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Biomedical subjects

F E Cohen

Publications and source records attributed to F E Cohen.

At least 145 records · Page 8Linked to original sources
PubMed1993

Origins of structural diversity within sequentially identical hexapeptides.

Efforts to predict protein secondary structure have been hampered by the apparent structural plasticity of local amino acid sequences. Kabsch and Sander (1984, Proc. Natl. Acad. Sci. USA 81, 1075-1078) articulated this problem by demonstrating that identical pentapeptide sequences can adopt distinct structures in different proteins. With the increased size of the protein structure database and the availability of new methods to characterize structural environments, we revisit this observation of structural plasticity. Within a set of proteins with less than 50% sequence identity, 59 pairs of identical hexapeptide sequences were identified. These local structures were compared and their surrounding structural environments examined. Within a protein structural class (alpha/alpha, beta/beta, alpha/beta, alpha + beta), the structural similarity of sequentially identical hexapeptides usually is preserved. This study finds eight pairs of identical hexapeptide sequences that adopt beta-strand structure in one protein and alpha-helical structure in the other. In none of the eight cases do the members of these sequences pairs come from proteins within the same folding class. These results have implications for class dependent secondary structure prediction algorithms.

Algorithms↗
PubMed1993

Mutational and secondary structural analysis of the basolateral sorting signal of the polymeric immunoglobulin receptor.

The 17-juxtamembrane cytoplasmic residues of the polymeric immunoglobulin receptor contain an autonomous basolateral targeting signal that does not mediate rapid endocytosis (Casanova, J. E., G. Apodaca, and K. E. Mostov. Cell. 66:65-75). Alanine-scanning mutagenesis identifies three residues in this region, His656, Arg657, and Val660, that are most essential for basolateral sorting and two residues, Arg655 and Tyr668, that play a lesser role in this process. Progressive truncations suggested that Ser664 and Ile665 might also play a role in basolateral sorting. However, mutation of these residues to Ala or internal deletions of these residues did not affect basolateral sorting, indicating that these residues are probably not required for basolateral sorting. Two-dimensional NMR spectroscopy of a peptide corresponding to the 17-mer signal indicates that the sequence Arg658-Asn-Val-Asp661 has a propensity to adopt a beta-turn in solution. Residues COOH-terminal to the beta-turn (Arg662 to Arg669) seem to take up a nascent helix structure in solution. Substitution of Val660 with Ala destabilizes the turn, while mutation of Arg657 to Ala does not appear to affect the turn structure. Neither mutation detectably altered the stability of the nascent helix in the COOH-terminal portion of the peptide.

Amino Acid Sequence↗
PubMed1993

MacMatch: a tool for pattern-based protein secondary structure prediction.

A program is described for predicting the secondary structure of globular proteins on an Apple Macintosh computer. MacMatch produces turn predictions using augmented regular expression pattern matching. Helix and strand predictions are based on a neural network. Protein structural class (alpha/alpha), beta/beta, alpha/beta can be exploited to improve secondary structure prediction. The program is simple to use, and the package includes sets of tested patterns and trained neural networks.

Microcomputers↗
PubMed1993

Modeling protein structures: construction and their applications.

Although no general solution to the protein folding problem exists, the three-dimensional structures of proteins are being successfully predicted when experimentally derived constraints are used in conjunction with heuristic methods. In the case of interleukin-4, mutagenesis data and CD spectroscopy were instrumental in the accurate assignment of secondary structure. In addition, the tertiary structure was highly constrained by six cysteines separated by many residues that formed three disulfide bridges. Although the correct structure was a member of a short list of plausible structures, the "best" structure was the topological enantiomer of the experimentally determined conformation. For many proteases, other experimentally derived structures can be used as templates to identify the secondary structure elements. In a procedure called modeling by homology, the structure of a known protein is used as a scaffold to predict the structure of another related protein. This method has been used to model a serine and a cysteine protease that are important in the schistosome and malarial life cycles, respectively. The model structures were then used to identify putative small molecule enzyme inhibitors computationally. Experiments confirm that some of these nonpeptidic compounds are active at concentrations of less than 10 microM.

Amino Acid Sequence↗
PubMed1993

New strategies for pharmaceutical design.

Parallel synthesis and testing procedures are being investigated to shorten the drug design and discovery process. These procedures have focused on peptides and nucleotides, although these compounds are unlikely to be useful therapeutics because of their low bioavailability and sensitivity to enzymatic degradation. More recently, the use of other modular systems with distinct linking chemistries have been explored. Structural data combined with computational screens of compound databases provides an alternative method to identify novel nonpeptide pharmaceuticals. When structural information is not available, homology-based models have proved to be sufficient to identify nonpeptide inhibitors active at low micromolar concentrations against important enzymes in parasite life cycles.

Bacteriophages↗
PubMed1992

A human gene (AHNAK) encoding an unusually large protein with a 1.2-microns polyionic rod structure.

We report here the identification and partial characterization of a human gene (designated AHNAK) that encodes an unusually large protein (approximately 700 kDa). AHNAK is expressed by means of a 17.5-kilobase mRNA in diverse cellular lineages but is typically repressed in cell lines derived from human neuroblastomas and in several other types of tumors. Unique-sequence domains at the two ends of the protein flank a large internal domain (approximately 4300 amino acids) composed of highly conserved repeated elements, most of which are 128 amino acids in length. The repeated elements in turn display a redundant motif, marked by the recurrence of proline at every seventh residue. Within these sequences, hydrophobic and hydrophilic residues alternate in a manner that is incompatible with a helical coiled-coil structure. Instead, we propose a structure resembling a beta-strand but with a periodicity of 2.33. The structure would engender a polyionic rod approximately 1.2 microns long. Preliminary evidence indicates that the protein resides predominantly within the nucleus, but no function has yet been discerned.

Adrenal Gland Neoplasms↗
PubMed1992

Taxonomy and conformational analysis of loops in proteins.

We propose a general classification scheme for loops, aperiodic segments of protein structure. In an effort to avoid the geometric complexity created by non-repeating phi psi angles, a morphologic definition that focuses upon the linearity and planarity of loops is utilized. Out of 432 loops (4 to 20 residues in length) extracted from 67 proteins, 205 are classified as linear (straps), 133 as non-linear and planar (omegas), and 86 as non-linear and non-planar (zetas). The remaining 8 are classified as compound loops because they contain a combination of strap, omega, and zeta morphologies. We introduce a structural alphabet as a shorthand notation for describing local conformation. The symbols of this alphabet are based on the virtual dihedral angle joining four consecutive alpha carbons. The notation is used to provide a compact description of loop motifs in phosphate binding and calcium binding proteins. Since similar loop conformations form similar "words", the structural sequence facilitates the search for common structural motifs in a family of loops. Contrary to the view of loops as "random coils", we find loops to have positional preferences for amino acid residues analogous to those previously described for beta-turns.

Amino Acid Sequence↗
PubMed1992

A segment-based approach to protein secondary structure prediction.

Amino acid sequence patterns have been used to identify the location of turns in globular proteins [Cohen et al. (1986) Biochemistry 25, 266-275]. We have developed sequence patterns that facilitate the prediction of helices in all helical proteins. Regular expression patterns recognize the component parts of a helix: the amino terminus (N-cap), the core of the helix (core), and the carboxy terminus (C-cap). These patterns recognize the core features of helices with a 95% success rate and the N- and C-capping features with success rates of 56% and 48%, respectively. A metapattern language, ALPPS, coordinates the recognition of turns and helical components in a scheme that predicts the location and extent of alpha-helices. On the basis of raw residue scoring, a 71% success rate is observed. By focusing on the recognition of core helical features, we achieve a 78% success rate. Amended scoring procedures are presented and discussed, and comparisons are made to other predictive schemes.

Algorithms↗
PubMed1991

Arresting tissue invasion of a parasite by protease inhibitors chosen with the aid of computer modeling.

Computer modeling of the three-dimensional structure of an enzyme, based upon its primary sequence alone, is a potentially powerful tool to elucidate the function of enzymes as well as design specific inhibitors. The cercarial (larval) protease from the blood fluke Schistosoma mansoni is a serine protease hypothesized to assist the schistosome parasite in invading the human circulatory system via the skin. A three-dimensional model of the protease was built, taking advantage of the similarity of the sequence of the cercarial enzyme to the trypsin-like class of serine proteases. A large hydrophobic S-1 binding pocket, suspected from previous kinetic studies, was located in the model and confirmed by new kinetic studies with both synthetic peptide substrates and inhibitors. Unexpected structural characteristics of the enzyme were also predicted by the model, including a large S-4 binding pocket, again confirmed by assays with synthetic peptides. The model was then used to design a peptide inhibitor with 4-fold increased solubility, and a series of synthetic inhibitors were tested against live cercariae invading human skin to confirm that predictions of the model were also applicable in a biologic assay.

Amino Acid Sequence↗
PubMed1991

Beta-breakers: an aperiodic secondary structure.

We have studied the architecture of parallel beta-sheets in proteins and focused on the residues that initiate and terminate the beta-strands. These beta-breaker residues are at the origin of the kink between the beta-strand and the turn that precedes or follows it. beta-Breakers can be located automatically using a consensus approach based on algorithmic secondary structure assignment, solvent accessibility and backbone dihedral angles. These beta-breakers are conformationally homogeneous with respect to side-chain solvent accessibility and backbone dihedral angle profile. A sequence-structure correlation is noted: a restricted subset of amino acids is observed at these positions. Analysis of homologous protein sequences shows that these residues are more highly conserved than other residues in the loop. We conclude that beta-breakers are the structural analogs of the N and C-terminal caps of alpha-helices. The identification of this aperiodic substructure suggests a strategy for improving secondary structure prediction and may guide site-directed mutagenesis experiments.

Amino Acid Sequence↗
PubMed1991

Protein folding. Effect of packing density on chain conformation.

Recent lattice polymer simulations by Chan & Dill suggest that compactness may be a significant driving force in the formation of secondary structure. We have addressed the robustness of this conclusion for non-lattice polymers using a rotational isomeric model of proteins. Boundary conditions are used to enforce compactness and excluded volume effects are explicitly incorporated. As in the cubic lattice studies, compactness is seen to influence secondary structure content. This effect is modest for densities comparable to native proteins but dramatic for chains that are approximately 30% more dense than native proteins. alpha-Helical structure is common but beta-sheet structure is rare. It appears that lattices impart to compact chains an organizational bias that favors beta-sheet structure. The strengths and weakness of various simplified representations of polypeptide chains are also discussed.

Crystallography↗
PubMed1991

Analogues of parathyroid hormone modified at positions 3 and 6. Effects on receptor binding and activation of adenylyl cyclase in kidney and bone.

Predictive and spectroscopic methods were used to develop a model of the structures of the 1-34 peptides of parathyroid hormone (PTH) and the PTH-related protein (PTHrP). Circular dichroism (CD) studies of bovine PTH-(1-34) and human PTHrP-(1-34)amide in the presence of trifluoroethanol suggest the presence of 24-26 alpha-helical residues. For both peptides, interactions between amino- and carboxyl-region alpha-helices are predicted to result in a hydrophobic core with externally facing hydrophilic residues that include probable determinants of receptor binding and activation. Two such residues, Ser3 and Gln6, are conserved in all known members of the PTH/PTHrP family. We have synthesized 13 novel analogues of bovine PTH-(1-34) monosubstituted at positions 3 and 6 and have determined their biological activities in renal and bone cell radioreceptor and adenylyl cyclase assays. Position 3 analogues displayed biological activity that was reduced in direct proportion to the volume of the substituent side-chain. Position 6 analogues also displayed reduced biological activity, but no simple correlation with side-chain volume or hydrophobicity was evident. The analogues fully displaced labeled PTH from binding sites in renal membranes and bone cells, but [Phe3]bPTH-(1-34), [Tyr3]bPTH-(1-34), [Phe6] bPTH-(1-34), and [Ser6]bPTH-(1-34) were only partial agonists in one or both adenylyl cyclase assays. Of these, [Phe3]bPTH-(1-34) and [Phe6]bPTH-(1-34) were tested for antagonist activity and were found to inhibit the activation of adenylyl cyclase in response to bPTH-(1-34) or hPTHrP-(1-34)amide. These results indicate that positions 3 and 6 contribute important determinants of PTH receptor binding and activation. Modification at these positions represents a novel approach to the development of antagonists of PTH action.

Adenylyl Cyclases↗
PubMed1991

Hydrogen bonds involving sulfur atoms in proteins.

Intrachain hydrogen bonds are a hallmark of globular proteins. Traditionally, these involve oxygen and nitrogen atoms. The electronic structure of sulfur is compatible with hydrogen bond formation as well. We surveyed a set of 85 high-resolution protein structures in order to evaluate the prevalence and geometry of sulfur-containing hydrogen bonds. This information should be of interest to experimentalists and theoreticians interested in protein structure and protein engineering.

Animals↗
PubMed1991

Experimental and theoretical studies of the three-dimensional structure of human interleukin-4.

The structure of human interleukin 4 (IL-4) was predicted utilizing a series of experimental and theoretical techniques. Circular Dichroism (CD) spectroscopy indicated that IL-4 belonged to the all alpha-helix class of protein structures. Secondary structure prediction, site-directed mutagenesis, and CD spectroscopy suggested a predominantly alpha-helical structure, consistent with a four-helix bundle structural motif. A human/mouse IL-4 chimera was constructed to qualitatively evaluate alternative secondary structure predictions. The four predicted helices were assembled into tertiary structures using established algorithms. The mapping of three disulfide bridges in IL-4 provided additional constraints on possible tertiary structures. Using accessible surface contact area as a criterion, the most suitable structures were right handed all antiparallel four-helix bundles with two overhand loop connections. Successful loop closure and incorporation of the three disulfide constraints were possible while maintaining the expected shape, solvent accessibility, and steric interactions between loops and helices. Lastly, energy minimization was used to regularize the chain.

Amino Acid Sequence↗
PubMed1990

Studies of synthetic helical peptides using circular dichroism and nuclear magnetic resonance.

We have designed a set of 17-residue synthetic peptides to be monomeric helices in aqueous solution. Circular dichrosim experiments indicate the presence of helical structure in aqueous solution at low temperature and low pH. The two-dimensional nuclear magnetic resonance results for one of the peptides show a segment of ten residues which clearly meets all of the criteria for the existence of helical structure at both 5 degrees C and 15 degrees C. The first four residues of the peptide are in a largely extended conformation. Calculations suggest that residues 5 through 14 are significantly helical at 5 degrees C. When the temperature is increased, circular dichroism spectra indicate that the helical content decreases. At 15 degrees C, the 3JN alpha coupling constants increase in the helical region, indicating an increase in motion or conformational averaging in the helical segment. None of the peptides has pH titration behavior consistent with salt bridge stabilization of helical conformation. Our data lend themselves to interpretation with the helix dipole model and specific side-chain interactions. When the N and C termini charges are removed the helical content of the peptides increases. The amount of helicity increases as the pH is lowered, due to the ionization of His16. Much of the helical stabilization appears to be due to a specific side-chain interaction between His16 and Tyr12.

Amino Acid Sequence↗
PubMed1990

Improvements in protein secondary structure prediction by an enhanced neural network.

Computational neural networks have recently been used to predict the mapping between protein sequence and secondary structure. They have proven adequate for determining the first-order dependence between these two sets, but have, until now, been unable to garner higher-order information that helps determine secondary structure. By adding neural network units that detect periodicities in the input sequence, we have modestly increased the secondary structure prediction accuracy. The use of tertiary structural class causes a marked increase in accuracy. The best case prediction was 79% for the class of all-alpha proteins. A scheme for employing neural networks to validate and refine structural hypotheses is proposed. The operational difficulties of applying a learning algorithm to a dataset where sequence heterogeneity is under-represented and where local and global effects are inadequately partitioned are discussed.

Artificial Intelligence↗