Lisa N Kinch

Summary

Affiliation: University of Texas Southwestern Medical Center
Country: USA

Publications

  1. pmc Structure of a conserved hypothetical protein SA1388 from S. aureus reveals a capped hexameric toroid with two PII domain lids and a dinuclear metal center
    Kumar 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
  2. pmc Realm of PD-(D/E)XK nuclease superfamily revisited: detection of novel families with modified transitive meta profile searches
    Lukasz Knizewski
    Interdisciplinary Centre for Mathematical and Computational Modelling, Warsaw University, Pawinskiego 5A, Warsaw, Poland
    BMC Struct Biol 7:40. 2007
  3. pmc Longin-like folds identified in CHiPS and DUF254 proteins: vesicle trafficking complexes conserved in eukaryotic evolution
    Lisa 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
  4. pmc Site-2 protease regulated intramembrane proteolysis: sequence homologs suggest an ancient signaling cascade
    Lisa 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
  5. pmc Identification of novel restriction endonuclease-like fold families among hypothetical proteins
    Lisa 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
  6. ncbi request reprint CASP5 assessment of fold recognition target predictions
    Lisa N Kinch
    Howard Hughes Medical Institute, University of Texas Southwestern Medical Center, Dallas, Texas 75390 9050, USA
    Proteins 53:395-409. 2003
  7. pmc CASP5 target classification
    Lisa N Kinch
    Howard Hughes Medical Institute, University of Texas Southwestern Medical Center, Dallas 75390 9050, USA
    Proteins 53:340-51. 2003
  8. pmc Fido, a novel AMPylation domain common to fic, doc, and AvrB
    Lisa N Kinch
    Howard Hughes Medical Institute, University of Texas Southwestern Medical Center, Dallas, Texas, United States of America
    PLoS ONE 4:e5818. 2009
  9. ncbi request reprint Evolution of protein structures and functions
    Lisa 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
  10. pmc CASP9 assessment of free modeling target predictions
    Lisa Kinch
    Howard Hughes Medical Institute, University of Texas, Southwestern Medical Center, Dallas, TX 75390 9050, USA
    Proteins 79:59-73. 2011

Collaborators

Detail Information

Publications39

  1. pmc Structure of a conserved hypothetical protein SA1388 from S. aureus reveals a capped hexameric toroid with two PII domain lids and a dinuclear metal center
    Kumar 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...
  2. pmc Realm of PD-(D/E)XK nuclease superfamily revisited: detection of novel families with modified transitive meta profile searches
    Lukasz Knizewski
    Interdisciplinary Centre for Mathematical and Computational Modelling, Warsaw University, Pawinskiego 5A, Warsaw, Poland
    BMC Struct Biol 7:40. 2007
    ....
  3. pmc Longin-like folds identified in CHiPS and DUF254 proteins: vesicle trafficking complexes conserved in eukaryotic evolution
    Lisa 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
    ....
  4. pmc Site-2 protease regulated intramembrane proteolysis: sequence homologs suggest an ancient signaling cascade
    Lisa 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...
  5. pmc Identification of novel restriction endonuclease-like fold families among hypothetical proteins
    Lisa 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...
  6. ncbi request reprint CASP5 assessment of fold recognition target predictions
    Lisa 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...
  7. pmc CASP5 target classification
    Lisa 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...
  8. pmc Fido, a novel AMPylation domain common to fic, doc, and AvrB
    Lisa 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...
  9. ncbi request reprint Evolution of protein structures and functions
    Lisa 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...
  10. pmc CASP9 assessment of free modeling target predictions
    Lisa 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/ ...
  11. pmc CASP9 target classification
    Lisa N Kinch
    Howard Hughes Medical Institute, University of Texas, Southwestern Medical Center, Dallas, TX 75390 9050, USA
    Proteins 79:21-36. 2011
    ....
  12. pmc The human Ago2 MC region does not contain an eIF4E-like mRNA cap binding motif
    Lisa 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...
  13. pmc Kinetic and structural insights into the mechanism of AMPylation by VopS Fic domain
    Phi 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...
  14. pmc EDD, a novel phosphotransferase domain common to mannose transporter EIIA, dihydroxyacetone kinase, and DegV
    Lisa 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
    ....
  15. ncbi request reprint Prediction of functional specificity determinants from protein sequences using log-likelihood ratios
    Jimin 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
    ....
  16. doi request reprint AMPylation of Rho GTPases by Vibrio VopS disrupts effector binding and downstream signaling
    Melanie 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...
  17. ncbi request reprint Effectors of animal and plant pathogens use a common domain to bind host phosphoinositides
    Dor Salomon
    Department of Molecular Biology, University of Texas Southwestern Medical Center, 5323 Harry Hines Boulevard, Dallas, Texas 75390 9148, USA
    Nat Commun 4:2973. 2013
    ..Thus, our findings suggest a possible mechanism for promoting refolding of Type III effectors after delivery into host cells. ..
  18. pmc 4SCOPmap: automated assignment of protein structures to evolutionary superfamilies
    Sara 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...
  19. ncbi request reprint Expanding the nitrogen regulatory protein superfamily: Homology detection at below random sequence identity
    Lisa N Kinch
    Howard Hughes Medical Institute, and Department of Biochemistry, University of Texas Southwestern Medical Center, Dallas, Texas, USA
    Proteins 48:75-84. 2002
    ....
  20. pmc An automatic method for CASP9 free modeling structure prediction assessment
    Qian 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...
  21. ncbi request reprint Deciphering a novel thioredoxin-like fold family
    Lisa 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)...
  22. doi request reprint Identification and assay of allosteric regulators of S-adenosylmethionine decarboxylase
    Erin K Willert
    Department of Pharmacology, University of Texas Southwestern Medical Center at Dallas, Dallas, TX, USA
    Methods Mol Biol 720:219-35. 2011
    ....
  23. pmc The ABC transporters in Candidatus Liberibacter asiaticus
    Wenlin 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...
  24. doi request reprint Bioinformatics perspective on rhomboid intramembrane protease evolution and function
    Lisa N Kinch
    Howard Hughes Medical Institute and Department of Biochemistry, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
    Biochim Biophys Acta 1828:2937-43. 2013
    ..This article is part of a Special Issue entitled: Intramembrane Proteases. ..
  25. pmc A database of domain definitions for proteins with complex interdomain geometry
    Indraneel 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...
  26. pmc An E3 ligase possessing an iron-responsive hemerythrin domain is a regulator of iron homeostasis
    Ameen 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...
  27. pmc Optimization of linear disorder predictors yields tight association between crystallographic disorder and hydrophobicity
    Nathan B Holladay
    Department of Biochemistry, University of Texas Southwestern Medical Center, Dallas, Texas 75390 9050, USA
    Protein Sci 16:2140-52. 2007
    ....
  28. pmc Pclust: protein network visualization highlighting experimental data
    Wenlin Li
    Departments of Biophysics and Biochemistry and Howard Hughes Medical Institute, University of Texas Southwestern Medical Center, Dallas, TX 75390 9050, USA
    Bioinformatics 29:2647-8. 2013
    ..articles in PubMed. The identification of 'reference proteins' and the ease of cross-database linkage will facilitate understanding the functions of protein clusters in the network, thus promoting interpretation of proteins of interest...
  29. pmc Seq2Ref: a web server to facilitate functional interpretation
    Wenlin 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...
  30. pmc Ubiquitin-induced oligomerization of the RNA sensors RIG-I and MDA5 activates antiviral innate immune response
    Xiaomo 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 revealĀ a unique mechanism by which ubiquitin regulates cell signaling and immune response...
  31. ncbi request reprint Sec61beta--a component of the archaeal protein secretory system
    Lisa 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...
  32. pmc C3PO, an endoribonuclease that promotes RNAi by facilitating RISC activation
    Ying 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...
  33. ncbi request reprint Purified NPC1 protein: II. Localization of sterol binding to a 240-amino acid soluble luminal loop
    Rodney 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...
  34. pmc Predictive sequence analysis of the Candidatus Liberibacter asiaticus proteome
    Qian 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...
  35. pmc cor, a novel carbon monoxide resistance gene, is essential for Mycobacterium tuberculosis pathogenesis
    Vineetha M Zacharia
    Department of Internal Medicine, University of Texas Southwestern Medical School, Dallas, Texas, USA
    MBio 4:e00721-13. 2013
    ..Taken together, this represents the first report of a role for HO1-derived CO in controlling infection of an intracellular pathogen and the first identification of a CO resistance gene in a pathogenic organism...
  36. ncbi request reprint Beclin 2 functions in autophagy, degradation of G protein-coupled receptors, and metabolism
    Congcong He
    Howard Hughes Medical Institute, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
    Cell 154:1085-99. 2013
    ..Our findings identify Beclin 2 as a converging regulator of autophagy and GPCR turnover and highlight the functional and mechanistic diversity of Beclin family membersĀ in autophagy, endolysosomal trafficking, and metabolism. ..
  37. pmc Genetic defects in surfactant protein A2 are associated with pulmonary fibrosis and lung cancer
    Yongyu 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...
  38. ncbi request reprint Putrescine activation of Trypanosoma cruzi S-adenosylmethionine decarboxylase
    Tracy 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...
  39. ncbi request reprint Mutations in the carboxyl-terminal domain of phospholipase C-beta 1 delineate the dimer interface and a potential Galphaq interaction site
    Olga 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)...