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F R Salemme

Publications and source records attributed to F R Salemme.

14 recordsLinked to original sources
PubMed1992

Structural studies of the retroviral proteinase from avian myeloblastosis associated virus.

The structure of the retroviral proteinase from avian myeloblastosis associated virus (MAV) has been determined and refined at 2.2 A resolution. This structure is compared with those of homologous proteinases from Rous sarcoma virus (RSV) and human immunodeficiency type 1 virus (HIV). Through comparison with the structure of a proteinase-inhibitor complex from HIV, a model of a complex between MAV proteinase and a peptide substrate has been generated. Examination of this model suggests structural basis for the diverse specifications of viral proteinases.

Amino Acid Sequence↗
PubMed1992

PROBIT: a statistical approach to modeling proteins from partial coordinate data using substructure libraries.

A program (PROBIT) has been developed that allows the reconstruction of a complete set of three-dimensional protein coordinates from alpha-carbon coordinates. The program generates a statistical measure of polypeptide conformational behavior for substructures in a defined structural context from a library of highly refined protein structures. These statistics provide a prescription for substructure substitution from the database to allow regeneration of the complete protein structure.

Computer Simulation↗
PubMed1992

Protein engineering for molecular electronics.

Recombinant DNA technology allows the manipulation of the physical properties of proteins that perform electron transport and photochemical processes. Recent work is reviewed that has a potential impact on the development of molecular electronic devices, within a general framework outlining strategies for device fabrication. This review is also published in Current Opinion in Structural Biology 1992, 2:587-592.

Bacteriorhodopsins↗
PubMed1992

Permuteins of interleukin 1 beta--a simplified approach for the construction of permutated proteins having new termini.

A technique for the rapid and simple generation of permutated versions of the interleukin-1 beta (IL-1 beta) gene is described. In this method, the human IL-1 beta cDNA is twice amplified by the polymerase chain reaction (PCR) and the resulting DNA fragments are ligated in tandem. Between the two genes, the DNA sequence encodes a short four amino acid loop to link the native N- and C-terminal ends of the IL-1 beta protein. By using PCR amplification from this starting template, a new version of the IL-1 beta cDNA was obtained that encodes a permutated form of the IL-1 beta protein where the new N- and C-terminal amino acids correspond to residues 65 and 64 of the native IL-1 beta sequence, respectively. The name 'permutein' is proposed to describe proteins generated by this technology. The molecular profile (IL-1 receptor binding, biologic activity and solution properties) of the IL-1 permutein produced by this technology, permutein 65/64, is shown to be identical to that of native IL-1 beta. The approach should be useful to define further the structural features of this protein that are important for its function.

Amino Acid Sequence↗
PubMed1991

Crystallographic refinement of bovine pro-phospholipase A2 at 1.6 A resolution.

Bovine pro-phospholipase A2 (Mr = 14,520), trigonal, P3(1)21, a = b = 46.5, c = 102.0 A, one molecule per asymmetric unit, lambda (Cu K alpha) = 1.54 A. The model incorporating 895 protein atoms, two molecules of 2-methyl-2,4-pentanediol, and 60 solvent water molecules, was refined by restrained least squares to a residual R = 0.194 for 14,667 reflections from 5 to 1.6 A resolution.

Enzyme Precursors↗
PubMed1991

Cooperative ligand reorientations in cytochrome c3: a molecular dynamics simulation.

Molecular dynamics simulations of a tetraheme cytochrome c3 were performed to investigate dynamic aspects of the motion of the axial heme iron ligands. It was found that persistent transitions between alternate axial imidazole orientations of the histidine incorporated in the CXXCH heme binding sequence occurred via correlated motions. The correlated motions involved virtually all of the atoms comprising the polypeptide backbone of the heme binding sequence as well as the histidine imidazole side-chain.

Amino Acid Sequence↗
PubMed1991

The identification of tyrosine as a common key residue in unrelated H-2Kd restricted antigenic peptides.

We have compared the activity of several Kd- or Ld-restricted antigenic peptides as competitors in a functional competition assay using cytolytic T lymphocyte (CTL) clones. All of four unrelated Kd-restricted peptides tested could compete with each other but not with the Ld-restricted peptide P91A-. 12-24 (P91A). Moreover, the P91A peptide failed to compete with the four Kd-restricted peptides. In contrast, another Ld-restricted peptide [mouse cytomegalovirus (MCMV) pp89 167-176] could clearly compete with both Kd- and Ld-restricted peptides. The comparison of a series of modified MCMV pp89 peptides suggested that distinct structural features allow the interaction of the peptide with the two different MHC class I molecules. We showed previously that the competitor activity of two different Kd-restricted antigenic peptides was reduced substantially upon Ala substitution of the single Tyr residues present in these peptides. We now show a similar effect for two additional Kd-restricted peptides. Our results thus suggest that Tyr may function as an 'anchor' residue for many antigenic peptides that bind to the Kd molecule. Molecular modeling of the presumed antigen-binding site of the Kd molecule revealed the presence of two deep cavities that may be involved in binding peptide amino acid side chains. A model illustrating one possible interaction of a Tyr-containing peptide with the Kd molecule is presented.

Alanine↗
PubMed1979

Conformations of twisted parallel beta-sheets and the origin of chirality in protein structures.

An analysis of the conformational properties of parallel beta-pleated sheets suggests that an important factor in the generation of beta-sheet twist is the preference for nonplanar peptide bond distortions that impart local left-handed helical character to polypeptide chains. It is demonstrated that the introduction of such chiral distortions, which result from the tetrahedral deformation of the peptide nitrogen atoms, naturally produces right-twisted beta-sheet structures with optimal hydrogen bond geometry.

Computers↗
PubMed1977

Structure of cytochrome c555 of Chlorobium thiosulfatophilum: primitive low-potential cytochrome c.

Cytochrome c555 is an 86-residue type c cytochrome derived from Chlorobium thiosulfatophilum, an obligately anaerobic green sulfur bacterium which is among the most primitive of living organisms. Here is presented a preliminary structural description of the cytochrome c555 molecule based on its crystallographic structure determination at 2.7-A resolution by multiple isomorphous replacement methods. This structure is of interest not only because of its evolutionary significance but also because the cytochrome c555 molecule possesses an unusually low physiologic oxidoreduction potential (Em,7 = +145 mV) compared with related members of the cytochrome c family. Consequently, determination of its structure may permit a direct assessment of the structural factors responsible for prosthetic group redox potential regulation in type c cytochromes.

Bacteria↗
PubMed1977

Structural convergence during protein evolution.

Several recent protein crystallographic structure determinations have demonstrated the existence of considerable tertiary structural similarity among proteins otherwise having little similarity in either amino acid sequence or biological function. In order to assess the possibility that such proteins may have arisen through processes of divergent evolution from a common ancestor, a graphical presentation is given which correlates the pattern of allowed single base substitutions defined by the genetic code with the associated changes in the structural properties of the encoded amino acids. The results show that while a large degree of structural conservation is evident due to codon synonomy, there is, in general, little tendency for the code to be structurally conservative in the majority of the cases where codon single-base changes result in amino acid substitutions. The possible consequences of this pattern of potential amino acid substitutions are discussed in relation to protein evolutionary processes.

Amino Acids↗