that these are truly surface collisions in that neon penetration into the organic boundary layer does not occur, even for the highest incident energies explored, 560 meV.

Journal Article↗

Ab initio folding of multiple-chain proteins.

Our previous methodology for ab initio prediction of protein structure is extended here to treat multiple-chain proteins. This involved modification of our united-residue (UNRES) force field and our Conformational Space Annealing (CSA) Global Optimization procedure. Good results have been obtained for both a four- and a three-helix protein from the CASP3 exercise.

Dimerization↗

Conformation-family Monte Carlo: a new method for crystal structure prediction.

A new global optimization method, Conformation-family Monte Carlo, has been developed recently for searching the conformational space of macromolecules. In the present paper, we adapted this method for prediction of crystal structures of organic molecules without assuming any symmetry constraints except the number of molecules in the unit cell. This method maintains a database of low energy structures that are clustered into families. The structures in this database are improved iteratively by a Metropolis-type Monte Carlo procedure together with energy minimization, in which the search is biased toward the regions of the lowest energy families. The Conformation-family Monte Carlo method is applied to a set of nine rigid and flexible organic molecules by using two popular force fields, AMBER and W99. The method performed well for the rigid molecules and reasonably well for the molecules with torsional degrees of freedom.

Crystallization↗

Recent improvements in prediction of protein structure by global optimization of a potential energy function.

Recent improvements of a hierarchical ab initio or de novo approach for predicting both alpha and beta structures of proteins are described. The united-residue energy function used in this procedure includes multibody interactions from a cumulant expansion of the free energy of polypeptide chains, with their relative weights determined by Z-score optimization. The critical initial stage of the hierarchical procedure involves a search of conformational space by the conformational space annealing (CSA) method, followed by optimization of an all-atom model. The procedure was assessed in a recent blind test of protein structure prediction (CASP4). The resulting lowest-energy structures of the target proteins (ranging in size from 70 to 244 residues) agreed with the experimental structures in many respects. The entire experimental structure of a cyclic alpha-helical protein of 70 residues was predicted to within 4.3 A alpha-carbon (C(alpha)) rms deviation (rmsd) whereas, for other alpha-helical proteins, fragments of roughly 60 residues were predicted to within 6.0 A C(alpha) rmsd. Whereas beta structures can now be predicted with the new procedure, the success rate for alpha/beta- and beta-proteins is lower than that for alpha-proteins at present. For the beta portions of alpha/beta structures, the C(alpha) rmsd's are less than 6.0 A for contiguous fragments of 30-40 residues; for one target, three fragments (of length 10, 23, and 28 residues, respectively) formed a compact part of the tertiary structure with a C(alpha) rmsd less than 6.0 A. Overall, these results constitute an important step toward the ab initio prediction of protein structure solely from the amino acid sequence.

Models, Molecular↗

Assessment of a policy to reduce placement of prosthetic hemodialysis access.

BACKGROUND: The aim of this study was to evaluate the determinants of access patency and revision, including the effects of reducing the placement of prosthetic hemodialysis access. METHODS: A retrospective cohort study of all hemodialysis accesses placed at the Veteran's Administration Puget Sound Health Care System between 1992 and 1999 was conducted. A policy was instituted in 1996 that maximized the use of autogenous hemodialysis access. The impacts of the policy change, demographics, and comorbid factors on access type and patency, were examined. Primary and secondary patency rates were examined using the Kaplan--Meier method, and factors associated with failure and revision were examined using Cox proportional hazard models and Poisson regression. RESULTS: During the study, 104 accesses (61 prosthetic grafts and 43 autogenous fistulas) were placed prior to 1996, and 118 (31 prosthetic grafts and 87 autogenous fistulas) were placed after 1996. There was a significant increase in autogenous fistulas placed after 1996 (87 out of 118) compared with before 1996 (43 out of 104, P < 0.001). At one year, autogenous fistulas demonstrated superior primary patency (56 vs. 36%, P = 0.001) and secondary patency (72 vs. 58%, P = 0.003) compared with prosthetic grafts. After adjustment for age, race, side of access placement, and history of prior access placement, patients with a prosthetic graft were estimated to experience a 78% increase in the risk of primary access failure when compared with similar patients having an autogenous access [adjusted relative risk (aRR) = 1.78, 95% CI 1.21--2.62, P = 0.003)]. Similarly, the adjusted relative risk of secondary access failure for comparing prosthetic grafts with autogenous fistulas was estimated to be 2.21 (95% CI 1.38--3.54, P = 0.001). The adjusted risk of access revision was 2.89-fold higher for prosthetic grafts than for autogenous fistulas (95% CI 1.88--4.44, P < 0.001). CONCLUSIONS: Autogenous conduits demonstrated superior performance when compared with prosthetic grafts in terms of primary and secondary patency and number of revisions. A policy emphasizing the preferential placement of autogenous fistulas over prosthetic grafts may result in improved patency and a reduction in the number of procedures required to maintain dialysis access patency.

Adult↗

Use of the vascular diagnostic laboratory in improving the success of angioaccess procedures.

The goal of hemodialysis access placement is long-term patency with as few revisions as possible. Autogenous fistulas have superior performance compared with prosthetic grafts, but up to 70% fail to mature sufficiently for dialysis. Accurate preoperative evaluation of arterial and venous anatomy can increase the successful use of autogenous fistulas, thereby increasing long-term access patency. Duplex ultrasonography has an important role in identifying usable autogenous conduit and detecting venous outflow disease, another important cause of access failure. The use of the vascular diagnostic laboratory in preoperative planning can increase the percentage of autogenous fistulas placed, increase the percentage that mature, and reduce the rate of negative explorations for vein at the time of surgery.

Angiography↗

Identification of factors predictive of lower extremity vein graft thrombosis.

OBJECTIVE: The objective of this study was to assess the prognostic value of hemodynamic parameters measured with duplex ultrasound scan, together with other important graft and patient characteristics, in predicting lower extremity vein graft thrombosis. METHODS: A total of 165 lower extremity vein grafts were entered prospectively into a postoperative duplex ultrasound scan surveillance program with examinations performed at 1, 2, 3, 4, 6, 9, 12, 18, and 24 months, and annually thereafter. Duplex scan-derived blood flow velocity measurements were recorded at 1562 patient visits over 7 years. Graft patency was determined after each visit, and an analysis of factors predictive of vein graft thrombosis was performed with Poisson regression. RESULTS: Thirty-two episodes of first-time graft thrombosis occurred, 23 of which were permanent. One-, 3-, and 5-year secondary graft patency rates were 90%, 86%, and 79%, respectively. In multivariate analyses, duplex scan velocity measurements predictive of lower extremity graft thrombosis included the maximum velocity ratio (Vr) in association with a graft stenosis and the mean graft peak systolic velocity (MGV) within nonstenotic portions of the body of the graft. The incidence of graft thrombosis among grafts without inflow/outflow stenoses, with Vr less than 3.5, and with MGV 50 cm/s or more, was 2.9% per year. Incidence rates were considerably higher among grafts with a of Vr of 3.5 or more (incidence rate ratio = 7.0; 95% CI, 3.4-14.6) or an MGV less than 50 cm/s (incidence rate ratio = 6.5; 95% CI, 3.3-13.1). In grafts without identifiable inflow, outflow, or graft stenoses, there was no association between MGV and the risk of graft thrombosis. CONCLUSION: Duplex scan velocity measurements are valid predictors of impending graft thrombosis. A Vr of 3.5 or more and an MGV less than 50 cm/s are the best predictive measures. Repair of correctable graft lesions with a Vr of 3.5 or more, or inflow, outflow, or graft lesions associated with an MGV less than 50 cm/s are recommended. Grafts without detectable inflow, outflow, or graft stenoses, regardless of MGV, may be safely followed.

Adolescent↗

Vascular access survival and incidence of revisions: a comparison of prosthetic grafts, simple autogenous fistulas, and venous transposition fistulas from the United States Renal Data System Dialysis Morbidity and Mortality Study.

OBJECTIVE: The study's aim was to evaluate access patency and incidence of revisions in patients initiating hemodialysis and to determine differences in access performance by type of access among patient subgroups. METHODS: The study used data from the United States Renal Data System Dialysis Morbidity and Mortality Study Wave 2, which contained a random sample of dialysis patients initiating dialysis in 1996 and early 1997. Failures and revisions were evaluated among 2247 newly placed hemodialysis accesses by using Cox proportional hazards regression model and Poisson regression. Primary and secondary patency rates were estimated using the Kaplan-Meier method. RESULTS: Fifteen hundred seventy-four prosthetic grafts, 492 simple autogenous fistulas, and 181 venous transposition fistulas were available for evaluation. Prosthetic grafts had a 41% greater risk of primary failure compared with simple fistulas (relative risk, 1.41; 95% CI, 1.22-1.64; P < .001) and a 91% higher incidence of revision (relative risk, 1.91; 95% CI, 1.60-2.28; P <.001). At 2 years, autogenous fistulas demonstrated superior primary patency (39.8% versus 24.6%, P < .001) and equivalent secondary patency (64.3% versus 59.5%, P = .24) compared with prosthetic grafts. When compared with simple fistulas, vein transpositions demonstrated equivalent secondary patency at 2 years (61.5% versus 64.3%, P = .43) but inferior primary patency (27.7% versus 39.8%, P = .008) and had a 32% increased incidence of revision (P = .04). Autogenous fistulas had superior primary patency compared with prosthetic grafts in all patient subgroups except for patients with previously failed access. Vein transpositions showed the greatest benefit in terms of patency and incidence of revision in women and in patients with previously failed access. CONCLUSIONS: The preferential placement of autogenous fistulas may increase primary patency and decrease the incidence of revisions. Vein transpositions had similar secondary patency compared with simple fistulas, but required more revisions. The greatest benefit of a vein transposition fistula was seen in women and in patients with a history of access failure.

Adult↗

Theoretical prediction of a crystal structure.

The diffusion equation method of global minimization is applied to compute the crystal structure of S6, with no a priori knowledge about the system. The experimental lattice parameters and positions and orientations of the molecules in the unit cell are predicted correctly.

Journal Article↗

Computer-aided discrimination between active and inactive mutants of the N-terminal domain of the bacteriophage lambda repressor.

Binding of the N-terminal domain of the lambda repressor to DNA is coupled to dimerization. Hydrophobic interactions between helix-5 and helix-5' drive the packing at the dimer interface. We have carried out computations of the conformational energy of packing of the fifth helices (and of the helix-4-loop-helix-5 portions) of variants of the lambda repressor operator binding domain, using an ECEPP/3-based packing algorithm. Here, we report the results for 26 mutants chosen among those that hve been characterized experimentally. We find that the relative orientation of the fifth helices for active mutants is very similar to the wild-type. The fifth helices of the inactive mutants have a significantly different relative orientation. This result illustrates that a unique specific orientation pattern of helix-5 relative to helix-5' is required for dimerization-coupled DNA binding activity. This finding is further supported by computational studies of the whole N-terminal domain of ten variants that showed that the active mutants, including the wild-type protein, have similar values of the number of contacts between the two monomers in the dimer, involving two amino acid residues of the fifth helices (positions 84 and 87 in each monomer). A decrease in the number of such contacts abolishes DNA-binding activity. Furthermore, all active mutants have their "DNA-recognition helices", numbers 3 and 3' positioned so that they can fit in the DNA operator like those of the wild-type protein, while some inactive mutants exhibit a substantial change in the relative orientation of their recognition helices.

Algorithms↗

Effects on protein structure and function of replacing tryptophan with 5-hydroxytryptophan: single-tryptophan mutants of the N-terminal domain of the bacteriophage lambda repressor.

Conformational energy computations have been carried out on the N-acetyl-N'-methylamide of 5-hydroxytryptophan (5OH-Trp) using ECEPP/3. As observed with tryptophan (Trp), the most preferred conformation about the C alpha-C beta bond of the side chain is g+ or t. This preference is reduced to only the t conformational state when 5-hydroxyTrp is in the middle of a right-handed poly(L-alanine) alpha-helix. A similar result has been obtained with Trp [Piela et al. (1987), Biopolymers 1987, 1273-1286]. These results suggest that replacement of Trp by its analog 5-hydroxyTrp may be tolerated in an alpha-helix. To test this hypothesis, we have replaced Trp by 5OH-Trp in the fifth helices of two functionally active mutants of the N-terminal domain of the bacteriophage lambda repressor. Computations on the packing of these helices have shown that no significant structural changes results from the replacement of Trp by 5OH-Trp. The DNA-binding activity of these mutants, as assessed indirectly through geometrical parameters, is also unaltered.

5-Hydroxytryptophan↗

The effect of the l-azetidine-2-carboxylic acid residue on protein conformation. IV. Local substitutions in the collagen triple helix.

The properties of collagen are affected by the replacement of Pro by imino acid analogues. The structural effect of the low-level local substitution of L-azetidine-2-carboxylic acid (Aze) has been analyzed by computing the energy of CH3CO-(Gly-Pro-Pro)4-NHCH3 triple helices in which a single residue of one strand has been replaced by Aze. When Aze is in position Y of a (Gly-X-Y) unit, low-energy local deformations are introduced in the triple helix, i.e., it becomes more flexible. On the other hand, the flexibility of the triple helix is not increased with Aze in position X. The energy of the triple helix to coil transition is not changed significantly by this amount of substitution. In an earlier study, we have demonstrated that the regular substitution of Aze in every tripeptide distorts or destabilizes the triple helix to a large extent [A. Zagari, G. Némethy, & H. A. Scheraga (1990) Biopolymers, Vol. 30, pp. 967-974]. Thus, it appears that a high level of substitution is required to cause the observed chemical and biological effects of Aze on collagen.

Amino Acid Sequence↗

Comparison of the low energy conformations of an oncogenic and a non-oncogenic p21 protein, neither of which binds GTP or GDP.

Oncogenic p21 protein, encoded by the ras-oncogene, that causes malignant transformation of normal cells and many human tumors, is almost identical in sequence to its normal protooncogene-encoded counterpart protein, except for the substitution of arbitrary amino acids for the normally occurring amino acids at critical positions such as Gly 12 and Gln 61. Since p21 is normally activated by the binding of GTP in place of GDP, it has been postulated that oncogenic forms must retain bound GTP for prolonged time periods. However, two multiply substituted p21 proteins have been cloned, neither of which binds GDP or GTP. One of these mutant proteins with Val for Gly 10, Arg for Gly 12, and Thr for Ala 59 causes cell transformation, while the other, similar protein with Gly 10, Arg 12, Val for Gly 13 and Thr 59 does not transform cells. To define the critical conformational changes that occur in the p21 protein that cause it to become oncogenic, we have calculated the low energy conformations of the two multiply substituted mutant p21 proteins using a new adaptation of the electrostatically driven Monte Carlo (EDMC) technique, based on the program ECEPP. We have used this method to explore the conformational space available to both proteins and to compute the average structures for both using statistical mechanical averaging. Comparison of the average structures allows us to detect the major differences in conformation between the two proteins. Starting structures for each protein were calculated using the recently deposited x-ray crystal coordinates for the p21 protein, that was energy-refined using ECEPP, and then perturbed using the EDMC method to compute its average structure. The specific amino acid substitutions for both proteins were then generated into the lowest energy structure generated by this procedure, subjected to energy minimization and then to full EDMC perturbations. We find that both mutant proteins exhibit major differences in conformation in specific regions, viz., residues 35-47, 55-78, 81-93, 96-110, 115-126, and 123-134, compared with the EDMC-refined x-ray structure of the wild-type protein. These regions have been found to be the most flexible in the p21 protein bound to GDP from prior molecular dynamics calculations (Dykes et al., 1993). Comparison of the EDMC-average structure of the transforming mutant with that of the nontransforming mutant reveals major structural differences at residues 10-16, 32-40, and 60-68. These structural differences appear to be the ones that are critical in activation of the p21 protein.(ABSTRACT TRUNCATED AT 400 WORDS)

Crystallography, X-Ray↗

Solution structure of murine epidermal growth factor determined by NMR spectroscopy and refined by energy minimization with restraints.

The solution structure of murine epidermal growth factor (mEGF) at pH 3.1 and a temperature of 28 degrees C has been determined from NMR data, using distance geometry calculations and restrained energy minimization. The structure determination is based on 730 conformational constraints derived from NMR data, including 644 NOE-derived upper bound distance constraints, constraints on the ranges of 32 dihedral angles based on measurements of vicinal coupling constants, and 54 upper and lower bound constraints associated with nine hydrogen bonds and the three disulfide bonds. The distance geometry interpretation of the NMR data is based on previously published sequence-specific 1H resonance assignments [Montelione et al. (1988) Biochemistry 27, 2235-2243], supplemented here with individual assignments for some side-chain amide, methylene, and isopropyl methyl protons. The molecular architecture of mEGF is the same as that described previously [Montelione et al. (1987) Proc. Natl. Acad. Sci. U.S.A. 84, 5226-5230], but the structure is overall more precisely determined by a more extensive set of NMR constraints. Analysis of proton NMR line widths, amide proton exchange rates, and side-chain 3J(H alpha-H beta) coupling constants provides evidence for internal motion in several regions of the mEGF molecule. Because mEGF is one member of a large family of homologous growth factors and protein domains for which X-ray crystal structures are not yet available, the atomic coordinates resulting from the present structure refinement (which we have deposited in the Brookhaven Protein Data Bank) are important data for understanding the structures of EGF-like proteins and for further detailed comparisons of these structures with mEGF.

Amino Acid Sequence↗

Fluorescence resonance energy transfer mapping of the fourth of six nucleotide-binding sites of chloroplast coupling factor 1.

Equilibrium dialysis measurements of adenine nucleotide binding to chloroplast coupling factor 1 suggest that the enzyme has six binding sites for ADP, adenylyl-beta,gamma-imidodiphosphate (AMP-PNP), and 2'(3')-O-2,4,6-trinitrophenyl-ATP (TNP-ATP). High affinity binding at all six sites requires the divalent cation, Mg2+. Three of the nucleotide-binding sites, sites 1, 2, and 3, have been mapped by fluorescence resonance energy transfer distance measurements (see McCarty, R. E., and Hammes, G. G. (1987) Trends Biochem. Sci. 12, 234-237). Using the same technique, we mapped the location of nucleotide-binding site 4, a tight, exchangeable site (Shapiro, A. B., Huber, A. H., and McCarty, R. E. (1991) J. Biol. Chem. 266, 4194-4200). Two arrangements of the energy transfer map of coupling factor 1 were found which are compatible with the available data. The two arrangements make different predictions about which sites interact in cooperative catalysis.

Adenosine Diphosphate↗