Biomedical subjects

Brendan J McConkey

Publications and source records attributed to Brendan J McConkey.

5 recordsLinked to original sources

PubMed2006

Ordered surface carbons distinguish antifreeze proteins and their ice-binding regions.

Antifreeze proteins (AFPs) are found in cold-adapted organisms and have the unusual ability to bind to and inhibit the growth of ice crystals. However, the underlying molecular basis of their ice-binding activity is unclear because of the difficulty of studying the AFP-ice interaction directly and the lack of a common motif, domain or fold among different AFPs. We have formulated a generic ice-binding model and incorporated it into a physicochemical pattern-recognition algorithm. It successfully recognizes ice-binding surfaces for a diverse range of AFPs, and clearly discriminates AFPs from other structures in the Protein Data Bank. The algorithm was used to identify a novel AFP from winter rye, and the antifreeze activity of this protein was subsequently confirmed. The presence of a common and distinct physicochemical pattern provides a structural basis for unifying AFPs from fish, insects and plants.

Algorithms↗

PubMed2006

Cold-active winter rye glucanases with ice-binding capacity.

Extracellular pathogenesis-related proteins, including glucanases, are expressed at cold temperatures in winter rye (Secale cereale) and display antifreeze activity. We have characterized recombinant cold-induced glucanases from winter rye to further examine their roles and contributions to cold tolerance. Both basic beta-1,3-glucanases and an acidic beta-1,3;1,4-glucanase were expressed in Escherichia coli, purified, and assayed for their hydrolytic and antifreeze activities in vitro. All were found to be cold active and to retain partial hydrolytic activity at subzero temperatures (e.g. 14%-35% at -4 degrees C). The two types of glucanases had antifreeze activity as measured by their ability to modify the growth of ice crystals. Structural models for the winter rye beta-1,3-glucanases were developed on which putative ice-binding surfaces (IBSs) were identified. Residues on the putative IBSs were charge conserved for each of the expressed glucanases, with the exception of one beta-1,3-glucanase recovered from nonacclimated winter rye in which a charged amino acid was present on the putative IBS. This protein also had a reduced antifreeze activity relative to the other expressed glucanases. These results support the hypothesis that winter rye glucanases have evolved to inhibit the formation of large, potentially fatal ice crystals, in addition to having enzymatic activity with a potential role in resisting infection by psychrophilic pathogens. Glucanases of winter rye provide an interesting example of protein evolution and adaptation aimed to combat cold and freezing conditions.

Amino Acid Sequence↗

PubMed2004

Importance of solvent accessibility and contact surfaces in modeling side-chain conformations in proteins.

Contact surface area and chemical properties of atoms are used to concurrently predict conformations of multiple amino acid side chains on a fixed protein backbone. The combination of surface complementarity and solvent-accessible surface accounts for van der Waals forces and solvation free energy. The scoring function is particularly suitable for modeling partially buried side chains. Both iterative and stochastic searching approaches are used. Our programs (Sccomp-I and Sccomp-S), with relatively fast execution times, correctly predict chi1 angles for 92-93% of buried residues and 82-84% for all residues, with an RMSD of approximately 1.7 A for side chain heavy atoms. We find that the differential between the atomic solvation parameters and the contact surface parameters (including those between noncomplementary atoms) is positive; i.e., most protein atoms prefer surface contact with other protein atoms rather than with the solvent. This might correspond to the driving force for maximizing packing of the protein. The influence of the crystal packing, completeness of rotamer library and precise positioning of Cbeta atoms on the accuracy of side-chain prediction are examined. The Sccomp-S and Sccomp-I programs can be accessed through the Web (http://sgedg.weizmann.ac.il/sccomp.html) and are available for several platforms.

Algorithms↗

PubMed2003

Discrimination of native protein structures using atom-atom contact scoring.

We introduce a method for discriminating correctly folded proteins from well designed decoy structures using atom-atom and atom-solvent contact surfaces. The measure used to quantify contact surfaces integrates the solvent accessible surface and interatomic contacts into one quantity, allowing solvent to be treated as an atom contact. A scoring function was derived from statistical contact preferences within known protein structures and validated by using established protein decoy sets, including the "Rosetta" decoys and data from the CASP4 structure predictions. The scoring function effectively distinguished native structures from all corresponding decoys in >90% of the cases, using isolated protein subunits as target structures. If contacts between subunits within quaternary structures are included, the accuracy increases to 97%. Interactions beyond atom-atom contact range were not required to distinguish native structures from the decoys using this method. The contact scoring performed as well or better than existing statistical and physicochemical potentials and may be applied as an independent means of evaluating putative structural models.

Cations↗

PubMed2002

Measurement of short- and long-term toxicity of polycyclic aromatic hydrocarbons using luminescent bacteria.

Growing concern over environmental contamination has stimulated rigorous efforts to establish reliable biological monitoring assays. Methodology was developed for measuring photoinduced short- and long-term toxicity of an important group of contaminants, polycyclic aromatic hydrocarbons (PAHs), using the luminescent bacterium Vibrio fischeri. The toxicity of most PAHs can be greatly enhanced on exposure of a living organism and/or the chemicals to ultraviolet (UV) radiation. There are two major mechanisms involved in photoinduced toxicity of PAHs: photosensitization and photomodification. In the former, production of singlet oxygen leads to cellular damage. In the latter, photooxidation of PAHs results in new compounds (usually oxygenated PAHs) that are often more toxic than their parent PAHs. Microbial toxicity assays were developed to measure short- and long-term photoinduced toxicity of PAHs. The bioassays were based on inhibition of luminescence and growth of V. fischeri. The short-term assay should detect toxicity of chemicals that are taken up rapidly and/or whose photosensitization activity is immediate. The long-term assay should identify chemicals where the rate of assimilation is slow and/or time is required for photoinduced effects to be realized. The assays were tested with 12 different PAHs. The short-term assay did not reveal photoinduced toxicity for any of the test chemicals. However, photoinduced toxicity was apparent in the long-term assay, indicating that short-term assays may be opaque to this key mechanism of PAH toxicity.

Biological Assay↗