Harry A. Saroff

Gas chromatography of the N-trifluoroacetylmethyl esters of the amino acids

Abstract The N-trifluoroacetylmethyl esters were found to yield single peaks on gas chromatography for the amino acids: alanine, valine, isoleucine, leucine, glycine, proline, aspartic acid, threonine, methionine, serine, glutamic acid, phenylalanine, hydroxyproline, and lysine. Improved yields of the derivatives were prepared by the use of sulfonated polystyrene resin in the hydrogen form as a catalyst for the formation of the methyl ester.

The multiple origins of cooperativity in binding to multi-site lattices

Binding events involving the reversible association of ligands with polymeric lattices of binding sites are common in biology and frequently exhibit significant cooperativity in binding. Positive and negative cooperativity in binding may be detected by characteristic changes in binding curves for multiple binding, compared to the binding expected for simple, independent binding events that are based on combinatorial considerations only. Cooperativity arises from ligand‐dependent interactions distinct from binding per se. Ligand‐dependent nearest neighbor interactions may be of two types referred to as ligand‐lattice (which can only occur if a bound ligand is unneighbored) and ligand‐ligand (which can occur if two or more bound ligands are adjacent). The molecular mechanisms underlying these two sources of cooperativity are not the same. Identical cooperative binding curves may be produced by changes from unity in parameters representing either one or both of these interaction types. Positive cooperativity may equally result from destabilizing ligand‐lattice interactions that disfavor initial, unneighbored binding, stabilizing ligand‐ligand interactions that favor subsequent, neighbored binding, or both. The structural origins of these are different, and cooperativity may emerge from multiple structural interactions.

Evaluation of uncertainties for parameters in binding studies: the sum-of-squares profile and Monte Carlo estimation.

Methods for characterization and evaluation of uncertainties in the parameter values for binding experiments are presented. A sum-of-squares profile is defined and illustrated. Sum-of-squares profiles give a qualitative description of both the uncertainties and correlation of parameters. The Monte Carlo method is developed as an accurate means of evaluating uncertainties in parameter values for nonlinear models. Examples are given for both actual and synthetic data.

The uniqueness of protein sequences. Uniqueness diagrams for the dayhoff file—1984

Protein sequences of the Dayhoff databank of 1984 have been analyzed to evaluate the occurrences of the 400 dipeptides and 8000 tripeptides. Expected values and standard deviations for the di- and tripeptides were determined by Monte Carlo and binomial approximation. A condensed format containing this information, labeled a uniqueness diagram, is presented and made available in the form of a microfiche.

The binding of ions to the muscle proteins. A theory for K+ and Na+ binding based on a hydrogen-bonded and chelated model

Abstract Binding equations are developed for the association of cations with proteins using a model in which hydrogen bonded and chelated forms are considered. The sodium- and potassium-ion binding data to myosin are analyzed with the result that the binding of sodium and potassium ions appears to involve carboxyl-alkali metal-imidazole and carboxyl-alkali metal-amino chelates. The association constants of these chelates are compared with those of known compounds.

The ionization of clusters II. Pairwise isotropic interactions and individual site binding data

Evaluation of the parameters describing the binding of protons to clusters of interacting sites requires some reasonable assumptions and procedures because it is impossible to observe an unperturbed site in its interacting environment. When the unperturbed sites are not identical, individual site binding data allow for the evaluation of the differences (or ratios) between the unperturbed (or intrinsic) binding constants but not their actual values (or the interaction energies). In this paper we extend our previous treatment of the ionization of clusters in order to generalize pairwise isotropic interactions and take into account the present availability of individual site binding data.

Ionization of clusters: III. Evaluation of interaction parameters from binding data

Interactions between ionizable groups on the same molecule modulate the binding of protons to an extent where the binding constants may be shifted by orders of magnitude. The first two papers of this series discussed the family of carboxylic acids, pairwise isotropic interactions, and evaluation of single site binding data. This paper presents an extended group of hypothetical binding isotherms. Procedures are illustrated for deriving interaction parameters from binding data. The interaction parameters for about 25 representative compounds with two and three interacting ionizable groups are evaluated and tabulated.

Application of the ising model to hemoglobin

Abstract This communication discusses an equation of Thompson (1968) for the binding of oxygen to hemoglobin and compares it with that of Pauling (1935) . Since the interactions assumed for the king model are not analogous to those assumed to apply in hemoglobin, the use of the Ising model yields unreasonable results in that an oxygenated site sometimes favors and sometimes hinders oxygenation at another site. It is shown that with some modification in the matrix representing the interactions between binding sites, the formalism of the Ising model leads to Paulings equation for the square model of hemoglobin.

The structure of ribonuclease derived from the clustering of its ionizable groups

Abstract A three dimensional structure of bovine ribonuclease is proposed and illustrated based on (1) the sequence of amino acids, (2) data on the active site, (3) the interpretation of proton and chloride binding yielding six clusters of five amino acids each, and (4) chemical evidence linking together distant parts of the polypeptide backbone. The model presented is examined for consistency with the data available on ribonuclease.

A continuous membrane diffusion column.

Abstract The construction and operation of a continuous membrane diffusion column are described. The column allowed the suspension of large areas of cellophane in a zig-zag fashion so that thin films of solutions could be made to flow continuously on both sides of the membrane. Data are presented on the dialyzing efficiency of the apparatus and on the concentration contours of solutions processed. Thickness of the solutions, mixing, and time of travel on the column were found to give conditions such that the diffusion coefficients of the solutes rather than pore size of the cellophane could be made the controlling factor in the operation of the apparatus. On the basis of experimental data found, one design for use of the apparatus as a molecular rectifier is proposed.