@article {2435,
	title = {A molecular barcoded yeast ORF library enables mode-of-action analysis of bioactive compounds},
	journal = {Nature Biotechnology},
	volume = {27},
	number = {4},
	year = {2009},
	note = {ISI Document Delivery No.: 430EOTimes Cited: 27Cited Reference Count: 60Ho, Cheuk Hei Magtanong, Leslie Barker, Sarah L. Gresham, David Nishimura, Shinichi Natarajan, Paramasivam Koh, Judice L. Y. Porter, Justin Gray, Christopher A. Andersen, Raymond J. Giaever, Guri Nislow, Corey Andrews, Brenda Botstein, David Graham, Todd R. Yoshida, Minoru Boone, Charles},
	month = {Apr},
	pages = {369-377},
	type = {Article},
	abstract = {We present a yeast chemical-genomics approach designed to identify genes that when mutated confer drug resistance, thereby providing insight about the modes of action of compounds. We developed a molecular barcoded yeast open reading frame (MoBY-ORF) library in which each gene, controlled by its native promoter and terminator, is cloned into a centromere-based vector along with two unique oligonucleotide barcodes. The MoBY-ORF resource has numerous genetic and chemical-genetic applications, but here we focus on cloning wild-type versions of mutant drug-resistance genes using a complementation strategy and on simultaneously assaying the fitness of all transformants with barcode microarrays. The complementation cloning was validated by mutation detection using whole-genome yeast tiling microarrays, which identified unique polymorphisms associated with a drug-resistant mutant. We used the MoBY-ORF library to identify the genetic basis of several drug-resistant mutants and in this analysis discovered a new class of sterol-binding compounds.},
	keywords = {1, 2, 3-BETA-D-GLUCAN SYNTHASE, CYCLOHEXIMIDE, DELETION MUTANTS, ELONGATION-FACTOR, GENE-DELETION, MAMMALIAN PROTEIN, ORDERED ARRAYS, OVEREXPRESSION STRAINS, resistance, SACCHAROMYCES-CEREVISIAE GENOME, SPONGE THEONELLA SP},
	isbn = {1087-0156},
	url = {<Go to ISI>://000264971800023},
	author = {Ho, C. H. and Magtanong, L. and Barker, S. L. and Gresham, D. and Nishimura, S. and Natarajan, P. and Koh, J. L. Y. and Porter, J. and Gray, C. A. and Andersen, R. J. and Giaever, G. and Nislow, C. and Andrews, B. and Botstein, D. and Graham, T. R. and Yoshida, M. and Boone, C.}
}
@article {2149,
	title = {Configurational entropy modulates the mechanical stability of protein GB1},
	journal = {Journal of Molecular Biology},
	volume = {379},
	number = {4},
	year = {2008},
	note = {ISI Document Delivery No.: 314NITimes Cited: 10Cited Reference Count: 39Li, Hongbin Wang, Hui-Chuan Cao, Yi Sharma, Deepak Wang, Meijia},
	month = {Jun},
	pages = {871-880},
	type = {Article},
	abstract = {Configurational entropy plays important roles in defining the thermodynamic stability as well as the folding/unfolding kinetics of proteins. Here we combine single-molecule atomic force microscopy and protein engineering techniques to directly examine the role of configurational entropy in the mechanical unfolding kinetics and mechanical stability of proteins. We used a small protein, GB1, as a model system and constructed four mutants that elongate loop 2 of GB1 by 2, 5, 24 and 46 flexible residues, respectively. These loop elongation mutants fold properly as determined by far-UV circular dichroism spectroscopy, suggesting that loop 2 is well tolerant of loop insertions without affecting GB1{\textquoteright}s native structure. Our single-molecule atomic force microscopy results reveal that loop elongation decreases the mechanical stability of GB1 and accelerates the mechanical unfolding kinetics. These results can be explained by the loss of configurational entropy upon closing an unstructured flexible loop using classical polymer theory, highlighting the important role of loop regions in the mechanical unfolding of proteins. This study not only demonstrates a general approach to investigating the structural deformation of the loop regions in mechanical unfolding transition state, but also provides the foundation to use configurational entropy as an effective means to modulate the mechanical stability of proteins, which is of critical importance towards engineering artificial elastomeric proteins with tailored nanomechanical properties. (C) 2008 Elsevier Ltd. All rights reserved.},
	keywords = {configurational entropy, DISULFIDE BONDS, FORCE, FORCE SPECTROSCOPY, FRAGMENT RECONSTITUTION, IMMUNOGLOBULIN BINDING DOMAIN, length, LOOP, MECHANICAL STABILITY, mechanical unfolding, MODULES, resistance, single molecule atomic force microscopy, SINGLE PROTEIN, SPECTROSCOPY, TITIN, TRANSITION-STATE},
	isbn = {0022-2836},
	url = {<Go to ISI>://000256815700018},
	author = {Li, H. B. and Wang, H. C. and Cao, Y. and Sharma, D. and Wang, M.}
}
@article {2247,
	title = {Stabilization provided by neighboring strands is critical for the mechanical stability of proteins},
	journal = {Biophysical Journal},
	volume = {95},
	number = {8},
	year = {2008},
	note = {ISI Document Delivery No.: 352NMTimes Cited: 5Cited Reference Count: 37Sharma, Deepak Feng, Gang Khor, Dingyue Genchev, Georgi Z. Lu, Hui Li, Hongbin},
	month = {Oct},
	pages = {3935-3942},
	type = {Article},
	abstract = {Single-molecule force spectroscopy studies and steered molecular dynamics simulations have revealed that protein topology and pulling geometry play important roles in determining the mechanical stability of proteins. Most studies have focused on local interactions that are associated with the force-bearing beta-strands. Interactions mediated by neighboring strands are often overlooked. Here we use Top7 and barstar as model systems to illustrate the critical importance of the stabilization effect provided by neighboring beta-strands on the mechanical stability. Using single-molecule atomic force microscopy, we showed that Top7 and barstar, which have similar topology in their force-bearing region, exhibit vastly different mechanical-stability characteristics. Top7 is mechanically stable and unfolds at similar to 150 pN, whereas barstar is mechanically labile and unfolds largely below 50 pN. Steered molecular dynamics simulations revealed that stretching force peels one force-bearing strand away from barstar to trigger unfolding, whereas Top7 unfolds via a substructure-sliding mechanism. This previously overlooked stabilization effect from neighboring beta-strands is likely to be a general mechanism in protein mechanics and can serve as a guideline for the de novo design of proteins with significant mechanical stability and novel protein topology.},
	keywords = {BARSTAR, DYNAMICS SIMULATIONS, IMMUNOGLOBULIN DOMAINS, MICROSCOPE, MOLECULE FORCE SPECTROSCOPY, resistance, SINGLE PROTEIN, TITIN, TOPOLOGY, UBIQUITIN},
	isbn = {0006-3495},
	url = {<Go to ISI>://000259503900036},
	author = {Sharma, D. and Feng, G. and Khor, D. and Genchev, G. Z. and Lu, H. and Li, H. B.}
}
@article {1333,
	title = {The bogorol family of antibiotics: Template-based structure elucidation and a new approach to positioning enantiomeric pairs of amino acids},
	journal = {Journal of Organic Chemistry},
	volume = {71},
	number = {16},
	year = {2006},
	note = {ISI Document Delivery No.: 067XTTimes Cited: 10Cited Reference Count: 29Barsby, Todd Warabi, Kaoru Sorensen, Dan Zimmerman, William T. Kelly, Michael T. Andersen, Raymond J.},
	month = {Aug},
	pages = {6031-6037},
	type = {Article},
	abstract = {The sequence positions of D and L Leu and Lys residues in bogorol A (1) have been defined by a simple and novel approach that utilizes small amounts of sample and focuses on detecting the order in which amino acids are liberated from the parent peptide during acid-catalyzed hydrolysis. This technique builds on a previously established relationship between the steric and electronic features of amino acids and their predilection for acidic liberation from polypeptides via dipeptides. The results, which complete the structure of bogorol A, have been confirmed by traditional degradation experiments. Utilizing the knowledge of the structure of bogorol A (1) as a template, we rapidly elucidated the structures of bogorols B-E (2-5) via analysis of ESI-MS and ESI-MS/ MS data and GC analysis of degradation products. The bogorol cationic peptide antibiotics contain a number of unusual structural features, which include the reduction of the C-terminal residue to valinol, an N-terminal residue of 2-hydroxy-3-methylpentanoic acid, the incorporation of four D amino acids, and the presence of a dehydroamino acid. Bogorols show selective and relatively potent activity against methicillin-resistant Staphylococcus aureus and vancomycin-resistant Enterococcus spp., as well as moderate activity against Escherichia coli.},
	keywords = {ANTIMICROBIAL PEPTIDE, BACILLUS, CONVERSION, CULTURE, resistance, SYSTEM, THREONINE, TROPICAL MARINE BACTERIUM},
	isbn = {0022-3263},
	url = {<Go to ISI>://000239336600025},
	author = {Barsby, T. and Warabi, K. and Sorensen, D. and Zimmerman, W. T. and Kelly, M. T. and Andersen, R. J.}
}
@article {1349,
	title = {Nonmechanical protein can have significant mechanical stability},
	journal = {Angewandte Chemie-International Edition},
	volume = {45},
	number = {4},
	year = {2006},
	note = {ISI Document Delivery No.: 004RFTimes Cited: 30Cited Reference Count: 44},
	pages = {642-645},
	type = {Article},
	keywords = {ADHESION, cell, DISULFIDE BONDS, DYNAMICS, ELASTICITY, mechanical properties, microscopy, MOLECULE FORCE-SPECTROSCOPY, protein unfolding, resistance, scanning probe microscopy, SIMULATION, SINGLE PROTEIN, single-molecule studies, TITIN IMMUNOGLOBULIN DOMAINS},
	isbn = {1433-7851},
	url = {<Go to ISI>://000234769200026},
	author = {Cao, Y. and Lam, C. and Wang, M. J. and Li, H. B.}
}
@article {1094,
	title = {Uncialamycin, a new enediyne antibiotic},
	journal = {Organic Letters},
	volume = {7},
	number = {23},
	year = {2005},
	note = {ISI Document Delivery No.: 983VATimes Cited: 27Cited Reference Count: 10},
	month = {Nov},
	pages = {5233-5236},
	type = {Article},
	abstract = {Laboratory cultures of an undescribed streptomycete obtained from the surface of a British Columbia lichen produce uncialamycin (1), a new enediyne antibiotic. The structure of uncialamycin (1) has been elucidated by analysis of spectroscopic data. Uncialamycin (1) exhibits potent in vitro antibacterial activity against Gram-positive and Gram-negative human pathogens, including Burkholderia cepacia, a major cause of morbidity and mortality in patients with cystic fibrosis.},
	keywords = {CALICHEAMICIN, DYNEMICIN-A, resistance},
	isbn = {1523-7060},
	url = {<Go to ISI>://000233259000031},
	author = {Davies, J. and Wang, H. and Taylor, T. and Warabi, K. and Huang, X. H. and Andersen, R. J.}
}
@article {998,
	title = {Identification and quantification of arsC genes in environmental samples by using real-time PCR},
	journal = {Journal of Microbiological Methods},
	volume = {58},
	number = {3},
	year = {2004},
	note = {ISI Document Delivery No.: 847SSTimes Cited: 24Cited Reference Count: 34},
	month = {Sep},
	pages = {335-349},
	type = {Article},
	abstract = {The arsC gene is responsible for the first step in arsenate biotransformation encoding the enzyme arsenate reductase. The quantitative real-time PCR method was developed to quantify the abundance of the arsC genes in environmental samples contaminated with arsenic. Two sets of primers that showed high specificity for the target arsC gene were designed based on consensus sequences from 13 bacterial species. The arsC gene was used as an external standard instead of total DNA in the calibration curve for real-time PCR, which was linear over six orders of magnitude and the detection limit was estimated to be about three copies of the gene. Soil samples from arsenic contaminated sites were screened for arsC genes by using PCR and showed the presence of this gene. The copy numbers of the gene ranging from 0.88 x 10(4) to 1.56 x 10(5) per ng total DNA were found in eight arsenic contaminated samples. Soil samples from a bioreactor containing pulp mill biomass and high concentration of arsenate showed a tenfold higher count of arsC gene copies than soil samples collected underground from an arsenic-rich gold mine. (C) 2004 Elsevier B.V. All rights reserved.},
	keywords = {arsC gene, arsenate reduction, ASSAY, BACTERIA, DNA, ESCHERICHIA-COLI, group-specific primers, QUANTITATION, real-time PCR, REDUCTION, resistance, SOIL, SYBR (R) Green 1},
	isbn = {0167-7012},
	url = {<Go to ISI>://000223415800006},
	author = {Sun, Y. M. and Polishchuk, E. A. and Radoja, U. and Cullen, W. R.}
}
@article {5010,
	title = {Bogorol A produced in culture by a marine Bacillus sp reveals a novel template for cationic peptide antibiotics},
	journal = {Organic Letters},
	volume = {3},
	number = {3},
	year = {2001},
	note = {ISI Document Delivery No.: 398WETimes Cited: 12Cited Reference Count: 25},
	month = {Feb},
	pages = {437-440},
	type = {Article},
	abstract = {[GRAPHICS] Bogorol A (1), a novel peptide antibiotic active against MRSA and VRE, has been isolated from cultures of a marine Bacillus sp, collected in Papua New Guinea, The structure of bogorol A was elucidated by a combination of spectroscopic analyses and chemical degradation. Bogorol A illustrates a new structural template for "cationic peptide antibiotics".},
	keywords = {BACTERIUM, DEFENSINS, HELIX, resistance},
	isbn = {1523-7060},
	url = {<Go to ISI>://000166778800032},
	author = {Barsby, T. and Kelly, M. T. and Gagne, S. M. and Andersen, R. J.}
}
@article {3983,
	title = {The inhibition of glutamate racemase by D-N-hydroxyglutamate},
	journal = {Bioorganic \& Medicinal Chemistry Letters},
	volume = {7},
	number = {17},
	year = {1997},
	note = {ISI Document Delivery No.: XX507Times Cited: 20Cited Reference Count: 30},
	month = {Sep},
	pages = {2265-2270},
	type = {Article},
	abstract = {We report that D-N-hydroxyglutamate is ii competitive inhibitor of glutamate racemase (K-I=56 mu M). The compound acts as an alternate substrate and is converted into a-ketoglutarate and ammonia (K-M=57 mu M, k(cat)/K-M=3.2x10(3) M(-1)sec(-1)), An imine intermediate is likely the species causing the inhibition. L-N-hydroxyglutamate is a weak inhibitor and is slowly converted to alpha-ketoglutarate (k(cat)/K-M=30 M(-1)sec(-1)). (C) 1997 Elsevier Science Ltd.},
	keywords = {CLONING, DIAMINOPIMELIC ACID, EPIMERASE, ESCHERICHIA-COLI, GENE, L-ALANINE, LACTOBACILLUS, MURI, PEDIOCOCCUS-PENTOSACEUS, resistance},
	isbn = {0960-894X},
	url = {<Go to ISI>://A1997XX50700025},
	author = {Glavas, S. and Tanner, M. E.}
}
@article {3447,
	title = {Increased potency of vanadium using organic ligands},
	journal = {Molecular and Cellular Biochemistry},
	volume = {153},
	number = {1-2},
	year = {1995},
	note = {ISI Document Delivery No.: TM620Times Cited: 45Cited Reference Count: 46Vanadium SymposiumJUL 29-31, 1994MONTREAL, CANADACanadian Diabet Assoc, Fonds Rech Sante Quebec, Juvenile Diabet Fdn Canada, Marion Merrell Dow Canada, McGill Univ, Med Res Council Canada, Medisense Canada Inc, Merck Frosst, Canada Inc, Miles Canada Inc},
	month = {Dec},
	pages = {175-180},
	type = {Proceedings Paper},
	abstract = {The in vivo glucose lowering effect of orally administered inorganic vanadium compounds in diabetes was first reported in our laboratory in 1985. While both vanadate and vanadyl forms of vanadium are orally active, they are still not well absorbed. We have synthesized several organic vanadium compounds and one compound, bis(maltolato)oxovanadium(lv) or BMOV, has been extensively investigated. BMOV proved effective in lowering plasma glucose and lipids in STZ-diabetic: rats when administered in drinking water over a 25 week period. The maintenance dose (0.18 mmol/kg/day) was approximately 50\% of that required for vanadyl sulfate (VS). Secondary complications of diabetes were prevented by BMOV and no marked toxicity was noted. Oral gavage of STZ-diabetic rats with BMOV also reduced blood glucose levels. The ED(50) for BMOV was 0.5 mmol/kg, while for VS the estimated ED(50) was 0.9 mmol/kg. BMOV was also effective by the intraperitoneal route in STZ-diabetic rats. The ED(50) was 0.08 mmol/kg compared to 0.22 mmol/kg for VS. Some animals treated p.o. or i.p. remained euglycemic for up to 14 weeks. An i.v. infusion of BMOV of 0.05 mmol/kg over a 30 min period reduced plasma glucose levels by 50\% while VS was not effective.},
	keywords = {ADIPOCYTES, BIS(MALTOLATO)OXOVANADIUM(IV), diabetes, DIABETIC, GLUCOSE, HYPERTENSION, IMPROVEMENT, INSULIN ACTION, insulin-mimetic, RATS, RECEPTOR TYROSINE KINASE, resistance, SPONTANEOUSLY HYPERTENSIVE RATS, VANADATE, VANADIUM},
	isbn = {0300-8177},
	url = {<Go to ISI>://A1995TM62000024},
	author = {McNeill, J. H. and Yuen, V. G. and Dai, S. T. and Orvig, Chris}
}
