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F E Cohen

Publications and source records attributed to F E Cohen.

At least 163 records · Page 9Linked to original sources
PubMed1990

Novel method for the rapid evaluation of packing in protein structures.

There has been considerable effort to predict the structure of proteins from their amino acid sequences. A major problem in all prediction efforts has been that, short of a direct comparison with crystallographic co-ordinates, it is often difficult to evaluate the merit of a model, or "proposed" protein structure. Here, we present a method for evaluating proposed protein structures that does not require a structural model of complete atomic detail. Our method evaluates residue-residue packing density using a simplified model of the polypeptide chain where amino acids are represented as one, two (histidine, tyrosine and phenylalanine), or three (tryptophan) spheres. This method also gives a measure of the appropriateness of residue-residue contacts, thus giving a measure of the amino acid distribution throughout the protein. Amino acid packing and amino acid distribution, as evaluated by this technique, are consistent with the accuracy of model-built structures. We have been able to select the best structures from a set of combinatorially generated models using this method, and we anticipate that it will be useful as a general tool for model-building.

Amino Acid Sequence↗
PubMed1990

Protein model structure evaluation using the solvation free energy of folding.

A systematic study of solvation free energy of folding for proteins with known crystallographic structures is presented. There is a linear relationship between the solvation free energy of folding and the protein size. This relationship, which can be rationalized by a simple model of chain folding, allows prediction of the solvation free energy of folding for proteins for which no high resolution structures are available. All misfolded structures analyzed show solvation free energies higher than predicted; however, some of the misfolded structures have values close enough to the predicted values so that one must be very careful when using such a criterion to check the correctness of a protein model.

Enzymes↗
PubMed1989

Structural significance of the C-terminal amphiphilic helix of interleukin-2.

The structural significance of C-terminal amphiphilic alpha-helix of human interleukin-2 has been investigated using principles of protein design. Employing disulfide-mediated semi-synthesis, several multiple residue substitution patterns were studied in order to provide rapid insight into the most appropriate features to incorporate into fully recombinant proteins. Substitutions directed toward both stabilization and destabilization of the helix resulted in proteins with modulated bioactivity. Circular dichroism verified the conformational integrity and thermal stability of the derivatives. The biologic characteristics of each derivative were evaluated in the standard murine CTLL-2 assay and compared to activities exhibited in both human T-cell bioactivity and binding assay. A strategy for the design of protein ligand agonists and antagonists without knowledge of receptor contact residues is discussed.

Binding, Competitive↗
PubMed1989

Topological distribution of four-alpha-helix bundles.

The four-alpha-helix bundle, a common structural motif in globular proteins, provides an excellent forum for the examination of predictive constraints for protein backbone topology. An exhaustive examination of the Brookhaven Crystallographic Protein Data Bank and other literature sources has lead to the discovery of 20 putative four-alpha-helix bundles. Application of an analytical method that examines the difference between solvent-accessible surface areas in packed and partially unpacked bundles reduced the number of structures to 16. Angular requirements further reduced the list of bundles to 13. In 12 of these bundles, all pairs of neighboring helices were oriented in an anti-parallel fashion. This distribution is in accordance with structure types expected if the helix macro dipole effect makes a substantial contribution to the stability of the native structure. The characterizations and classifications made in this study prompt a reevaluation of constraints used in structure prediction efforts.

Macromolecular Substances↗
PubMed1988

A design approach to the structural analysis of interleukin-2.

A semi-synthetic protein design approach has been employed for the structural investigation of a putative helical region at the C-terminus of Interleukin-2. With crystallographic or NMR derived conformational data as yet unavailable, we have relied only on primary sequence information and computer-assisted modelling to direct the analysis. By employing both chemical peptide synthesis and recombinant DNA methods, the C-terminus of IL-2 was modified according to a strategy designed to stabilize helical secondary structure. A semi-synthetic protein incorporating 12 simultaneous amino acid replacements was constructed, which possessed potentiated biological activity and displayed a far UV circular dichroism spectrum comparable to a hybrid protein with the authentic sequence. By comparison, another hybrid protein containing a C-terminal region designed to contain helix breaking residues was totally devoid of bioactivity. These findings provide evidence that the modelling method correctly identified a helix necessary for the formation of a bioactive tertiary fold. Moreover, by employing semi-synthesis it was possible to circumvent the difficulties associated with the preparation, purification and analysis of multiple recombinant proteins, and also to avoid the unreliability of total chemical synthesis for proteins greater than 100 residues.

Amino Acid Sequence↗
PubMed1988

Diffusion-collision model for the folding kinetics of myoglobin.

The diffusion-collision model has been used to analyze the folding kinetics of myoglobin. The microdomains, which are the basic units that coalesce during the folding, are identified with the helices and the stabilizing contacts between helices are determined from the native structure. Both association and dissociation reactions are included and a range of stabilization parameters is investigated to determine the variation in overall rate and the relative contributions made by different intermediates during the folding process. In a comparison of folding to the native state and to the midpoint of the folding transition (i.e., 50% native protein at the completion of the reaction) significant differences in the contributing intermediates are found.

Diffusion↗
PubMed1987

Prediction of the three-dimensional structure of human growth hormone.

In recent years, the protein-folding problem has attracted the attention of molecular biologists. Efforts have focused on developing heuristic and energy-based algorithms to predict the three-dimensional structure of a protein from its amino acid sequence. We have applied a series of heuristic algorithms to the sequence of human growth hormone. A family of five structures which are generically right-handed fourfold alpha-helical bundles are found from an investigation of approximately 10(8) structures. A plausible receptor binding site is suggested. Independent crystallographic analysis confirms some aspects of these predictions. These methods only deal with the "core" structure, and conformations of many residues are not defined. Further work is required to identify a unique set of coordinates and to clarify the topological alternative available to alpha-helical proteins.

Growth Hormone↗
PubMed1987

Prediction of the tertiary structure of the alpha-subunit of tryptophan synthase.

The tertiary structure of the alpha-subunit of tryptophan synthase was proposed using a combination of experimental data and computational methods. The vacuum-ultraviolet circular dichroism spectrum was used to assign the protein to the alpha/beta-class of supersecondary structures. The two-domain structure of the alpha-subunit (Miles et al.: Biochemistry 21:2586, 1982; Beasty and Matthews: Biochemistry 24:3547, 1985) eliminated consideration of a barrel structure and focused attention on a beta-sheet structure. An algorithm (Cohen et al.: Biochemistry 22:4894, 1983) was used to generate a secondary structure prediction that was consistent with the sequence data of the alpha-subunit from five species. Three potential secondary structures were then packed into tertiary structures using other algorithms. The assumption of nearest neighbors from second-site revertant data eliminated 97% of the possible tertiary structures; consideration of conserved hydrophobic packing regions on the beta-sheet eliminated all but one structure. The native structure is predicted to have a parallel beta-sheet flanked on both sides by alpha-helices, and is consistent with the available data on chemical cross-linking, chemical modification, and limited proteolysis. In addition, an active site region containing appropriate residues could be identified as well as an interface for beta 2-subunit association. The ability of experimental data to facilitate the prediction of protein structure is discussed.

Amino Acid Sequence↗
PubMed1986

Structure-activity studies of interleukin-2.

The critical role of interleukin-2 (IL-2) in immune response heightens the need to know its structure in order to understand its activity. New computer-assisted predictive methods for the assignment of secondary structure together with a method to predict the tertiary structure of a protein from data on its primary sequence and secondary structure were applied to IL-2. This method generated four topological families of structures, of which the most plausible is a right-handed fourfold alpha-helical bundle. Members of this family were shown to be compatible with existing structural data on disulfide bridges and monoclonal antibody binding for IL-2. Experimental estimates of secondary structure from circular dichroism and site-directed mutagenesis data support the model. A region likely to be important in IL-2 binding to its receptor was identified as residues Leu36, Met38, Leu40, Phe42, Phe44, and Met46.

Amino Acid Sequence↗
PubMed1986

Turn prediction in proteins using a pattern-matching approach.

We extend the use of amino acid sequence patterns [Cohen, F.E., Abarbanel, R. M., Kuntz, I. D., & Fletterick, R. J. (1983) Biochemistry 22, 4894-4904] to the identification of turns in globular proteins. The approach uses a conservative strategy, combined with a hierarchical search (strongest patterns first) and length-dependent masking, to achieve high accuracy (95%) on a test set of proteins of known structure. Applying the same procedure to homologous families gives a 90% success rate. Straightforward changes are suggested to improve the predictive power. The computer program, written in Lisp, provides a general pattern-recognition language well suited for a number of investigations of protein and nucleic acid sequences.

Amino Acid Sequence↗
PubMed1986

A "helix-scissors" mechanism for the hinge-bending conformational change in phosphoglycerate kinase.

X-ray studies of phosphoglycerate kinase (EC 2.7.2.3, PGK) have shown that the enzyme's single polypeptide chain is organized into two separate domains that correspond to the N- and C-terminal halves of the chain. Substrate binding studies and the incorporation of the complete amino acid sequence of horse-muscle PGK into its X-ray model suggest that the C-domain is an ADP/ATP binding unit and that the N-terminal domain contains the phosphoglycerate binding site and the active site located in a prominent cluster of positively charged residues. Because the distance between these two sites is 12-15 A, a hinge-bending of 10 degrees--20 degrees has been proposed to bring the two sites together for catalysis. Independent solution studies of yeast PGK have shown that the radius of gyration decreases significantly on the formation of the ternary complex. This change has been interpreted in terms of a 9 degrees--12 degrees rotation about a hinge in the interdomain region that brings the two domains together. We suggest here a structural basis for the proposed hinge-bending that involves the rotation of the two helices that form the domain interface about their contact normal carrying their respective domains with them.

Amino Acid Sequence↗
PubMed1983

Secondary structure assignment for alpha/beta proteins by a combinatorial approach.

We describe an algorithm for assigning the secondary structure of alpha/beta proteins. Turns are identified very accurately (98%) by simultaneously considering hydrophilicity and the ideal spacing of turns throughout the sequence. The segments bounded by these turns are labeled by a pattern-recognition scheme based on the physical properties of alpha-helices and beta-strands, in this class of proteins. Long-range, as well as local, information is incorporated to enhance the quality of the assignments. Although the assignment for any one sequence is not unique, at least one of the assignments bears a close resemblance to the native structure. The algorithm successfully divides protein sequences into two classes: alpha/beta and non-alpha/beta. The accuracy of the secondary-structure assignments in the alpha/beta class is sufficient to provide useful input for tertiary-structure assignments.

Isomerism↗
PubMed1981

Analysis and predication of structural motifs in the glycolytic enzymes.

Protein crystallography has determined the three-dimensional structures of 10 of the 13 enzymes of the glycolytic pathway. Diagrams and details of these enzyme structures are given in the paper. Most of the enzyme domains are variations and extensions of a many (4--9)-stranded, predominantly or totally parallel, beta-sheet that is shielded from solvent by alpha-helices (i.e. alpha/beta structures). There are strong structural similarities between the domains of some, but not all, of the enzymes. In particular the dinucleotide binding fold of lactate dehydrogenase and the beta-barrel of triose phosphate isomerase are found in other domains. General rules governing the topology and packing of alpha-helices against a beta-sheet provide a basis for the combinatorial prediction of the tertiary fold of glycolytic domains from their amino acid sequence and observed secondary structure. The predication algorithm demonstrates that there are severe restrictions on the number of possible structures. However, these restrictions do not fully explain some of the remarkable structural similarities between different enzymes that probably result from evolution from a common ancestor.

Animals↗