PubMed

Evolution of allostery in the cyclic nucleotide binding module.

Kannan N, Wu J, Anand GS, Yooseph S, Neuwald AF, Venter JC, Taylor SS.

Genome Biol. 2007;8(12):R264.PMID: 18076763 [PubMed - indexed for MEDLINE]Related articlesFree article

Analogous regulatory sites within the alphaC-beta4 loop regions of ZAP-70 tyrosine kinase and AGC kinases.

Kannan N, Neuwald AF, Taylor SS.

Biochim Biophys Acta. 2008 Jan;1784(1):27-32. Epub 2007 Sep 29. Review.PMID: 17977811 [PubMed - indexed for MEDLINE]Related articlesFree article

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.

Neuwald AF.

Protein Sci. 2007 Nov;16(11):2570-7.PMID: 17962409 [PubMed - indexed for MEDLINE]Related articlesFree article

The CHAIN program: forging evolutionary links to underlying mechanisms.

Neuwald AF.

Trends Biochem Sci. 2007 Nov;32(11):487-93. Epub 2007 Oct 24.PMID: 17962021 [PubMed - indexed for MEDLINE]Related articles

The hallmark of AGC kinase functional divergence is its C-terminal tail, a cis-acting regulatory module.

Kannan N, Haste N, Taylor SS, Neuwald AF.

Proc Natl Acad Sci U S A. 2007 Jan 23;104(4):1272-7. Epub 2007 Jan 16. Erratum in: Proc Natl Acad Sci U S A. 2008 Jul 1;105(26):9130. PMID: 17227859 [PubMed - indexed for MEDLINE]Related articlesFree article

Hypothesis: bacterial clamp loader ATPase activation through DNA-dependent repositioning of the catalytic base and of a trans-acting catalytic threonine.

Neuwald AF.

Nucleic Acids Res. 2006;34(18):5280-90. Epub 2006 Sep 29.PMID: 17012286 [PubMed - indexed for MEDLINE]Related articlesFree article

Bayesian shadows of molecular mechanisms cast in the light of evolution.

Neuwald AF.

Trends Biochem Sci. 2006 Jul;31(7):374-82.PMID: 16766187 [PubMed - indexed for MEDLINE]Related articles

Evolutionary clues to eukaryotic DNA clamp-loading mechanisms: analysis of the functional constraints imposed on replication factor C AAA+ ATPases.

Neuwald AF.

Nucleic Acids Res. 2005;33(11):3614-28.PMID: 16082778 [PubMed - indexed for MEDLINE]Related articlesFree article

Did protein kinase regulatory mechanisms evolve through elaboration of a simple structural component?

Kannan N, Neuwald AF.

J Mol Biol. 2005 Sep 2;351(5):956-72.PMID: 16051269 [PubMed - indexed for MEDLINE]Related articles

Computational analysis of protein tyrosine phosphatases: practical guide to bioinformatics and data resources.

Andersen JN, Del Vecchio RL, Kannan N, Gergel J, Neuwald AF, Tonks NK.

Methods. 2005 Jan;35(1):90-114. Review.PMID: 15588990 [PubMed - indexed for MEDLINE]Related articles

Gapped alignment of protein sequence motifs through Monte Carlo optimization of a hidden Markov model.

Neuwald AF, Liu JS.

BMC Bioinformatics. 2004 Oct 25;5:157.PMID: 15504234 [PubMed - indexed for MEDLINE]Related articlesFree article

Evolutionary constraints associated with functional specificity of the CMGC protein kinases MAPK, CDK, GSK, SRPK, DYRK, and CK2alpha.

Kannan N, Neuwald AF.

Protein Sci. 2004 Aug;13(8):2059-77.PMID: 15273306 [PubMed - indexed for MEDLINE]Related articlesFree article

Differential contributions of condensin I and condensin II to mitotic chromosome architecture in vertebrate cells.

Ono T, Losada A, Hirano M, Myers MP, Neuwald AF, Hirano T.

Cell. 2003 Oct 3;115(1):109-21.PMID: 14532007 [PubMed - indexed for MEDLINE]Related articles

Evolutionary clues to DNA polymerase III beta clamp structural mechanisms.

Neuwald AF.

Nucleic Acids Res. 2003 Aug 1;31(15):4503-16.PMID: 12888511 [PubMed - indexed for MEDLINE]Related articlesFree article

Ran's C-terminal, basic patch, and nucleotide exchange mechanisms in light of a canonical structure for Rab, Rho, Ras, and Ran GTPases.

Neuwald AF, Kannan N, Poleksic A, Hata N, Liu JS.

Genome Res. 2003 Apr;13(4):673-92.PMID: 12671004 [PubMed - indexed for MEDLINE]Related articlesFree article

HEAT repeats associated with condensins, cohesins, and other complexes involved in chromosome-related functions.

Neuwald AF, Hirano T.

Genome Res. 2000 Oct;10(10):1445-52.PMID: 11042144 [PubMed - indexed for MEDLINE]Related articlesFree article

PSI-BLAST searches using hidden markov models of structural repeats: prediction of an unusual sliding DNA clamp and of beta-propellers in UV-damaged DNA-binding protein.

Neuwald AF, Poleksic A.

Nucleic Acids Res. 2000 Sep 15;28(18):3570-80.PMID: 10982878 [PubMed - indexed for MEDLINE]Related articlesFree article

The hexamerization domain of N-ethylmaleimide-sensitive factor: structural clues to chaperone function.

Neuwald AF.

Structure. 1999 Feb 15;7(2):R19-23. Review.PMID: 10368290 [PubMed - indexed for MEDLINE]Related articles

AAA+: A class of chaperone-like ATPases associated with the assembly, operation, and disassembly of protein complexes.

Neuwald AF, Aravind L, Spouge JL, Koonin EV.

Genome Res. 1999 Jan;9(1):27-43.PMID: 9927482 [PubMed - indexed for MEDLINE]Related articlesFree article