Research Topics
Genomes and Genes | Lisa N KinchSummaryAffiliation: University of Texas Southwestern Medical Center Country: USA Publications
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Publications
Structure of a conserved hypothetical protein SA1388 from S. aureus reveals a capped hexameric toroid with two PII domain lids and a dinuclear metal centerKumar Singh Saikatendu
Department of Biochemistry, University of Texas Southwestern Medical Center, 5323 Harry Hines Blvd, Dallas TX 75390 8816, USA
BMC Struct Biol 6:27. 2006..Proteins like SA1388 remain a poorly studied group and their structural characterization could guide future investigations aimed at understanding their function...- Realm of PD-(D/E)XK nuclease superfamily revisited: detection of novel families with modified transitive meta profile searchesLukasz Knizewski
Interdisciplinary Centre for Mathematical and Computational Modelling, Warsaw University, Pawinskiego 5A, Warsaw, Poland
BMC Struct Biol 7:40. 2007.... - CASP9 assessment of free modeling target predictionsLisa Kinch
Howard Hughes Medical Institute, University of Texas, Southwestern Medical Center, Dallas, TX 75390 9050, USA
Proteins 79:59-73. 2011..The details of evaluation are available at http://prodata.swmed.edu/CASP9/ ... - Fido, a novel AMPylation domain common to fic, doc, and AvrBLisa N Kinch
Howard Hughes Medical Institute, University of Texas Southwestern Medical Center, Dallas, Texas, United States of America
PLoS ONE 4:e5818. 2009..The VopS fic domain includes a conserved sequence motif (HPFx[D/E]GN[G/K]R) that contributes to AMPylation. Fic domains are found in a variety of species, including bacteria, a few archaea, and metazoan eukaryotes... - The human Ago2 MC region does not contain an eIF4E-like mRNA cap binding motifLisa N Kinch
Howard Hughes Medical Institute and Department of Biochemistry, University of Texas Southwestern Medical Center, 5323 Harry Hines Blvd, Dallas, TX 75390 9050, USA
Biol Direct 4:2. 2009..The corresponding Ago2 aromatic residues (F450 and F505) were hypothesized to perform the same cap-binding function. However, the detected similarity between the MC sequence and the eIF4E cap-binding motif was questionable... - CASP9 target classificationLisa N Kinch
Howard Hughes Medical Institute, University of Texas, Southwestern Medical Center, Dallas, TX 75390 9050, USA
Proteins 79:21-36. 2011.... - Longin-like folds identified in CHiPS and DUF254 proteins: vesicle trafficking complexes conserved in eukaryotic evolutionLisa N Kinch
Howard Hughes Medical Institute and Department of Biochemistry, University of Texas Southwestern Medical Center, Dallas, Texas 75390 9050, USA
Protein Sci 15:2669-74. 2006.... - Site-2 protease regulated intramembrane proteolysis: sequence homologs suggest an ancient signaling cascadeLisa N Kinch
Howard Hughes Medical Institute and Department of Biochemistry, University of Texas Southwestern Medical Center, 5323 Harry Hines Blvd, Dallas, TX 75390 9050, USA
Protein Sci 15:84-93. 2006..Finally, conserved genomic neighborhoods of S2P homologs allow functional predictions for PDZ-containing transmembrane proteases in extra-cytoplasmic stress response and lipid metabolism... - Identification of novel restriction endonuclease-like fold families among hypothetical proteinsLisa N Kinch
Department of Biochemistry, Howard Hughes Medical Institute, University of Texas Southwestern Medical Center, 5323 Harry Hines Boulevard, Dallas, TX 75390 9050, USA
Nucleic Acids Res 33:3598-605. 2005..Finally, our method identifies a novel restriction endonuclease-like domain in the C-terminus of RecC that is not detected with structure-based searches of the existing PDB database... 
Evolution of protein structures and functionsLisa N Kinch
Howard Hughes Medical Institute and Department of Biochemistry, University of Texas Southwestern Medical Center, 5323 Harry Hines Boulevard, Dallas, TX 75390 9050, USA
Curr Opin Struct Biol 12:400-8. 2002..The mechanisms by which protein folds change often include the fusion of duplicated domains, followed by divergence through mutation. Such changes reflect both the stability of protein folds and the requirements of protein function...- CASP5 assessment of fold recognition target predictionsLisa N Kinch
Howard Hughes Medical Institute, University of Texas Southwestern Medical Center, Dallas, Texas 75390 9050, USA
Proteins 53:395-409. 2003..We also compared the results of manual groups to those of automatic servers evaluated in parallel by CAFASP, showing that the top performing automated server structure predictions approached those of the best manual predictors... - CASP5 target classificationLisa N Kinch
Howard Hughes Medical Institute, University of Texas Southwestern Medical Center, Dallas 75390 9050, USA
Proteins 53:340-51. 2003..CASP5 domains are illustrated in Figure 1. Examples of nontrivial links between CASP5 target domains and existing structures that support our classifications are provided... - Kinetic and structural insights into the mechanism of AMPylation by VopS Fic domainPhi Luong
Department of Molecular Biology, University of Texas Southwestern Medical Center, Dallas, Texas 75390, USA
J Biol Chem 285:20155-63. 2010..Discovery of a ternary reaction mechanism along with structural insight provides critical groundwork for future studies for the family of AMPylators that modify hydroxyl-containing residues with AMP... - EDD, a novel phosphotransferase domain common to mannose transporter EIIA, dihydroxyacetone kinase, and DegVLisa N Kinch
Howard Hughes Medical Institute, University of Texas Southwestern Medical Center, 5323 Harry Hines Blvd, Dallas, TX 75390-9050, USA
Protein Sci 14:360-7. 2005.... - Prediction of functional specificity determinants from protein sequences using log-likelihood ratiosJimin Pei
Howard Hughes Medical Institute, University of Texas Southwestern Medical Center 5323 Harry Hines Boulevard, Dallas, TX 75390-9050, USA
Bioinformatics 22:164-71. 2006..AVAILABILITY: SPEL is freely available for non-commercial use. Its pre-compiled versions for several platforms and alignments used in this work are available at ftp://iole.swmed.edu/pub/SPEL/.. 
AMPylation of Rho GTPases by Vibrio VopS disrupts effector binding and downstream signalingMelanie L Yarbrough
Department of Molecular Biology, University of Texas UT Southwestern Medical Center, Dallas, TX 75390, USA
Science 323:269-72. 2009..Eukaryotic proteins were also directly modified with AMP, potentially expanding the repertoire of posttranslational modifications for molecular signaling...- 4SCOPmap: automated assignment of protein structures to evolutionary superfamiliesSara Cheek
Howard Hughes Medical Institute, University of Texas Southwestern Medical Center, 5323 Harry Hines Blvd, Dallas, Texas 75390, USA
BMC Bioinformatics 5:197. 2004..To address this issue, we have developed an algorithm to map protein domains to an existing structural classification scheme and have applied it to the SCOP database... - Expanding the nitrogen regulatory protein superfamily: Homology detection at below random sequence identityLisa N Kinch
Howard Hughes Medical Institute, and Department of Biochemistry, University of Texas Southwestern Medical Center, Dallas, Texas, USA
Proteins 48:75-84. 2002.... - An automatic method for CASP9 free modeling structure prediction assessmentQian Cong
Department of Biochemistry, University of Texas Southwestern Medical Center, Dallas, TX 75390 9050, USA
Bioinformatics 27:3371-8. 2011..It is beneficial to incorporate the ideas behind manual inspection to an automatic score system, which could provide objective and reproducible assessment of structure models... - Deciphering a novel thioredoxin-like fold familyLisa N Kinch
Howard Hughes Medical Institute, and Department of Biochemistry, University of Texas Southwestern Medical Center, Dallas, Texas 75390-9050, USA
Proteins 52:323-31. 2003..Finally, the rosetta-derived model structure assists us in assembling a global multiple-sequence alignment of COG3019 with two other thioredoxin-like fold families, the thioltransferases and the bacterial arsenate reductases (ArsC)... - Identification and assay of allosteric regulators of S-adenosylmethionine decarboxylaseErin K Willert
Department of Pharmacology, University of Texas Southwestern Medical Center at Dallas, Dallas, TX, USA
Methods Mol Biol 720:219-35. 2011.... - The ABC transporters in Candidatus Liberibacter asiaticusWenlin Li
Department of Biochemistry and Department of Biophysics, University of Texas Southwestern Medical Center, Dallas, TX 75390 9050, USA
Proteins 80:2614-28. 2012..L. asiaticus pathogenicity and the ABC transporter systems responsible for bacterial OM biosynthesis that are good drug targets... - A database of domain definitions for proteins with complex interdomain geometryIndraneel Majumdar
Department of Biochemistry, University of Texas Southwestern Medical Center at Dallas, Dallas, Texas, United States of America
PLoS ONE 4:e5084. 2009..Additionally, the database can be used for training and testing domain delineation algorithms. Since our domains represent structurally compact evolutionary units, the database may be useful for studying domain properties and evolution... - Optimization of linear disorder predictors yields tight association between crystallographic disorder and hydrophobicityNathan B Holladay
Department of Biochemistry, University of Texas Southwestern Medical Center, Dallas, Texas 75390 9050, USA
Protein Sci 16:2140-52. 2007.... - An E3 ligase possessing an iron-responsive hemerythrin domain is a regulator of iron homeostasisAmeen A Salahudeen
Department of Biochemistry, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
Science 326:722-6. 2009..These observations suggest a mechanistic link between iron sensing via the FBXL5 hemerythrin domain, IRP2 regulation, and cellular responses to maintain mammalian iron homeostasis... - Ubiquitin-induced oligomerization of the RNA sensors RIG-I and MDA5 activates antiviral innate immune responseXiaomo Jiang
Department of Molecular Biology, University of Texas Southwestern Medical Center, Dallas, TX 75390 9148, USA
Immunity 36:959-73. 2012..These results suggest a unified mechanism of RIG-I and MDA5 activation and reveal a unique mechanism by which ubiquitin regulates cell signaling and immune response... - C3PO, an endoribonuclease that promotes RNAi by facilitating RISC activationYing Liu
Department of Biochemistry, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
Science 325:750-3. 2009..These studies establish an in vitro RNAi reconstitution system and identify C3PO as a key activator of the core RNAi machinery... - Sec61beta--a component of the archaeal protein secretory systemLisa N Kinch
Howard Hughes Medical Institute and Dept of Biochemistry, University of Texas Southwestern Medical Center, 5323 Harry Hines Boulevard, Dallas, TX 75390-9050, USA
Trends Biochem Sci 27:170-1. 2002..With the identification of the Sec61beta motif, functions for a universal family of archaeal proteins can be predicted and the archaeal translocon system can be definitively detected... - Purified NPC1 protein: II. Localization of sterol binding to a 240-amino acid soluble luminal loopRodney E Infante
Department of Molecular Genetics, University of Texas Southwestern Medical Center at Dallas, Dallas, Texas 75390, USA
J Biol Chem 283:1064-75. 2008..Thus, the sterol binding site on luminal loop-1 is not essential for NPC1 function in fibroblasts, but it may function in other cells where NPC1 deficiency produces more complicated lipid abnormalities... - Predictive sequence analysis of the Candidatus Liberibacter asiaticus proteomeQian Cong
Department of Biophysics, University of Texas Southwestern Medical Center, Dallas, Texas, United States of America
PLoS ONE 7:e41071. 2012..L. asiaticus proteome function and its relationship to disease. Pilot studies based on the information from our website have revealed several potential virulence factors, discussed herein... - Seq2Ref: a web server to facilitate functional interpretationWenlin Li
Howard Hughes Medical Institute, University of Texas Southwestern Medical Center, Dallas, TX 75390 9050, USA
BMC Bioinformatics 14:30. 2013..Instead of such error-prone automatic annotations, functional interpretation should rely on annotations of 'reference proteins' that have been experimentally characterized or manually curated... - Genetic defects in surfactant protein A2 are associated with pulmonary fibrosis and lung cancerYongyu Wang
Eugene McDermott Center for Human Growth and Development, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
Am J Hum Genet 84:52-9. 2009..These data are consistent with SFTPA2 germline mutations that interfere with protein trafficking and cause familial IPF and lung cancer... - Putrescine activation of Trypanosoma cruzi S-adenosylmethionine decarboxylaseTracy Clyne
Department of Pharmacology, The University of Texas Southwestern Medical Center at Dallas, 5323 Harry Hines Boulevard, Dallas, Texas 75390-9041, USA
Biochemistry 41:13207-16. 2002..cruzi enzyme contains only limited elements (D174) in common with the human enzyme and that the diamine plays different roles in the function of the mammalian and parasite enzymes... - Mutations in the carboxyl-terminal domain of phospholipase C-beta 1 delineate the dimer interface and a potential Galphaq interaction siteOlga Ilkaeva
Department of Pharmacology, University of Texas Southwestern Medical Center, Dallas, Texas 75390-9041
J Biol Chem 277:4294-300. 2002..Its location in the molecule suggests that moving the attachment point of the catalytic domain can disrupt its ability to be activated by Galpha(q)...