ANDREW NEUWALD

Summary

Affiliation: University of Maryland
Country: USA

Publications

  1. pmc Automated hierarchical classification of protein domain subfamilies based on functionally-divergent residue signatures
    Andrew F Neuwald
    Institute for Genome Sciences and Department of Biochemistry and Molecular Biology, University of Maryland School of Medicine, BioPark II, Room 617, 801 West Baltimore St, Baltimore, MD 21201, USA
    BMC Bioinformatics 13:144. 2012
  2. pmc Evolution of allostery in the cyclic nucleotide binding module
    Natarajan Kannan
    Department of Chemistry and Biochemistry, University of California, Gilman Drive, La Jolla, California 92093 0654, USA
    Genome Biol 8:R264. 2007
  3. pmc Bayesian classification of residues associated with protein functional divergence: Arf and Arf-like GTPases
    Andrew F Neuwald
    Department of Biochemistry and Molecular Biology, Institute for Genome Sciences, University of Maryland School of Medicine, BioPark II, Room 617, 801 West Baltimore St, Baltimore, MD 21201, USA
    Biol Direct 5:66. 2010
  4. pmc Rapid detection, classification and accurate alignment of up to a million or more related protein sequences
    Andrew F Neuwald
    Department of Biochemistry and Molecular Biology and The Institute for Genome Sciences, University of Maryland, School of Medicine, BioPark II, Baltimore, MD 21201, USA
    Bioinformatics 25:1869-75. 2009
  5. pmc The charge-dipole pocket: a defining feature of signaling pathway GTPase on/off switches
    Andrew F Neuwald
    Institute for Genome Sciences and Department of Biochemistry and Molecular Biology, University of Maryland School of Medicine, Baltimore, 21201, USA
    J Mol Biol 390:142-53. 2009
  6. pmc The glycine brace: a component of Rab, Rho, and Ran GTPases associated with hinge regions of guanine- and phosphate-binding loops
    Andrew F Neuwald
    Institute for Genome Sciences and Department of Biochemistry and Molecular Biology, University of Maryland School of Medicine, 801 West Baltimore St, BioPark II, Baltimore, MD 21201, USA
    BMC Struct Biol 9:11. 2009
  7. pmc Galpha Gbetagamma dissociation may be due to retraction of a buried lysine and disruption of an aromatic cluster by a GTP-sensing Arg Trp pair
    Andrew F Neuwald
    J Craig Venter Institute, Rockville, MD 20850, USA
    Protein Sci 16:2570-7. 2007
  8. ncbi request reprint The CHAIN program: forging evolutionary links to underlying mechanisms
    Andrew F Neuwald
    The J Craig Venter Institute, 9704 Medical Center Drive, Rockville, MD 20850, USA
    Trends Biochem Sci 32:487-93. 2007
  9. pmc A typhus group-specific protease defies reductive evolution in rickettsiae
    Nicole C Ammerman
    Department of Microbiology and Immunology, University of Maryland School of Medicine, Baltimore, Maryland 21201, USA
    J Bacteriol 191:7609-13. 2009
  10. ncbi request reprint Did protein kinase regulatory mechanisms evolve through elaboration of a simple structural component?
    Natarajan Kannan
    Cold Spring Harbor Laboratory, 1 Bungtown Road, P O Box 100, Cold Spring Harbor, NY 11724, USA
    J Mol Biol 351:956-72. 2005

Collaborators

Detail Information

Publications20

  1. pmc Automated hierarchical classification of protein domain subfamilies based on functionally-divergent residue signatures
    Andrew F Neuwald
    Institute for Genome Sciences and Department of Biochemistry and Molecular Biology, University of Maryland School of Medicine, BioPark II, Room 617, 801 West Baltimore St, Baltimore, MD 21201, USA
    BMC Bioinformatics 13:144. 2012
    ..These domain models are annotated to provide insights into the relationships between sequence, structure and function via web-based BLAST searches...
  2. pmc Evolution of allostery in the cyclic nucleotide binding module
    Natarajan Kannan
    Department of Chemistry and Biochemistry, University of California, Gilman Drive, La Jolla, California 92093 0654, USA
    Genome Biol 8:R264. 2007
    ..In this study, we analyze the evolutionary information embedded in genomic sequences to explore the diversity of signaling through the CNB domain and also how the CNB domain elicits a cellular response upon binding to cAMP...
  3. pmc Bayesian classification of residues associated with protein functional divergence: Arf and Arf-like GTPases
    Andrew F Neuwald
    Department of Biochemistry and Molecular Biology, Institute for Genome Sciences, University of Maryland School of Medicine, BioPark II, Room 617, 801 West Baltimore St, Baltimore, MD 21201, USA
    Biol Direct 5:66. 2010
    ....
  4. pmc Rapid detection, classification and accurate alignment of up to a million or more related protein sequences
    Andrew F Neuwald
    Department of Biochemistry and Molecular Biology and The Institute for Genome Sciences, University of Maryland, School of Medicine, BioPark II, Baltimore, MD 21201, USA
    Bioinformatics 25:1869-75. 2009
    ..However, multiply-aligning vast numbers of sequences in this way is clearly impractical...
  5. pmc The charge-dipole pocket: a defining feature of signaling pathway GTPase on/off switches
    Andrew F Neuwald
    Institute for Genome Sciences and Department of Biochemistry and Molecular Biology, University of Maryland School of Medicine, Baltimore, 21201, USA
    J Mol Biol 390:142-53. 2009
    ....
  6. pmc The glycine brace: a component of Rab, Rho, and Ran GTPases associated with hinge regions of guanine- and phosphate-binding loops
    Andrew F Neuwald
    Institute for Genome Sciences and Department of Biochemistry and Molecular Biology, University of Maryland School of Medicine, 801 West Baltimore St, BioPark II, Baltimore, MD 21201, USA
    BMC Struct Biol 9:11. 2009
    ..How these families have evolutionarily diverged from each other at the sequence level provides clues to underlying mechanisms associated with their functional specialization...
  7. pmc Galpha Gbetagamma dissociation may be due to retraction of a buried lysine and disruption of an aromatic cluster by a GTP-sensing Arg Trp pair
    Andrew F Neuwald
    J Craig Venter Institute, Rockville, MD 20850, USA
    Protein Sci 16:2570-7. 2007
    ..Other structural features associated with Galpha functional divergence further support the proposed mechanism...
  8. ncbi request reprint The CHAIN program: forging evolutionary links to underlying mechanisms
    Andrew F Neuwald
    The J Craig Venter Institute, 9704 Medical Center Drive, Rockville, MD 20850, USA
    Trends Biochem Sci 32:487-93. 2007
    ..This is illustrated here by its application to bacterial clamp-loader ATPases...
  9. pmc A typhus group-specific protease defies reductive evolution in rickettsiae
    Nicole C Ammerman
    Department of Microbiology and Immunology, University of Maryland School of Medicine, Baltimore, Maryland 21201, USA
    J Bacteriol 191:7609-13. 2009
    ..As a possible determinant of host pathogenicity, ppcE warrants consideration in the development of therapeutics against epidemic and murine typhus...
  10. ncbi request reprint Did protein kinase regulatory mechanisms evolve through elaboration of a simple structural component?
    Natarajan Kannan
    Cold Spring Harbor Laboratory, 1 Bungtown Road, P O Box 100, Cold Spring Harbor, NY 11724, USA
    J Mol Biol 351:956-72. 2005
    ....
  11. pmc Hypothesis: bacterial clamp loader ATPase activation through DNA-dependent repositioning of the catalytic base and of a trans-acting catalytic threonine
    Andrew F Neuwald
    Cold Spring Harbor Laboratory, 1 Bungtown Road PO Box 100, Cold Spring Harbor, NY 11724, USA
    Nucleic Acids Res 34:5280-90. 2006
    ..As eukaryotic and archaeal clamp loaders lack most of these key residues, it appears that eubacteria utilize a fundamentally different mechanism for clamp loader activation than do these other organisms...
  12. pmc Evolutionary clues to DNA polymerase III beta clamp structural mechanisms
    Andrew F Neuwald
    Cold Spring Harbor Laboratory, 1 Bungtown Road, PO Box 100, Cold Spring Harbor, NY 11724, USA
    Nucleic Acids Res 31:4503-16. 2003
    ..Q149 and K198 appear to sense DNA within the clamp's central hole while other residues may relay this information to the delta binding site. Mutagenesis experiments designed to explore possible mechanisms are proposed...
  13. pmc Proteomic analysis of interchromatin granule clusters
    Noriko Saitoh
    Cold Spring Harbor Laboratory, Cold Spring Harbor, New York 11724, USA
    Mol Biol Cell 15:3876-90. 2004
    ..However, the predominance of pre-mRNA processing factors supports the proposed role of IGCs as assembly, modification, and/or storage sites for proteins involved in pre-mRNA processing...
  14. pmc Evolutionary constraints associated with functional specificity of the CMGC protein kinases MAPK, CDK, GSK, SRPK, DYRK, and CK2alpha
    Natarajan Kannan
    Cold Spring Harbor Laboratory, Cold Spring Harbor, New York 11724, USA
    Protein Sci 13:2059-77. 2004
    ..Analysis of other CMGC kinases similarly suggests candidate family-specific residues for experimental follow-up...
  15. pmc Gapped alignment of protein sequence motifs through Monte Carlo optimization of a hidden Markov model
    Andrew F Neuwald
    Cold Spring Harbor Laboratory, 1 Bungtown Road, P, O, Box 100, Cold Spring Harbor, NY 11724, USA
    BMC Bioinformatics 5:157. 2004
    ....
  16. ncbi request reprint Computational analysis of protein tyrosine phosphatases: practical guide to bioinformatics and data resources
    Jannik N Andersen
    Cold Spring Harbor Laboratory, Demerec Building, 1 Bungtown Road, Cold Spring Harbor, NY 11724 2208, USA
    Methods 35:90-114. 2005
    ..Our annotated sequences, along with a web service for phylogenetic classification of PTP domains, are available online (http://ptp.cshl.edu and http://science.novonordisk.com/ptp)...
  17. pmc Analogous regulatory sites within the alphaC-beta4 loop regions of ZAP-70 tyrosine kinase and AGC kinases
    Natarajan Kannan
    Department of Chemistry and Biochemistry, University of California San Diego, La Jolla, CA 92093 0654, USA
    Biochim Biophys Acta 1784:27-32. 2008
    ..Such cis regulation of protein kinase activity may be a feature of other eukaryotic protein kinase families as well...
  18. ncbi request reprint Bayesian shadows of molecular mechanisms cast in the light of evolution
    Andrew F Neuwald
    Cold Spring Harbor Laboratory, 1 Bungtown Road, PO Box 100, Cold Spring Harbor, NY 11724, USA
    Trends Biochem Sci 31:374-82. 2006
    ..This approach is demonstrated by considering how DNA polymerase clamp-loader AAA+ ATPases couple DNA recognition to ATP hydrolysis and clamp loading...
  19. pmc The hallmark of AGC kinase functional divergence is its C-terminal tail, a cis-acting regulatory module
    Natarajan Kannan
    Howard Hughes Medical Institute, Department of Chemistry and Biochemistry, University of California at San Diego, 9500 Gilman Drive, La Jolla, CA 92093 0654, USA
    Proc Natl Acad Sci U S A 104:1272-7. 2007
    ....
  20. pmc Ran's C-terminal, basic patch, and nucleotide exchange mechanisms in light of a canonical structure for Rab, Rho, Ras, and Ran GTPases
    Andrew F Neuwald
    Cold Spring Harbor Laboratory, Cold Spring Harbor, New York 11724, USA
    Genome Res 13:673-92. 2003
    ..Other core components of the cellular machinery are likewise amenable to this approach, which we term Contrast Hierarchical Alignment and Interaction Network (CHAIN) analysis...

Research Grants15

  1. Predicting common protein mechanisms by the light of evolution
    ANDREW NEUWALD; Fiscal Year: 2007
    ..And (v) propose molecular mechanisms based on these analyses. ..
  2. Advanced Sequence-Based Prediction of Protein Function
    ANDREW NEUWALD; Fiscal Year: 2005
    ..abstract_text> ..
  3. ADVANCED SEQUENCE BASED PREDICTION OF PROTEIN FUNCTION
    ANDREW NEUWALD; Fiscal Year: 2000
    ..A comprehensive database of protein domains will be made available to the biomedical community through the National Center for Biotechnology Information. ..
  4. Predicting common protein mechanisms by the light of evolution
    ANDREW NEUWALD; Fiscal Year: 2009
    ..And (v) propose molecular mechanisms based on these analyses. ..