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Sean D. Mooney1,2,*, Mike Hsin-Ping Liang1, Rob DeConde1 andRuss B. Altman1,*DOI:&10.1002/prot.20661
Proteins: Structure, Function, and Bioinformatics pages 741&747, Author Information1Department of Genetics, Stanford University, Stanford, California2Center for Computational Biology and Bioinformatics, Department of Medical and Molecular Genetics, Indiana University School of Medicine, Indianapolis, IndianaEmail: Sean D. Mooney (sdmooney@iupui.edu), Russ B. Altman (russ.altman@stanford.edu)*Center for Computational Biology and Bioinformatics, Department of Medical and Molecular Genetics, Indiana University School of Medicine, Indianapolis, IN 46202Publication HistoryIssue published online: 17 NOV 2005Article first published online: 21 OCT 2005Manuscript Accepted: 12 MAY 2005Manuscript Received: 8 NOV 2004
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Bernard Collins1 andIan A. Wilson1,2,*DOI:&10.1002/prot.24616
Proteins: Structure, Function, and Bioinformatics pages , Author Information1Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, California2Skaggs Institute for Chemical Biology, The Scripps Research Institute, La Jolla, California*Correspondence to: Ian A. W Department of Integrative Structural and Computational Biology, BCC206, 10550 N. Torrey Pines Rd., La Jolla, CA 92037. E-mail: Publication HistoryIssue published online: 24 SEP 2014Article first published online: 16 JUN 2014Accepted manuscript online: 30 MAY AM ESTManuscript Accepted: 20 MAY 2014Manuscript Revised: 14 MAY 2014Manuscript Received: 5 MAY 2014
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Toll-TLR;TLR9;DNA;leucine-LRRABSTRACTToll-like receptors (TLRs) are important pattern recognition receptors that function in innate immunity. Elucidating the structure and signaling mechanisms of TLR9, a sensor of foreign and endogenous DNA, is essential for understanding its key role in immunity against microbial pathogens as well as in autoimmunity. Abundant evidence suggests that the TLR9-CTD (C-terminal domain) by itself is capable of DNA binding and signaling. The crystal structure of unliganded mouse TLR9-CTD is presented. TLR9-CTD exhibits one unique feature, a cluster of stacked aromatic and arginine side chains on its concave face. Overall, its structure is most related to the TLR8-CTD, suggesting a similar mode of ligand binding and signaling. Proteins 4&2878. & 2014 Wiley Periodicals, Inc.JOURNAL MENUFIND ISSUES
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Proteins: Structure, Function, and BioinformaticsEdited By: Bertrand Garcia-MorenoImpact Factor: 2.921ISI Journal Citation Reports & Ranking:
(Biophysics); 139/291 (Biochemistry & Molecular Biology)Online ISSN:
Aims and Scope
PROTEINS : Structure, Function, and Bioinformatics
publishes original reports of significant experimental and analytic
research in all areas of protein research: structure, function,
computation, genetics, and design. The journal encourages reports
that present new experimental or computational approaches for
interpreting and understanding data from biophysical chemistry,
structural studies of proteins and macromolecular assemblies,
alterations of protein structure and function engineered through
techniques of molecular biology and genetics, functional analyses
under physiologic conditions, as well as the interactions of
proteins with receptors, nucleic acids, or other specific ligands
or substrates. Research in protein and peptide biochemistry
directed toward synthesizing or characterizing molecules that
simulate aspects of the activity of proteins, or that act as
inhibitors of protein function, is also within the scope of
PROTEINS. In addition to full-length reports, short
communications (usually not more than 4 printed pages) and
prediction reports are welcome. Reviews are typically by
authors are encouraged to submit proposed topics for
consideration.
Proteins is bringing web-based technology to bear to
speed and simplify the entire publication process. Proteins now
offers online submission and peer review and encourages electronic
submission of manuscripts, which expedites the review process. In
addition, individual articles are published online as rapidly as
possible after acceptance. Please see the Author Instructions for
Proteins is pleased to announce that online access to the
full-text content of all Structure Notes is
commencing 2003. Structure Notes, first launched in 1999, are
one-to-two-page articles describing a novel protein structure of
unknown function and/or those with recurring topology. Structure
Notes are published within three months of receipt at the
Proteins office by expediting all stages of editorial review
and production. Please see the Author Instructions for details.
Readership
Protein scientists & biochemists & biophysicists & cell and
molecular biologists & biomolecular chemists & computational
chemists & crystallographers & structural biologists &
biotechnologists & pharmaceutical chemists
proteins, structural genomics, x-ray crystallography, molecular
modeling, binding, CASP, structure prediction, bioinformatics,
docking, thermodynamics, protein structure, molecular dynamics,
journal, online journal, Wiley Online Library
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Jason A. Wallace, Yuhang Wang, Chuanyin Shi, Kevin J. Pastoor, Bao-Linh Nguyen, Kai Xia andJana K. Shen*DOI:&10.1002/prot.23080
Proteins: Structure, Function, and BioinformaticsSpecial Issue: Protein Electrostatics Calculations: Critical Assessment of Progress and Problems pages , Author InformationDepartment of Chemistry and Biochemistry, University of Oklahoma, Norman, Oklahoma 73019Email: Jana K. Shen (jana.k.shen@ou.edu)*Department of Chemistry and Biochemistry, University of Oklahoma, Norman, OK 73019Publication HistoryIssue published online: 10 NOV 2011Article first published online: 11 JUL 2011Accepted manuscript online: 17 MAY PM ESTManuscript Accepted: 4 MAY 2011Manuscript Revised: 23 APR 2011Manuscript Received: 11 JAN 2011
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pr pKaimplicit-Poisson-Bprotein mutationsAbstractProton uptake or release controls many important biological processes, such as energy transduction, virus replication, and catalysis. Accurate pKa prediction informs about proton pathways, thereby revealing detailed acid-base mechanisms. Physics-based methods in the framework of molecular dynamics simulations not only offer pKa predictions but also inform about the physical origins of pKa shifts and provide details of ionization-induced conformational relaxation and large-scale transitions. One such method is the recently developed continuous constant pH molecular dynamics (CPHMD) method, which has been shown to be an accurate and robust pKa prediction tool for naturally occurring titratable residues. To further examine the accuracy and limitations of CPHMD, we blindly predicted the pKa values for 87 titratable residues introduced in various hydrophobic regions of staphylococcal nuclease and variants. The predictions gave a root-mean-square deviation of 1.69 pK units from experiment, and there were only two pKa's with errors greater than 3.5 pK units. Analysis of the conformational fluctuation of titrating side-chains in the context of the errors of calculated pKa values indicate that explicit treatment of conformational flexibility and the associated dielectric relaxation gives CPHMD a distinct advantage. Analysis of the sources of errors suggests that more accurate pKa predictions can be obtained for the most deeply buried residues by improving the accuracy in calculating desolvation energies. Furthermore, it is found that the generalized Born implicit-solvent model underlying the current CPHMD implementation slightly distorts the local conformational environment such that the inclusion of an explicit-solvent representation may offer improvement of accuracy. Proteins 2011. & 2011 Wiley-Liss, Inc.