%0 Journal Article %J Cell Cycle (Georgetown, Tex.) %D 2008 %T Uncharacterized DUF1574 leptospira proteins are SGNH hydrolases %A Lukasz Knizewski %A Kamil Steczkiewicz %A Krzysztof Kuchta %A Lucjan Wyrwicz %A Dariusz Plewczynski %A Andrzej Koliński %A Leszek Rychlewski %A Krzysztof Ginalski %K Amino Acid Sequence %K Bacterial Proteins %K Bacterial Proteins: genetics %K Base Sequence %K Computational Biology %K DNA %K Hydrolases %K Hydrolases: genetics %K Leptospira %K Leptospira: enzymology %K Models %K Molecular %K Molecular Sequence Data %K Sequence Alignment %K Sequence Analysis %B Cell Cycle (Georgetown, Tex.) %V 7 %P 542–4 %8 feb %G eng %U http://www.ncbi.nlm.nih.gov/pubmed/18235229 %0 Journal Article %J Biophysical Journal %D 2003 %T Unfolding of globular proteins: monte carlo dynamics of a realistic reduced model %A Andrzej Koliński %A Piotr Klein %A Piotr Romiszowski %A Jeffrey Skolnick %K Apoproteins %K Apoproteins: chemistry %K Bacterial Proteins %K Chemical %K DNA-Binding Proteins %K DNA-Binding Proteins: chemistry %K Leghemoglobin %K Leghemoglobin: chemistry %K Models %K Molecular %K Monte Carlo Method %K Myoglobin %K Myoglobin: chemistry %K Nerve Tissue Proteins %K Nerve Tissue Proteins: chemistry %K Plastocyanin %K Plastocyanin: chemistry %K Protein Denaturation %K Protein Folding %K Proteins %K Proteins: chemistry %K Statistical %X Reduced lattice models of proteins and Monte Carlo dynamics were used to simulate the initial stages of the unfolding of several proteins of various structural types, and the results were compared to experiment. The models semiquantitatively reproduce the approximate order of events of unfolding as well as subtle mutation effects and effects resulting from differences in sequences of similar folds. The short-time mobility of particular residues, observed in simulations, correlates with the crystallographic temperature factor. The main factor controlling unfolding is the native state topology, with sequence playing a less important role. The correlation with various experiments, especially for sequence-specific effects, strongly suggests that properly designed reduced models of proteins can be used for qualitative studies (or prediction) of protein unfolding pathways. %B Biophysical Journal %V 85 %P 3271–3278 %8 nov %G eng %U http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=1303603&tool=pmcentrez&rendertype=abstract %R 10.1016/S0006-3495(03)74745-6 %0 Journal Article %J Journal of Molecular Biology %D 1997 %T MONSSTER: a method for folding globular proteins with a small number of distance restraints %A Jeffrey Skolnick %A Andrzej Koliński %A Angel. R. Ortiz %K Algorithms %K Aprotinin %K Aprotinin: chemistry %K Bacterial Proteins %K Bacterial Proteins: chemistry %K Computer Graphics %K Computer Simulation %K Flavodoxin %K Flavodoxin: chemistry %K Models %K Molecular %K Myoglobin %K Myoglobin: chemistry %K Plastocyanin %K Plastocyanin: chemistry %K Protein Conformation %K Protein Folding %K Protein Structure %K Secondary %K Tertiary %K Thioredoxins %K Thioredoxins: chemistry %X The MONSSTER (MOdeling of New Structures from Secondary and TEritary Restraints) method for folding of proteins using a small number of long-distance restraints (which can be up to seven times less than the total number of residues) and some knowledge of the secondary structure of regular fragments is described. The method employs a high-coordination lattice representation of the protein chain that incorporates a variety of potentials designed to produce protein-like behaviour. These include statistical preferences for secondary structure, side-chain burial interactions, and a hydrogen-bond potential. Using this algorithm, several globular proteins (1ctf, 2gbl, 2trx, 3fxn, 1mba, 1pcy and 6pti) have been folded to moderate-resolution, native-like compact states. For example, the 68 residue 1ctf molecule having ten loosely defined, long-range restraints was reproducibly obtained with a C alpha-backbone root-mean-square deviation (RMSD) from native of about 4. A. Flavodoxin with 35 restraints has been folded to structures whose average RMSD is 4.28 A. Furthermore, using just 20 restraints, myoglobin, which is a 146 residue helical protein, has been folded to structures whose average RMSD from native is 5.65 A. Plastocyanin with 25 long-range restraints adopts conformations whose average RMSD is 5.44 A. Possible applications of the proposed approach to the refinement of structures from NMR data, homology model-building and the determination of tertiary structure when the secondary structure and a small number of restraints are predicted are briefly discussed. %B Journal of Molecular Biology %V 265 %P 217–241 %8 jan %G eng %U http://www.ncbi.nlm.nih.gov/pubmed/9020984 %R 10.1006/jmbi.1996.0720