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Structure, Function, and Evolution in Proteins: Report of Symposium held June 3-5, 1968, Volume 1

Description: Report issued by the Brookhaven National Laboratory containing conference proceedings from the first three sessions of the Symposium in Biology, held June 3-5, 1968. It includes research and papers discussing developments in the structure, function, and evolution in proteins with tables, illustrations, and photographs.
Date: February 1969
Creator: Brookhaven National Laboratory
Partner: UNT Libraries Government Documents Department

Biomedical Research Group, Health Division annual report 1954

Description: This report covers the activities of the Biomedical Research Group (H-4) of the Health Division during the period January 1 through December 31, 1954. Organizationally, Group H-4 is divided into five sections, namely, Biochemistry, Radiobiology, Radiopathology, Biophysics, and Organic Chemistry. The activities of the Group are summarized under the headings of the various sections. The general nature of each section`s program, publications, documents and reports originating from its members, and abstracts and summaries of the projects pursued during the year are presented.
Date: December 1955
Creator: Langham, W. H. & Storer, J. B.
Partner: UNT Libraries Government Documents Department

Fast events in protein folding

Description: The primary objective of this work was to develop a molecular understanding of how proteins achieve their native three-dimensional (folded) structures. This requires the identification and characterization of intermediates in the protein folding process on all relevant timescales, from picoseconds to seconds. The short timescale events in protein folding have been entirely unknown. Prior to this work, state-of-the-art experimental approaches were limited to milliseconds or longer, when much of the folding process is already over. The gap between theory and experiment is enormous: current theoretical and computational methods cannot realistically model folding processes with lifetimes longer than one nanosecond. This unique approach to employ laser pump-probe techniques that combine novel methods of laser flash photolysis with time-resolved vibrational spectroscopic probes of protein transients. In this scheme, a short (picosecond to nanosecond) laser photolysis pulse was used to produce an instantaneous pH or temperature jump, thereby initiating a protein folding or unfolding reaction. Structure-specific, time-resolved vibrational probes were then used to identify and characterize protein folding intermediates.
Date: April 1, 1996
Creator: Woodruff, W.; Callender, R.; Causgrove, T.; Dyer, R. & Williams, S.
Partner: UNT Libraries Government Documents Department

Designed supramolecular assemblies for biosensors and photoactive devices. LDRD final report

Description: The objective of this project is the development of a new class of supramolecular assemblies for applications in biosensors and biodevices. The supramolecular assemblies are based on membranes and Langmuir-Blodgett (LB) films composed of naturally-occurring or synthetic lipids, which contain electrically and/or photochemically active components. The LB films are deposited onto electrically-active materials (metal, semiconductors). The active components film components (lipo-porphyrins) at the surface function as molecular recognition sites for sensing proteins and other biomolecules, and the porphyrins and other components (e.g., fullerenes) incorporated into the films serve as photocatalysts and vectorial electron-transport agents. Computer-aided molecular design (CAMD) methods are used to tailor the structure of these film components to optimize function. Molecular modeling is also used to predict the location, orientation, and motion of these molecular components within the films. The result is a variety of extended, self-assembled molecular structures that serve as devices for sensing proteins and biochemicals or as other bioelectronic devices.
Date: February 1, 1997
Creator: Song, X.Z.; Shelnutt, J.A.; Hobbs, J.D. & Cesarano, J.
Partner: UNT Libraries Government Documents Department

Bioinformatics Symposium of the Analytical Division of the American Chemical Society Meeting. Final Technical Report from 03/15/2000 to 03/14/2001 [sample pages of agenda, abstracts, index]

Description: Sparked by the Human Genome Project, biological and biomedical research has become an information science. Information tools are now being generated for proteins, cell modeling, and genomics. The opportunity for analytical chemistry in this new environment is profound. New analytical techniques that can provide the information on genes, SNPs, proteins, protein modifications, cells, and cell chemistry are required. In this symposium, we brought together both informatics experts and leading analytical chemists to discuss this interface. Over 200 people attended this highly successful symposium.
Date: March 28, 2000
Creator: Kennedy, Robert T.
Partner: UNT Libraries Government Documents Department

Final Report [Function of the Arabidopsis TIR1 gene in auxin response]

Description: During this grant period substantial progress was made in the characterization of the TIR1 gene in Arabidopsis. Studies showed that the TIR1 protein is part of a protein complex that includes AtCUL1, ASK1 and RBX1. This complex, called SCF-TIR1, functions in the ubiquitin-mediated protein degradation pathway. Our work is the first report of an SCF complex in a plant system. The results of our studies are described in more detail in the report together with a publication resulting from this study.
Date: December 18, 2000
Creator: Estelle, Mark
Partner: UNT Libraries Government Documents Department

Bacterial nickel metabolism and storage. Final report for the period January 1, 1999 - March 31, 2002

Description: Nickel is an element required for the growth of many microorganisms, as the metal functions as a key component of a metal center for several enzymes. For the organisms that rely on nickel, the metal must be transported, temporarily stored or sequestered, and then processed by accessory proteins for proper metal center assembly into the designated enzyme. The research conducted for this project addressed the nature and roles of key proteins that are involved in the above Ni-enzyme expression/synthesis process.
Date: August 15, 2002
Creator: Maier, Robert J.
Partner: UNT Libraries Government Documents Department

Functional genomics, an integrated approach. Final report for the Trieste component

Description: Phage display offers the possibility of selecting polypeptides (and the genes which encode them) from libraries of 10 billion or more different polypeptides on the basis of their abilities to bind target proteins and subdomains. The general principle of phage display relies on the coupling of phenotype and genotype in the phage. The specific aims of this project were threefold: (1) to produce a large phagemid antibody library; (2) to develop a general method for deriving antibodies against the protein products of cloned genes; (3) to develop technologies which permit the display of gene fragment libraries on phage. Accomplishments in each of these areas are presented.
Date: November 1, 1999
Creator: Bradbury, Andrew
Partner: UNT Libraries Government Documents Department

The Dictyostelium discoideum cellulose synthase: Structure/function analysis and identification of interacting proteins

Description: OAK-B135 The major accomplishments of this project were: (1) the initial characterization of dcsA, the gene for the putative catalytic subunit of cellulose synthase in the cellular slime mold Dictyostelium discoideum; (2) the detection of a developmentally regulated event (unidentified, but perhaps a protein modification or association with a protein partner) that is required for cellulose synthase activity (i.e., the dcsA product is necessary, but not sufficient for cellulose synthesis); (3) the continued exploration of the developmental context of cellulose synthesis and DcsA; (4) the isolation of a GFP-DcsA-expressing strain (work in progress); and (5) the identification of Dictyostelium homologues for plant genes whose products play roles in cellulose biosynthesis. Although our progress was slow and many of our results negative, we did develop a number of promising avenues of investigation that can serve as the foundation for future projects.
Date: February 19, 2004
Creator: Blanton, Richard L.
Partner: UNT Libraries Government Documents Department

Development of protein based bioremediation and drugs for heavy metal toxicity

Description: Structural studies were performed on several proteins of the bacterial detoxification system. These proteins are responsible for binding (MerP) and transport of heavy metals, including mercury, across membranes. The structural information obtained from NMR experiments provides insight into the selectivity and sequestration processes towards heavy metal toxins.
Date: September 18, 2001
Creator: Opella, Stanley J.
Partner: UNT Libraries Government Documents Department

Predicting Function of Biological Macromolecules: A Summary of LDRD Activities: Project 10746

Description: This LDRD project has involved the development and application of Sandia's massively parallel materials modeling software to several significant biophysical systems. They have been successful in applying the molecular dynamics code LAMMPS to modeling DNA, unstructured proteins, and lipid membranes. They have developed and applied a coupled transport-molecular theory code (Tramonto) to study ion channel proteins with gramicidin A as a prototype. they have used the Towhee configurational bias Monte-Carlo code to perform rigorous tests of biological force fields. they have also applied the MP-Sala reacting-diffusion code to model cellular systems. Electroporation of cell membranes has also been studied, and detailed quantum mechanical studies of ion solvation have been performed. In addition, new molecular theory algorithms have been developed (in FasTram) that may ultimately make protein solvation calculations feasible on workstations. Finally, they have begun implementation of a combined molecular theory and configurational bias Monte-Carlo code. They note that this LDRD has provided a basis for several new internal (e.g. several new LDRD) and external (e.g. 4 NIH proposals and a DOE/Genomes to Life) proposals.
Date: November 1, 2002
Partner: UNT Libraries Government Documents Department

Protein Data Bank Project at Rutgers University

Description: The central activities of the Protein Data Base continue to be the collection, archiving and distribution of high quality structural data to the scientific community on a timely basis. The systems that have been developed for doing this has become increasingly reliable and stable. We have completed the inventory of magnetic and paper media that was received from Brookhaven National Laboratory.
Date: July 18, 2002
Creator: Berman, Helen
Partner: UNT Libraries Government Documents Department

Low-Level Detection of a Bacillus Anthracis Simulant using Love-Wave Biosensors on 36 Degree YX LiTaO3

Description: Crucial to low-level detection of biowarfare agents in aqueous environments is the mass sensitivity optimization of Love-wave acoustic sensors. The present work is an experimental study of 36{sup o} YX cut LiTaO{sub 3} based Love-wave devices for detection of pathogenic spores in aqueous conditions. Given that the detection limit (DL) of Love-wave based sensors is a strong function of the overlying waveguide, two waveguide materials have been investigated, which are polyimide and polystyrene. To determine the mass sensitivity of Love-wave sensor, bovine serum albumin (BSA) protein was injected into the Love-wave test cell while recording magnitude and phase shift across each sensor. Polyimide had the lowest mass detection limit with an estimated value of 1-2 ng/cm{sup 2}, as compared to polystyrene where DL = 2.0 ng/cm{sup 2}. Suitable chemistries were used to orient antibodies on the Love-wave sensor using adsorbed protein G. The thickness of each biofilm was measured using ellipsometry from which the surface concentrations were calculated. The monoclonal antibody BD8 with a high degree of selectivity for anthrax spores was used to capture the non-pathogenic simulant B. thuringiensis B8 spores. Bacillus Subtilis spores were used as a negative control to determine whether significant non-specific binding would occur. Spore aliquots were prepared using an optical counting method, which permitted removal of background particles for consistent sample preparation. This work demonstrates that Love-wave devices can be used to detect B. anthracis simulant below reported infectious levels.
Date: March 1, 2003
Partner: UNT Libraries Government Documents Department

Human macrophage differentiation involves an interaction between integrins and fibronectin

Description: The authors have examined the role of the {beta}{sub 1} integrin family of adhesion receptors (VLA) and the extracellular matrix protein fibronectin (FN) in macrophage differentiation of (1) human HL-60 myeloid leukemia cells induced by phorbol 12-myristate 13-acetate (PMA) and (2) human peripheral blood monocytes induced by either PMA or macrophage-colony stimulating factor (M=CSF). Increased VLA and FN gene expression was observed as early as 4 h after PMA treatment of HL-60 cells and PMA- or M-CSF-treatment of monocytes, and it preceded the manifestation of macrophage markers. Treated HL-60 cells and monocytes also released and deposited FN on the surface of the tissue culture dishes. An HL-60 cell variant, HL-525, which is deficient in protein kinase C {beta} and resistant to PMA-induced differentiation, exhibited elevated levels of the VLA antigen but failed to express the FN gene. Incubation of HL-525 cells on dishes precoated with exogenous FN resulted in a macrophage differentiation. The macrophage phenotype induced in HL-60 cells, HL-525 cells, or monocytes was attenuated to various degrees by anti-VLA or anti-FN MAbs or by exogenous RGDS, a VLA-binding motif on FN. The authors suggest that macrophage differentiation is initiated by the activation of protein kinase C, which leads to the expression of the integrin, FN and related genes. The integrins mediate cell attachment and spreading on appropriate substrates by binding to deposited extracellular proteins such as FN. This attachment and spreading, in turn, leads to the expression of genes that code for the macrophage functions.
Date: November 15, 1996
Creator: Laouar, A.; Chubb, C.B.H.; Collart, F. & Huberman, E.
Partner: UNT Libraries Government Documents Department

Lattice and off-lattice side chain models of protein folding: Linear time structure prediction better than 86% of optimal

Description: This paper considers the protein structure prediction problem for lattice and off-lattice protein folding models that explicitly represent side chains. Lattice models of proteins have proven extremely useful tools for reasoning about protein folding in unrestricted continuous space through analogy. This paper provides the first illustration of how rigorous algorithmic analyses of lattice models can lead to rigorous algorithmic analyses of off-lattice models. The authors consider two side chain models: a lattice model that generalizes the HP model (Dill 85) to explicitly represent side chains on the cubic lattice, and a new off-lattice model, the HP Tangent Spheres Side Chain model (HP-TSSC), that generalizes this model further by representing the backbone and side chains of proteins with tangent spheres. They describe algorithms for both of these models with mathematically guaranteed error bounds. In particular, the authors describe a linear time performance guaranteed approximation algorithm for the HP side chain model that constructs conformations whose energy is better than 865 of optimal in a face centered cubic lattice, and they demonstrate how this provides a 70% performance guarantee for the HP-TSSC model. This is the first algorithm in the literature for off-lattice protein structure prediction that has a rigorous performance guarantee. The analysis of the HP-TSSC model builds off of the work of Dancik and Hannenhalli who have developed a 16/30 approximation algorithm for the HP model on the hexagonal close packed lattice. Further, the analysis provides a mathematical methodology for transferring performance guarantees on lattices to off-lattice models. These results partially answer the open question of Karplus et al. concerning the complexity of protein folding models that include side chains.
Date: August 9, 1996
Creator: Hart, W.E. & Istrail, S.
Partner: UNT Libraries Government Documents Department

Membrane boenergetics of salt tolerant organisms. Progress report, June 1993--June 1995

Description: Substantial progress was made on describing the pathway of the transported proton in bacteriorhodopsin, and the thermodynamics of the proton transfers. The underlying principle of the transport was identified as the alternating access of the retinal Schiff base toward the two membrane surfaces, regulated by electrostatic interaction between the retinylidene nitrogen and its counterion. Consistent with a shared transport mechanism for both retinal proteins, bacteriorhodopsin was converted into a balorhodopsin-like chloride pump by replacing asp-85 with threonine. This region is thereby identified as the active site that determines ion specificity. Description of the metal ion-dependent kinetics of the ATP hydrolysis provided clues to the structure of active site in the halobacterial ATPase.
Date: June 1, 1996
Creator: Lanyi, J.K.
Partner: UNT Libraries Government Documents Department

Theories of hydrophobic effects and the description of free volume in complex liquids

Description: Recent progress on molecular theories of hydration of nonpolar solutes in liquid aqueous solution has lead to new ways to thinking about the old issue of free volume in liquids. This article surveys the principal new results with particular attention to the context of general issues of packing in liquids.
Date: December 1998
Creator: Pratt, L. R.; Garde, S. & Hummer, G.
Partner: UNT Libraries Government Documents Department

Bifunctional chelates of RH-105 and AU199 as potential radiotherapeutic agents

Description: Research is presented on new bifunctional chelating ligand systems with stability on the macroscopic and radiochemical levels. The synthesis of the following complexes are described: rhodium 105, palladium 109, and gold 198.
Date: March 1, 1997
Creator: Droege, P.
Partner: UNT Libraries Government Documents Department

Structural mechanisms of nonplanar hemes in proteins

Description: The objective is to assess the occurrence of nonplanar distortions of hemes and other tetrapyrroles in proteins and to determine the biological function of these distortions. Recently, these distortions were found by us to be conserved among proteins belonging to a functional class. Conservation of the conformation of the heme indicates a possible functional role. Researchers have suggested possible mechanisms by which heme distortions might influence biological properties; however, no heme distortion has yet been shown conclusively to participate in a structural mechanism of hemoprotein function. The specific aims of the proposed work are: (1) to characterize and quantify the distortions of the hemes in all of the more than 300 hemoprotein X-ray crystal structures in terms of displacements along the lowest-frequency normal coordinates, (2) to determine the structural features of the protein component that generate and control these nonplanar distortions by using spectroscopic studies and molecular-mechanics calculations for the native proteins, their mutants and heme-peptide fragments, and model porphyrins, (3) to determine spectroscopic markers for the various types of distortion, and, finally, (4) to discover the functional significance of the nonplanar distortions by correlating function with porphyrin conformation for proteins and model porphyrins.
Date: May 1, 1997
Creator: Shelnutt, J.A.
Partner: UNT Libraries Government Documents Department

International summer school on macromolecular crystallographic computing. Final report

Description: The School was the seventh in a series of International Union of Crystallography (IUCr) Crystallographic Symposia. The format of the School was formal lectures in the morning, tutorials in the afternoon, and software demonstrations and more lectures in the evening. The full program which left both the organizers and attendees exhausted, reflects the current state of excitement in the field of macromolecular structure determination using the technique of X-ray crystallography. The new and improved technologies and techniques described in these Proceedings are contributing to that growth and at the same time, as pointed out in the paper given by Sussman, creating challenges for the Protein Data Bank (PDB). As the School progressed, the authors were struck by the similarities to events which took place in small molecule crystallography beginning some 20 to 25 years ago. Growth then was fueled by the advent of new algorithms, affordable computer hardware, and good software. So it is today for macromolecular crystallography, but with the added bonus of the Internet which is changing how scientist conduct their research. Flack presented this view as part of his on-going contribution to how crystallographers use the Internet. After presentations discussing structures en masse they returned to the more traditional mode of presentation which parallels the determination of a single macromolecular structure: data collection -- phasing -- model building and visualization -- refinement.
Date: August 1, 1998
Partner: UNT Libraries Government Documents Department

Models of the solvent-accessible surface of biopolymers

Description: Many biopolymers such as proteins, DNA, and RNA have been studied because they have important biomedical roles and may be good targets for therapeutic action in treating diseases. This report describes how plastic models of the solvent-accessible surface of biopolymers were made. Computer files containing sets of triangles were calculated, then used on a stereolithography machine to make the models. Small (2 in.) models were made to test whether the computer calculations were done correctly. Also, files of the type (.stl) required by any ISO 9001 rapid prototyping machine were written onto a CD-ROM for distribution to American companies.
Date: September 1, 1996
Creator: Smith, R.E.
Partner: UNT Libraries Government Documents Department

Similarity landscapes: An improved method for scientific visualization of information from protein and DNA database searches

Description: This is the final report of a three-year, Laboratory Directed Research and Development (LDRD) project at the Los Alamos National Laboratory (LANL). The authors have used computer simulations and examination of a variety of databases to answer questions about a wide range of evolutionary questions. The authors have found that there is a clear distinction in the evolution of HIV-1 and HIV-2, with the former and more virulent virus evolving more rapidly at a functional level. The authors have discovered highly non-random patterns in the evolution of HIV-1 that can be attributed to a variety of selective pressures. In the course of examination of microsatellite DNA (short repeat regions) in microorganisms, the authors have found clear differences between prokaryotes and eukaryotes in their distribution, differences that can be tied to different selective pressures. They have developed a new method (topiary pruning) for enhancing the phylogenetic information contained in DNA sequences. Most recently, the authors have discovered effects in complex rainforest ecosystems that indicate strong frequency-dependent interactions between host species and their parasites, leading to the maintenance of ecosystem variability.
Date: December 1, 1998
Creator: Dogget, N.; Myers, G. & Wills, C.J.
Partner: UNT Libraries Government Documents Department

Structural biology research at the National Synchroton Light Source

Description: The world`s foremost facility for scientific research using x-rays and ultraviolet and infrared radiation is operated by the national synchrotron Light Source Department. This year alone, a total of 2200 guest researchers performed experiments at the world`s largest source of synchrotron light. Researchers are trying to define the three- dimensional structures of biological macromolecules to create a map of life, a guide for exploring the biological and chemical interactions of the vast variety of molecules found in living organisms. Studies in structural biology may lead to new insights into how biological systems are formed and nourished, how they survive and grow, how they are damaged and die. This document discusses some the the structural biological research done at the National Synchrotron Light Source.
Date: May 1, 1996
Partner: UNT Libraries Government Documents Department

The chlorophyll-binding protein CP47 in photosystem II. Final report

Description: Generally, light-harvesting chlorophyll-binding proteins (LHCP) of the Cab family that are prevalent antenna systems in plants are thought to be absent in cyanobacteria. Therefore, it often is tacitly assumed that in cyanobacteria all chlorophyll is associated with the PS II and PS I core antenna. For this reason, it was of interest to investigate what the effect would be of genetic deletion of both the PS I core complex and the PS II core antenna in Synechocystis. Therefore, a mutant was made in which the psaAB genes for the PS I core were deleted, in addition to deletion or inactivation of psbB and/or psbC (coding for CP43). In this series of mutants, also apcE was deleted. In the absence of both CP47 and CP43, also the PS II reaction center proteins D1 and D2 were not detectable in the thylakoid membrane. Thus, both PS II and PS I were deleted in the resulting strains. Nonetheless, a significant amount of chlorophyll (about 15% of that present when PS II was left intact) was found to remain in the PS I-less, psbB{sup {minus}}, psbC{sup {minus}}, apcE{sup {minus}} mutant. This chlorophyll had fluorescence characteristics resembling those of LHC II in higher plants, with a 678 nm emission maximum at 77 K. The properties of this chlorophyll remaining in the absence of PS II and PS I in Synechocystis did not resemble those of chlorophyll bound to a CP43-like protein that has been found in cyanobacteria and that is expressed under iron-stress conditions. However, some similarities in terms of fluorescence emission were observed with the isolated 22 kDa protein encoded by psbS. The role and association of the remaining chlorophyll in the PS I-less, psbB{sup {minus}}, psbC{sup {minus}}, apcE{sup {minus}} mutant remains unclear, however, this chlorophyll protein is expected to be functionally connected to ...
Date: December 31, 1995
Creator: Vermaas, W.F.J.
Partner: UNT Libraries Government Documents Department