M. Thomas Record

Bio: M. Thomas Record is an academic researcher from University of Wisconsin-Madison. The author has contributed to research in topics: RNA polymerase & DNA. The author has an hindex of 53, co-authored 119 publications receiving 9388 citations. Previous affiliations of M. Thomas Record include St. Olaf College & University of California, San Diego.

Hofmeister salt effects on surface tension arise from partitioning of anions and cations between bulk water and the air-water interface.

Abstract: We apply a recently developed surface-bulk partitioning model to interpret the effects of individual Hofmeister cations and anions on the surface tension of water. The most surface-excluded salt (Na2SO4) provides a minimum estimate for the number of water molecules per unit area of the surface region of 0.2 H2O A-2. This corresponds to a lower bound thickness of the surface region of ∼6 A, which we assume is a property of this region and not of the salt investigated. At salt concentrations ≲1 m, single-ion partition coefficients Kp,i, defined relative to Kp,Na+ = Kp,SO42− = 0, are found to be independent of bulk salt concentration and additive for different salt ions. Semiquantitative agreement with surface-sensitive spectroscopy data and molecular dynamics simulations is attained. In most cases, the rank orders of Kp,i for both anions and cations follow the conventional Hofmeister series, qualitative rankings of ions based on their effects on protein processes (folding, precipitation, assembly). Most ani...

Novel computer program for fast exact calculation of accessible and molecular surface areas and average surface curvature.

Abstract: New computer programs, SurfRace and FastSurf, perform fast calculations of the solvent accessible and molecular (solvent excluded) surface areas of macromolecules. Program SurfRace also calculates the areas of cavities inaccessible from the outside. We introduce the definition of average curvature of molecular surface and calculate average molecular surface curvatures for each atom in a structure. All surface area and curvature calculations are analytic and therefore yield exact values of these quantities. High calculation speed of this software is achieved primarily by avoiding computationally expensive mathematical procedures wherever possible and by efficient handling of surface data structures. The programs are written initially in the language C for PCs running Windows 2000/98/NT, but their code is portable to other platforms with only minor changes in input-output procedures. The algorithm is robust and does not ignore either multiplicity or degeneracy of atomic overlaps. Fast, memory-efficient and robust execution make this software attractive for applications both in computationally expensive energy minimization algorithms, such as docking or molecular dynamics simulations, and in stand-alone surface area and curvature calculations.

疟原虫var基因转换速率变化导致抗原变异[英]／Paul H, Robert P, Christodoulou Z, et al//Proc Natl Acad Sci U S A

Abstract: 抗原变异可使得多种致病微生物易于逃避宿主免疫应答。表达在感染红细胞表面的恶性疟原虫红细胞表面蛋白1（PfPMP1）与感染红细胞、内皮细胞、树突状细胞以及胎盘的单个或多个受体作用，在黏附及免疫逃避中起关键的作用。每个单倍体基因组var基因家族编码约60种成员，通过启动转录不同的var基因变异体为抗原变异提供了分子基础。

Rapid procedure for detection and isolation of large and small plasmids.

Abstract: Procedures are described for the detection and isolation of plasmids of various sizes (2.6 to 350 megadaltons) that are harbored in species of Agrobacterium, Rhizobium, Escherichia, Salmonella, Erwinia, Pseudomonas, and Xanthomonas. The method utilized the molecular characteristics of covalently closed circular deoxyribonucleic acid (DNA) that is released from cells under conditions that denature chromosomal DNA by using alkaline sodium dodecyl sulfate (pH 12.6) at elevated temperatures. Proteins and cell debris were removed by extraction with phenol-chloroform. Under these conditions chromosomal DNA concentrations were reduced or eliminated. The clarified extract was used directly for electrophoretic analysis. These procedures also permitted the selective isolation of plasmid DNA that can be used directly in nick translation, restriction endonuclease analysis, transformation, and DNA cloning experiments.

A unified view of polymer, dumbbell, and oligonucleotide DNA nearest-neighbor thermodynamics

Abstract: A unified view of polymer, dumbbell, and oligonucleotide nearest-neighbor (NN) thermodynamics is presented DNA NN DG° 37 parameters from seven laboratories are presented in the same format so that careful comparisons can be made The seven studies used data from natural polymers, synthetic polymers, oligonucleotide dumbbells, and oligonucleotide duplexes to derive NN parameters; used dif- ferent methods of data analysis; used different salt concen- trations; and presented the NN thermodynamics in different formats As a result of these differences, there has been much confusion regarding the NN thermodynamics of DNA poly- mers and oligomers Herein I show that six of the studies are actually in remarkable agreement with one another and explanations are provided in cases where discrepancies re- main Further, a single set of parameters, derived from 108 oligonucleotide duplexes, adequately describes polymer and oligomer thermodynamics Empirical salt dependencies are also derived for oligonucleotides and polymers

Classical Electrostatics in Biology and Chemistry

Abstract: A major revival in the use of classical electrostatics as an approach to the study of charged and polar molecules in aqueous solution has been made possible through the development of fast numerical and computational methods to solve the Poisson-Boltzmann equation for solute molecules that have complex shapes and charge distributions. Graphical visualization of the calculated electrostatic potentials generated by proteins and nucleic acids has revealed insights into the role of electrostatic interactions in a wide range of biological phenomena. Classical electrostatics has also proved to be successful quantitative tool yielding accurate descriptions of electrical potentials, diffusion limited processes, pH-dependent properties of proteins, ionic strength-dependent phenomena, and the solvation free energies of organic molecules.

The molecular theory of polyelectrolyte solutions with applications to the electrostatic properties of polynucleotides.

Abstract: Although the importance of the polyelectrolyte character of DNA has been recognized for some time (Felsenfeld & Miles 1967), few of the implications have been explored, primarily because of a lag in translating the breakthroughs in polyelectrolyte theory of the last decade into a form that is well adapted to the analysis of the specialized problems of biophysical chemistry. Perhaps an analogous situation existed in the field of protein chemistry during the period after the formulation and confirmation of the Debye—Huckel theory of ionic solutions but before Scatchard's incorporation of the theory into his analysis of the binding properties of proteins. An achievement for polynucleotide solutions parallel to Scatchard's was recently presented by Record, Lohman, & de Haseth (1976) and further developed and reviewed by Record, Anderson & Lohman (1978).