Nick Grishin

Summary

Affiliation: University of Texas Southwestern Medical Center
Country: USA

Publications

  1. pmc Protein structure prediction for the male-specific region of the human Y chromosome
    Krzysztof Ginalski
    Department of Biochemistry, University of Texas Southwestern Medical Center, 5323 Harry Hines Boulevard, Dallas, TX 75390 9038, USA
    Proc Natl Acad Sci U S A 101:2305-10. 2004
  2. pmc A putative RNA-interference-based immune system in prokaryotes: computational analysis of the predicted enzymatic machinery, functional analogies with eukaryotic RNAi, and hypothetical mechanisms of action
    Kira S Makarova
    National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA
    Biol Direct 1:7. 2006
  3. 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
  4. pmc Self consistency grouping: a stringent clustering method
    Bong Hyun Kim
    Biochemistry Department, UT Southwestern Medical Center, Dallas, TX, USA
    BMC Bioinformatics 13:S3. 2012
  5. pmc MESSA: MEta-Server for protein Sequence Analysis
    Qian Cong
    Department of Biophysics, University of Texas Southwestern Medical Center, Dallas, TX 75390 9050, USA
    BMC Biol 10:82. 2012
  6. pmc Membrane protein structure predictions for exploration
    Nick V Grishin
    Howard Hughes Medical Institute, Departments of Biophysics and Biochemistry, University of Texas Southwestern Medical Center, 6001 Forest Park Road, Dallas, TX, 75390 9050, USA
    Cell 149:1424-5. 2012
  7. pmc CREST--a large and diverse superfamily of putative transmembrane hydrolases
    Jimin Pei
    Howard Hughes Medical Institute, University of Texas Southwestern Medical Center, 6001 Forest Park Road, Dallas, TX 75390, USA
    Biol Direct 6:37. 2011
  8. 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
  9. pmc A tale of two ferredoxins: sequence similarity and structural differences
    S Sri Krishna
    Howard Hughes Medical Institute, University of Texas Southwestern Medical Center, Dallas, TX 75390 9050, USA
    BMC Struct Biol 6:8. 2006
  10. pmc A comprehensive update of the sequence and structure classification of kinases
    Sara Cheek
    Howard Hughes Medical Institute, University of Texas Southwestern Medical Center, 5323 Harry Hines Blvd, Dallas, Texas 75390, USA
    BMC Struct Biol 5:6. 2005

Collaborators

Detail Information

Publications94

  1. pmc Protein structure prediction for the male-specific region of the human Y chromosome
    Krzysztof Ginalski
    Department of Biochemistry, University of Texas Southwestern Medical Center, 5323 Harry Hines Boulevard, Dallas, TX 75390 9038, USA
    Proc Natl Acad Sci U S A 101:2305-10. 2004
    ..The data presented here set up the basis for additional scientific discoveries in human biology of the Y chromosome, which plays a fundamental role in sex determination...
  2. pmc A putative RNA-interference-based immune system in prokaryotes: computational analysis of the predicted enzymatic machinery, functional analogies with eukaryotic RNAi, and hypothetical mechanisms of action
    Kira S Makarova
    National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA
    Biol Direct 1:7. 2006
    ..However, the proximity of CRISPR and cas genes strongly suggests that they have related functions which is hard to reconcile with the repair hypothesis...
  3. 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...
  4. pmc Self consistency grouping: a stringent clustering method
    Bong Hyun Kim
    Biochemistry Department, UT Southwestern Medical Center, Dallas, TX, USA
    BMC Bioinformatics 13:S3. 2012
    ..Numerous types of clustering like single linkage and K-means have been widely studied and applied to a variety of scientific problems. However, the existing methods are not readily applicable for the problems that demand high stringency...
  5. pmc MESSA: MEta-Server for protein Sequence Analysis
    Qian Cong
    Department of Biophysics, University of Texas Southwestern Medical Center, Dallas, TX 75390 9050, USA
    BMC Biol 10:82. 2012
    ..However, as predictions of local sequence properties, three-dimensional structure and function are usually intertwined, it is beneficial to address them together...
  6. pmc Membrane protein structure predictions for exploration
    Nick V Grishin
    Howard Hughes Medical Institute, Departments of Biophysics and Biochemistry, University of Texas Southwestern Medical Center, 6001 Forest Park Road, Dallas, TX, 75390 9050, USA
    Cell 149:1424-5. 2012
    ..are publishing untested de novo structure models for 11 transmembrane protein families. Will their models stand the test of time and hold up to experimentation? The prospects are excellent...
  7. pmc CREST--a large and diverse superfamily of putative transmembrane hydrolases
    Jimin Pei
    Howard Hughes Medical Institute, University of Texas Southwestern Medical Center, 6001 Forest Park Road, Dallas, TX 75390, USA
    Biol Direct 6:37. 2011
    ..Recently, a group of putative transmembrane receptors called progestin and adipoQ receptors (PAQRs) were found to be distantly related to alkaline ceramidases, raising the possibility that they may also function as membrane enzymes...
  8. 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...
  9. pmc A tale of two ferredoxins: sequence similarity and structural differences
    S Sri Krishna
    Howard Hughes Medical Institute, University of Texas Southwestern Medical Center, Dallas, TX 75390 9050, USA
    BMC Struct Biol 6:8. 2006
    ..Profile-based methods for sequence comparison, such as PSI-BLAST and HMMer, suggest statistically significant similarity between these domains...
  10. pmc A comprehensive update of the sequence and structure classification of kinases
    Sara Cheek
    Howard Hughes Medical Institute, University of Texas Southwestern Medical Center, 5323 Harry Hines Blvd, Dallas, Texas 75390, USA
    BMC Struct Biol 5:6. 2005
    ..This survey presents a complete global picture of this large functional class of proteins and confirms the soundness of our initial kinase classification scheme...
  11. 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...
  12. pmc Exploring dynamics of protein structure determination and homology-based prediction to estimate the number of superfamilies and folds
    Ruslan I Sadreyev
    Howard Hughes Medical Institute, Department of Biochemistry, University of Texas Southwestern Medical Center, Dallas, TX 75390 8816, USA
    BMC Struct Biol 6:6. 2006
    ..random sample of all sequence families? Do targets solved by structural genomic initiatives (SGI) provide such a sample? What are approximate total numbers of structure-based superfamilies and folds among soluble globular domains?..
  13. 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
    ....
  14. pmc Genome trees constructed using five different approaches suggest new major bacterial clades
    Y I Wolf
    National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA
    BMC Evol Biol 1:8. 2001
    ..Such attempts are particularly relevant because of the major role of horizontal gene transfer and lineage-specific gene loss, at least in the evolution of prokaryotes...
  15. pmc Reconstruction of ancestral protein sequences and its applications
    Wei Cai
    Department of Biochemistry, University of Texas Southwestern Medical Center at Dallas, 5323 Harry Hines Blvd, Dallas, TX 75390 9050, USA
    BMC Evol Biol 4:33. 2004
    ..Additionally, reconstructed ancestral protein sequences could serve to fill in sequence space thus aiding remote homology inference...
  16. pmc Considering scores between unrelated proteins in the search database improves profile comparison
    Ruslan I Sadreyev
    Howard Hughes Medical Institute, University of Texas Southwestern Medical Center, 5323 Harry Hines Blvd, Dallas, TX 75390 9050, USA
    BMC Bioinformatics 10:399. 2009
    ..Here we analyze a novel approach to estimate the statistical significance of profile similarity: the explicit consideration of background score distributions for each database template (subject)...
  17. pmc PALSSE: a program to delineate linear secondary structural elements from protein structures
    Indraneel Majumdar
    Howard Hughes Medical Institute, University of Texas Southwestern Medical Center, 5323 Harry Hines Blvd, Dallas, TX 75390, USA
    BMC Bioinformatics 6:202. 2005
    ..Success of such structural comparison methods depends crucially on the accurate identification and delineation of secondary structure elements...
  18. pmc Estimates of statistical significance for comparison of individual positions in multiple sequence alignments
    Ruslan I Sadreyev
    Howard Hughes Medical Institute, Department of Biochemistry, University of Texas Southwestern Medical Center, 5323, Harry Hines Blvd, Dallas, TX 75390 9050, USA
    BMC Bioinformatics 5:106. 2004
    ....
  19. pmc A comprehensive system for evaluation of remote sequence similarity detection
    Yuan Qi
    Department of Biochemistry, University of Texas Southwestern Medical Center, 5323, Harry Hines Blvd, Dallas, TX 75390 9050, USA
    BMC Bioinformatics 8:314. 2007
    ....
  20. 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...
  21. ncbi request reprint Structural drift: a possible path to protein fold change
    S Sri Krishna
    Howard Hughes Medical Institute, University of Texas Southwestern Medical Center, 5323, Harry Hines Blvd, Dallas, TX 75390 9050, USA
    Bioinformatics 21:1308-10. 2005
    ....
  22. ncbi request reprint Mh1 domain of Smad is a degraded homing endonuclease
    N V Grishin
    Howard Hughes Medical Institute and Department of Biochemistry, University of Texas Southwestern Medical Center, 5323 Harry Hines Blvd, Dallas, TX 75390 9050, USA
    J Mol Biol 307:31-7. 2001
    ..MH1 is an example of transcription regulator derived from the ancient enzymatic domain that lost its catalytic activity but retained DNA-binding sites...
  23. ncbi request reprint Euclidian space and grouping of biological objects
    Vyacheslav N Grishin
    Department of Biochemistry Howard Hughes Medical Institute, University of Texas Southwestern Medical Center, 5323 Harry Hines Blvd, Dallas, TX 75390 9050, USA
    Bioinformatics 18:1523-34. 2002
    ..Such a space can also be a basis for model-based clustering strategies that typically produce results correlating better with biological properties of proteins...
  24. ncbi request reprint C-terminal domains of Escherichia coli topoisomerase I belong to the zinc-ribbon superfamily
    N V Grishin
    Biochemistry Department, University of Texas Southwestern Medical Center, 5323, Harry Hines Blvd, Dallas, TX, 75390 9038, USA
    J Mol Biol 299:1165-77. 2000
    ..Present analyses lead to the classification of the C-terminal fragment of E. coli topoisomerase I as a member of zinc ribbon superfamily, despite the absence of zinc-binding sites...
  25. pmc Two tricks in one bundle: helix-turn-helix gains enzymatic activity
    N V Grishin
    Biochemistry Department, University of Texas Southwestern Medical Center, Dallas, TX 75390 9038, USA
    Nucleic Acids Res 28:2229-33. 2000
    ....
  26. pmc Treble clef finger--a functionally diverse zinc-binding structural motif
    N V Grishin
    Howard Hughes Medical Institute and Department of Biochemistry, University of Texas Southwestern Medical Center, 5323 Harry Hines Boulevard, Dallas, TX 75390 9050, USA
    Nucleic Acids Res 29:1703-14. 2001
    ..Present analysis suggests that the treble clef motif defines a distinct structural fold found in proteins with diverse functional properties and forms one of the major zinc finger groups...
  27. pmc From complete genomes to measures of substitution rate variability within and between proteins
    N V Grishin
    National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894 USA
    Genome Res 10:991-1000. 2000
    ..The topology of the resulting tree is largely compatible with those of global rRNA-based trees and trees produced by other approaches to genome-wide comparison...
  28. pmc KH domain: one motif, two folds
    N V Grishin
    Howard Hughes Medical Institute and Department of Biochemistry, University of Texas Southwestern Medical Center, 5323 Harry Hines Boulevard, Dallas, TX 75390 9050, USA
    Nucleic Acids Res 29:638-43. 2001
    ..Current analysis offers a new look on how proteins can change fold in the course of evolution...
  29. 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
    ....
  30. ncbi request reprint Structural classification of thioredoxin-like fold proteins
    Yuan Qi
    Department of Biochemistry, University of Texas Southwestern Medical Center, Dallas, Texas 75390 9050, USA
    Proteins 58:376-88. 2005
    ..Considering these structurally similar domains together sheds new light on the relationships between sequence, structure, function and evolution of thioredoxins...
  31. 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
    ....
  32. ncbi request reprint PCOAT: positional correlation analysis using multiple methods
    Yuan Qi
    Department of Biochemistry, University of Texas Southwestern Medical Center, 5323 Harry Hines Blvd, Dallas, TX 75390 9050, USA
    Bioinformatics 20:3697-9. 2004
    ..AVAILABILITY: ftp://iole.swmed.edu/pub/PCOAT/. SUPPLEMENTARY INFORMATION: The PCOAT ftp site contains a detailed description of the program, and the results of PCOAT analysis on C2H2 alignment and ACT domain alignment...
  33. 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...
  34. pmc A DNA repair system specific for thermophilic Archaea and bacteria predicted by genomic context analysis
    Kira S Makarova
    National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Building 380, Bethesda, MD 20894, USA
    Nucleic Acids Res 30:482-96. 2002
    ....
  35. ncbi request reprint Searching for three-dimensional secondary structural patterns in proteins with ProSMoS
    Shuoyong Shi
    Howard Hughes Medical Institute, University of Texas Southwestern Medical Center, Dallas, TX 75390 9050, USA
    Bioinformatics 23:1331-8. 2007
    ..A brief analysis of all beta-Grasp-containing proteins is presented. Program availability: ProSMoS is freely available for non-commercial use from ftp://iole.swmed.edu/pub/ProSMoS...
  36. pmc Detecting distant homology with Meta-BASIC
    Krzysztof Ginalski
    Department of Biochemistry, University of Texas, Southwestern Medical Center, 5323 Harry Hines Boulevard, Dallas, Texas 75390 9038, USA
    Nucleic Acids Res 32:W576-81. 2004
    ..pl. Detailed discussion is provided for two of the most interesting assignments. DUF271 and DUF431 are predicted to be a nucleotide-diphospho-sugar transferase and an alpha/beta-knot SAM-dependent RNA methyltransferase, respectively...
  37. ncbi request reprint Combining evolutionary and structural information for local protein structure prediction
    Jimin Pei
    Department of Biochemistry, University of Texas Southwestern Medical Center, Dallas, Texas 75390 9050, USA
    Proteins 56:782-94. 2004
    ..77), suggesting that it is a valid method for local protein structure prediction. Mixture of predicted structural frequencies and evolutionary frequencies improve the quality of local profile-to-profile alignment by COMPASS...
  38. pmc Structure similarity measure with penalty for close non-equivalent residues
    Ruslan I Sadreyev
    Howard Hughes Medical Institute, University of Texas Southwestern Medical Center, 5323 Harry Hines Blvd, Dallas, TX 75390 9050, USA
    Bioinformatics 25:1259-63. 2009
    ....
  39. ncbi request reprint Crystal structure of Haemophilus influenzae NadR protein. A bifunctional enzyme endowed with NMN adenyltransferase and ribosylnicotinimide kinase activities
    S Kumar Singh
    Department of Biochemistry and Howard Hughes Medical Institute, University of Texas Southwestern Medical Center, Dallas, Texas 75390, USA
    J Biol Chem 277:33291-9. 2002
    ....
  40. 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)...
  41. pmc Profile-profile comparisons by COMPASS predict intricate homologies between protein families
    Ruslan I Sadreyev
    Howard Hughes Medical Institute and Department of Biochemistry, University of Texas Southwestern Medical Center, Dallas, Texas 75390 9050, USA
    Protein Sci 12:2262-72. 2003
    ....
  42. 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
    ....
  43. ncbi request reprint COMPASS: a tool for comparison of multiple protein alignments with assessment of statistical significance
    Ruslan Sadreyev
    Howard Hughes Medical Institute, and Department of Biochemistry, University of Texas Southwestern Medical Center, 5323 Harry Hines Blvd, Dallas, TX 75390 9050, USA
    J Mol Biol 326:317-36. 2003
    ..The potential value of COMPASS for structure/function predictions is illustrated by the detection of an intricate homology between the DNA-binding domain of the CTF/NFI family and the MH1 domain of the Smad family...
  44. ncbi request reprint Probabilistic scoring measures for profile-profile comparison yield more accurate short seed alignments
    David Mittelman
    Howard Hughes Medical Institute Department of Biochemistry, University of Texas Southwestern Medical Center, 5323 Harry Hines Blvd, Dallas, TX 75390 9050, USA
    Bioinformatics 19:1531-9. 2003
    ..We implemented several previously reported scoring functions as well as our own functions, and compared them on the basis of their ability to produce accurate short ungapped alignments of a given length...
  45. ncbi request reprint Structure of human nicotinamide/nicotinic acid mononucleotide adenylyltransferase. Basis for the dual substrate specificity and activation of the oncolytic agent tiazofurin
    Tianjun Zhou
    Department of Biochemistry, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
    J Biol Chem 277:13148-54. 2002
    ..The results from the analytical ultracentrifugation studies are consistent with the formation of a hexamer in solution under certain conditions...
  46. ncbi request reprint Structural classification of small, disulfide-rich protein domains
    Sara Cheek
    Department of Biochemistry, University of Texas Southwestern Medical Center, Dallas, 75390, USA
    J Mol Biol 359:215-37. 2006
    ..Examples of variations in disulfide bonding patterns found within families and fold groups are discussed...
  47. ncbi request reprint Three-dimensional structure of the rSly1 N-terminal domain reveals a conformational change induced by binding to syntaxin 5
    Demet Arac
    Department of Biochemistry, University of Texas Southwestern Medical Center, 5323 Harry Hines Boulevard, Dallas, TX 75390, USA
    J Mol Biol 346:589-601. 2005
    ....
  48. pmc PROCAIN server for remote protein sequence similarity search
    Yong Wang
    Biomedical Engineering Program, University of Texas Southwestern Medical Center, University of Texas Southwestern Medical Center, 5323 Harry Hines Blvd, Dallas, TX 75390 9050, USA
    Bioinformatics 25:2076-7. 2009
    ..The front page allows the user to adjust multiple options of input processing and output formatting, as well as search settings, including the relative weights assigned to the three types of assisting information...
  49. 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...
  50. pmc MALISAM: a database of structurally analogous motifs in proteins
    Hua Cheng
    Howard Hughes Medical Institute and Department of Biochemistry, University of Texas Southwestern Medical Center, 5323 Harry Hines Blvd, Dallas, TX 75390 9050, USA
    Nucleic Acids Res 36:D211-7. 2008
    ..The database is publicly available at http://prodata.swmed.edu/malisam...
  51. ncbi request reprint Genome trees and the tree of life
    Yuri I Wolf
    National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA
    Trends Genet 18:472-9. 2002
    ..However, this tree should be reinterpreted as a prevailing trend in the evolution of genome-scale gene sets rather than as a complete picture of evolution...
  52. pmc Unusually rapid evolution of Neuroligin-4 in mice
    Marc F Bolliger
    Departments of Neuroscience, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
    Proc Natl Acad Sci U S A 105:6421-6. 2008
    ....
  53. pmc Bifunctional NMN adenylyltransferase/ADP-ribose pyrophosphatase: structure and function in bacterial NAD metabolism
    Nian Huang
    Department of Biochemistry, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
    Structure 16:196-209. 2008
    ..The latter observation provided new insights into the ligand binding mode of ADPR-gated Ca2+ channel TRPM2...
  54. pmc Lysine acetylation is a highly abundant and evolutionarily conserved modification in Escherichia coli
    Junmei Zhang
    Department of Biochemistry, Howard Hughes Medical Institute, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
    Mol Cell Proteomics 8:215-25. 2009
    ..Furthermore, we demonstrate that bacterial lysine acetylation is regulated in response to stress stimuli...
  55. pmc PROMALS3D web server for accurate multiple protein sequence and structure alignments
    Jimin Pei
    Howard Hughes Medical Institute and Department of Biochemistry, University of Texas Southwestern Medical Center, 6001 Forest Park Road, Dallas, TX 75390 9050, USA
    Nucleic Acids Res 36:W30-4. 2008
    ..Intermediate results of sequence and structural database searches are also available. The PROMALS3D web server is available at: http://prodata.swmed.edu/promals3d/...
  56. pmc Double-stranded DNA bacteriophage prohead protease is homologous to herpesvirus protease
    Hua Cheng
    Department of Biochemistry, University of Texas Southwestern Medical Center, Dallas, Texas 75390, USA
    Protein Sci 13:2260-9. 2004
    ..Our study provides further support for the proposed evolutionary link between dsDNA bacteriophages and herpesviruses...
  57. ncbi request reprint Quality of alignment comparison by COMPASS improves with inclusion of diverse confident homologs
    Ruslan I Sadreyev
    Howard Hughes Medical Institute, and Department of Biochemistry, University of Texas Southwestern Medical Center, 5323, Harry Hines Blvd, Dallas, TX 75390 9050, USA
    Bioinformatics 20:818-28. 2004
    ....
  58. ncbi request reprint Effective scoring function for protein sequence design
    Shide Liang
    Department of Biochemistry, University of Texas Southwestern Medical Center, Dallas 75390 9050, USA
    Proteins 54:271-81. 2004
    ..The designed sequences were similar to the natural sequences of the family to which the template structure belonged. The profile of the designed sequences was helpful for identification of remote homologues of the native sequence...
  59. ncbi request reprint Efficient expansion, folding, and unfolding of proteins
    Erik D Nelson
    Howard Hughes Medical Institute, University of Texas Southwestern Medical Center, 5323 Harry Hines Boulevard, Dallas, TX 75235 9050, USA
    Phys Rev E Stat Nonlin Soft Matter Phys 70:051906. 2004
    ..The results suggest that certain topological "defects" in proteins lead to preferred, entropically favorable channels down their free energy landscapes...
  60. ncbi request reprint C-terminal domain of gyrase A is predicted to have a beta-propeller structure
    Yuan Qi
    Department of Biochemistry, University of Texas Southwestern Medical Center, Texas 75390 9050, USA
    Proteins 47:258-64. 2002
    ..The prediction rationalizes available experimental data and sheds light on the spatial properties of the largest topoisomerase domain that lacks structural information...
  61. pmc DOM-fold: a structure with crossing loops found in DmpA, ornithine acetyltransferase, and molybdenum cofactor-binding domain
    Hua Cheng
    Department of Biochemistry, University of Texas Southwestern Medical Center, Dallas, 75390 9050, USA
    Protein Sci 14:1902-10. 2005
    ..Contrary to previous reports, we conclude that functional similarities between DmpA/OAT proteins and N-terminal nucleophile (Ntn) hydrolases are convergent and are unlikely to be inherited from a common ancestor...
  62. pmc Remote homology between Munc13 MUN domain and vesicle tethering complexes
    Jimin Pei
    Howard Hughes Medical Institute, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
    J Mol Biol 391:509-17. 2009
    ....
  63. 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
    ....
  64. 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...
  65. pmc HangOut: generating clean PSI-BLAST profiles for domains with long insertions
    Bong Hyun Kim
    Department of Biochemistry, University of Texas Southwestern Medical Center, 5323 Harry Hines Boulevard, Dallas, TX 75390, USA
    Bioinformatics 26:1564-5. 2010
    ..We developed a procedure (HangOut) that, for a single domain with specified insertion position, cleans erroneously extended PSI-BLAST alignments to generate better profiles...
  66. pmc Structure and mechanism of a eukaryotic FMN adenylyltransferase
    Carlos Huerta
    Department of Biochemistry, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
    J Mol Biol 389:388-400. 2009
    ..Structure-based investigation of the kinetic properties of FMNAT should offer insights into the regulatory mechanisms of FAD homeostasis by FMNAT in eukaryotic organisms...
  67. pmc COMPASS server for homology detection: improved statistical accuracy, speed and functionality
    Ruslan I Sadreyev
    Howard Hughes Medical Institute, University of Texas Southwestern Medical Center, 5323 Harry Hines Blvd, Dallas, TX 75390 9050, USA
    Nucleic Acids Res 37:W90-4. 2009
    ..URL: http://prodata.swmed.edu/compass...
  68. 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...
  69. ncbi request reprint PCMA: fast and accurate multiple sequence alignment based on profile consistency
    Jimin Pei
    Howard Hughes Medical Institute, and Department of Biochemistry, University of Texas Southwestern Medical Center, 5323 Harry Hines Blvd, Dallas, TX 75390 9050, USA
    Bioinformatics 19:427-8. 2003
    ..PCMA balances speed and accuracy in a flexible way and is suitable for aligning large numbers of sequences...
  70. ncbi request reprint Structural characterization of a human cytosolic NMN/NaMN adenylyltransferase and implication in human NAD biosynthesis
    Xuejun Zhang
    Department of Biochemistry, University of Texas Southwestern Medical Center, Dallas, Texas 75390, USA
    J Biol Chem 278:13503-11. 2003
    ..The characterization of the cytosolic human PNAT-3 provided compelling evidence that the final steps of NAD biosynthesis pathways may exist in mammalian cytoplasm and mitochondria, potentially contributing to their NAD/NADP pool...
  71. ncbi request reprint The finger domain of the human deubiquitinating enzyme HAUSP is a zinc ribbon
    S Sri Krishna
    Department of Biochemistry, University of Texas Southwestern Medical Center, Dallas, Texas 75390 9050, USA
    Cell Cycle 3:1046-9. 2004
    ..By comparative sequence and structural analysis, we show that the previously uncharacterized finger domain insert to the catalytic core of HAUSP is a zinc ribbon that has lost its zinc-binding ability...
  72. ncbi request reprint BTLCP proteins: a novel family of bacterial transglutaminase-like cysteine proteinases
    Krzysztof Ginalski
    Department of Biochemistry, University of Texas, Southwestern Medical Center, 5323 Harry Hines Boulevard, Dallas, Texas 75390 9038, USA
    Trends Biochem Sci 29:392-5. 2004
    ..Inspection of neighboring genes encoding BTLCPs suggests a link between this predicted activity and a type-I secretion system resembling ATP-binding cassette exporters of toxins and proteases involved in bacterial pathogenicity...
  73. pmc The P5 protein from bacteriophage phi-6 is a distant homolog of lytic transglycosylases
    Jimin Pei
    Department of Biochemistry, University of Texas Southwestern Medical Center, 5323 Harry Hines Boulevard, Dallas, TX 75390 9038, USA
    Protein Sci 14:1370-4. 2005
    ....
  74. 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...
  75. ncbi request reprint The HicAB cassette, a putative novel, RNA-targeting toxin-antitoxin system in archaea and bacteria
    Kira S Makarova
    National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health Bethesda, MD 20894, USA
    Bioinformatics 22:2581-4. 2006
    ..Thus, the HicAB module is predicted to be a novel TAS whose mechanism involves RNA-binding and, possibly, cleavage...
  76. pmc Structural classification of zinc fingers: survey and summary
    S Sri Krishna
    Department of Biochemistry, University of Texas, Southwestern Medical Center, 5323 Harry Hines Boulevard, Dallas, TX 75390 9050, USA
    Nucleic Acids Res 31:532-50. 2003
    ..The classification helps in understanding the relationship between the structure, function and evolutionary history of these domains. The results are available as an online database of zinc finger structures...
  77. 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
    ....
  78. pmc Breaking the singleton of germination protease
    Jimin Pei
    Department of Biochemistry, University of Texas Southwestern Medical Center, Dallas, Texas 75390 9050, USA
    Protein Sci 11:691-7. 2002
    ..Our analysis helps localize the active site of GPRs and provides insight into the catalytic mechanisms of a superfamily of putative metal-regulated proteases...
  79. ncbi request reprint PROMALS: towards accurate multiple sequence alignments of distantly related proteins
    Jimin Pei
    Howard Hughes Medical Institute, The University of Texas Southwestern Medical Center at Dallas, 6001 Forest Park Road, Dallas, TX 75390 9050, USA
    Bioinformatics 23:802-8. 2007
    ..Although the alignment problem has attracted considerable attention, preparation of high-quality alignments for distantly related sequences remains a difficult task...
  80. ncbi request reprint Crystal structures of E. coli nicotinate mononucleotide adenylyltransferase and its complex with deamido-NAD
    Hong Zhang
    Department of Biochemistry, University of Texas Southwestern Medical Center, 5323 Harry Hines Boulevard, Dallas, TX 75390, USA
    Structure 10:69-79. 2002
    ..The bacterial NaMN adenylyltransferase structures described here provide a foundation for structure-based design of specific inhibitors that may have therapeutic potential...
  81. ncbi request reprint BOF: a novel family of bacterial OB-fold proteins
    Krzysztof Ginalski
    Department of Biochemistry, University of Texas, Southwestern Medical Center, 5323 Harry Hines Boulevard, Dallas, TX 75390 9038, USA
    FEBS Lett 567:297-301. 2004
    ....
  82. pmc BAP1 loss defines a new class of renal cell carcinoma
    Samuel Peña-Llopis
    Department of Internal Medicine, University of Texas Southwestern Medical Center, Dallas, Texas, USA
    Nat Genet 44:751-9. 2012
    ..0005). Our results establish the foundation for an integrated pathological and molecular genetic classification of RCC, paving the way for subtype-specific treatments exploiting genetic vulnerabilities...
  83. pmc Nuclear envelope phosphatase 1-regulatory subunit 1 (formerly TMEM188) is the metazoan Spo7p ortholog and functions in the lipin activation pathway
    Sungwon Han
    Department of Pharmacology, University of Texas Southwestern Medical Center, Dallas, Texas 75390, USA
    J Biol Chem 287:3123-37. 2012
    ..The nuclear fraction of lipin-1b is increased when CTDNEP1 and NEP1-R1 are co-expressed. Therefore, NEP1-R1 is functionally conserved from yeast to humans and functions in the lipin activation pathway...
  84. pmc COMPASS server for remote homology inference
    Ruslan I Sadreyev
    Howard Hughes Medical Institute, University of Texas Southwestern Medical Center, 5323 Harry Hines Blvd, Dallas, TX 75390 9050, USA
    Nucleic Acids Res 35:W653-8. 2007
    ..To illustrate the value of this tool for protein structure-functional prediction, we present two examples of detecting distant homologs for uncharacterized protein families. Available at http://prodata.swmed.edu/compass...
  85. pmc Peptidase family U34 belongs to the superfamily of N-terminal nucleophile hydrolases
    Jimin Pei
    Howard Hughes Medical Institute, Department of Biochemistry, University of Texas Southwestern Medical Center, Dallas, Texas 75390, USA
    Protein Sci 12:1131-5. 2003
    ....
  86. 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...
  87. ncbi request reprint DCC proteins: a novel family of thiol-disulfide oxidoreductases
    Krzysztof Ginalski
    Department of Biochemistry, University of Texas, Southwestern Medical Center, 5323 Harry Hines Boulevard, Dallas, TX 75390 9038, USA
    Trends Biochem Sci 29:339-42. 2004
  88. ncbi request reprint Structurally analogous proteins do exist!
    S Sri Krishna
    Structure 12:1125-7. 2004
  89. ncbi request reprint Raptor protein contains a caspase-like domain
    Krzysztof Ginalski
    Biochemistry Department, University of Texas Southwestern Medical Center, 5323 Harry Hines Boulevard, Dallas, Texas 75390 9038, USA
    Trends Biochem Sci 29:522-4. 2004
    ..This finding suggests several unexpected aspects of raptor function in the target of rapamycin (TOR) signaling pathway...
  90. pmc PROMALS3D: a tool for multiple protein sequence and structure alignments
    Jimin Pei
    Howard Hughes Medical Institute, Dallas, TX 75390, USA
    Nucleic Acids Res 36:2295-300. 2008
    ..PROMALS3D outperforms a number of existing methods for constructing multiple sequence or structural alignments using both reference-dependent and reference-independent evaluation methods...
  91. pmc MUMMALS: multiple sequence alignment improved by using hidden Markov models with local structural information
    Jimin Pei
    Howard Hughes Medical Institute, University of Texas Southwestern Medical Center at Dallas, 5323 Harry Hines Boulevard, Dallas, TX 75390 9050, USA
    Nucleic Acids Res 34:4364-74. 2006
    ....
  92. 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...
  93. pmc PROMALS web server for accurate multiple protein sequence alignments
    Jimin Pei
    Howard Hughes Medical Institute, University of Texas Southwestern Medical Center, 6001 Forest Park Road, Dallas, Texas 75390 9050, USA
    Nucleic Acids Res 35:W649-52. 2007
    ..The output includes a colored alignment augmented with information about sequence grouping, predicted secondary structures and positional conservation. The PROMALS web server is available at: http://prodata.swmed.edu/promals/..
  94. pmc Accurate statistical model of comparison between multiple sequence alignments
    Ruslan I Sadreyev
    Howard Hughes Medical Institute, Dallas, TX 75390 9050, USA
    Nucleic Acids Res 36:2240-8. 2008
    ..Third, we apply this random model to database searches and show that it surpasses conventional models in the accuracy of detecting remote protein similarities...

Research Grants5

  1. Computations of Fold Changes in Evolution of Proteins
    Nick Grishin; Fiscal Year: 2006
    ..Finally, we will perform in silico evolution of model proteins under functional constraints and compare the results to those deduced from the analysis of natural sequences and structures. ..
  2. Computational methods for structural-functional studies of proteins
    Nick V Grishin; Fiscal Year: 2010
    ..We will improve alignment accuracy and using the new method will analyze kinases, which are a medically important group of enzymes attracting high interest because of their relevance to many diseases, cancer in particular. ..