A5025532762- DNA and Nucleic Acid Chemistry
- RNA and protein synthesis mechanisms
- Bacteriophages and microbial interactions
- Enzyme Structure and Function
- Bacterial Genetics and Biotechnology
- Protein Structure and Dynamics
- Amino Acid Enzymes and Metabolism
- Advanced biosensing and bioanalysis techniques
- CRISPR and Genetic Engineering
- RNA Interference and Gene Delivery
- Ion channel regulation and function
- Diffusion and Search Dynamics
- Ion Transport and Channel Regulation
- Pancreatic function and diabetes
- Pharmaceutical Practices and Patient Outcomes
- Theoretical and Computational Physics
- Biomedical Text Mining and Ontologies
- Statistical Mechanics and Entropy
- Scientific Computing and Data Management
- Advanced Database Systems and Queries
- Nanopore and Nanochannel Transport Studies
- Data Mining Algorithms and Applications
- Photosynthetic Processes and Mechanisms
- Cardiac electrophysiology and arrhythmias
- Machine Learning in Materials Science
University of Pittsburgh
2012-2024
Brigham Young University
2019
Pittsburg State University
2018
Massachusetts Institute of Technology
1973-2018
University of Southern California
2017
Monash University
2000-2003
Indiana University Bloomington
2003
European Molecular Biology Laboratory
2003
Australian Regenerative Medicine Institute
2000
Smithsonian Astrophysical Observatory
1997
Abstract The Weighted Histogram Analysis Method (WHAM), an extension of Ferrenberg and Swendsen's Multiple Technique, has been applied for the first time on complex biomolecular Hamiltonians. method is presented here as Umbrella Sampling free‐energy Potential Mean Force calculations. This algorithm possesses following advantages over methods that are currently employed: (1) It provides a built‐in estimate sampling errors thereby yielding objective estimates optimal location length additional...
The base pairs in double helical nucleic acids have been compared to see how they can be recognized by proteins. We conclude that a single hydrogen bond is inadequate for uniquely identifying any particular pair, as this leads numerous degeneracies. However, using two bonds, fidelity of pair recognition may achieved. propose specific amino-acid side chain interactions involving bonds component the system pairs. In major groove we suggest asparagine or glutamine binds adenine arginine...
Abstract The recently formulated weighted histogram analysis method (WHAM) 1 is an extension of Ferrenberg and Swendsen's multiple technique for free‐energy potential mean force calculations. As illustration the method, we have calculated two‐dimensional surface dihedrals gamma chi in deoxyadenosine with Monte Carlo simulations using all‐atom united‐atom representation AMBER fields. This also demonstrates one major advantages WHAM over umbrella sampling techniques. provides statistical...
The crystal structure of the complex between Eco RI endonuclease and cognate oligonucleotide TCGCGAATTCGCG provides a detailed example structural basis sequence-specific DNA-protein interactions. was determined, to 3 Å resolution, by ISIR (iterative single isomorphous replacement) method with platinum derivative. has twofold symmetry. Each subunit is organized into an α/β domain consisting five-stranded β sheet, α helices, extension, called "arm," which wraps around DNA. large sheet consists...
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The Eco R1 endonuclease and methylase recognize the same hexanucleotide substrate sequence.We have determined sequence of a fragment DNA which encodes these enzymes using chain-termination method Sanger (Sanger, F.,
The innately heterodimeric K 2P filter permits two C-type gating mechanisms, pinching and dilation, to operate in one channel.
Optimum coordinate sets have been obtained for ferrocytochrome c and the two symmetry-independent molecules of ferricytochrome from tuna at 2.0 A resolution by making best fit models with standard bond lengths angles to experimental electron density maps (1977) J. Biol. Chem. 252, 759-785, as a preliminary full refinement 1.5 data. Both Diamond model-building programs locally developed minicomputer routines were tried, latter preferred economy ease operation, although both gave satisfactory...
The sodium salt of guanylyl-3',5'-cytidine crystallizes in a monoclinic unit cell with one molecule the asymmetric unit. Each is related to another by 2-fold rotation axis which results formation an antiparallel, right-handed double helix complementary hydrogen bonding between guanine and cytosine residues. crystal heavily hydrated 36 water molecules cell. geometry this crystalline very similar those have been derived from studies fiber x-ray diffraction patterns double-stranded RNA, even...
The free energy of the binding reaction between EcoRI restriction endonuclease and a specific cognate dodecadeoxynucleotide (d(CGCGAATTCGCG)) has contributions from both electrostatic nonelectrostatic components.These were dissected by measuring effects varying salt concentration on equilibrium constant applying thermodynamic analyses Record et al. (Record, M.
The characteristics of inducer binding to lactose repressor protein in the presence a small (29 base pair) operator DNA fragment have been examined. fragments decreases affinity for molecules. maximum change observed is 20-fold increase concentration necessary half-saturation protein. non-linearity Scatchard type plots and slopes Hill data indicate that exhibits cooperative behavior fragments, while free binds noncooperative fashion. experimental both absence saturating amounts were compared...
A procedure has been developed which eliminates the commonly observed inactivation of DNA binding activity lac repressor during purification. The operator obtained by this method is 100 ±10%. can be stored frozen indefinitely without losing its affinity for DNA.
Significance The potential energy stored in ion gradients across cell membranes drives nutrients and out of cells by cotransport proteins, e.g., uphill glucose accumulation sodium cotransporters. Insight into the mechanism has been obtained from high-resolution atomic structures transporters, but further progress requires dynamic information about substrate movements through proteins. We have used multiple long molecular-dynamic simulations electrophysiological assays to explore dynamics...