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Items: 17

1.

Clusters of isoleucine, leucine, and valine side chains define cores of stability in high-energy states of globular proteins: Sequence determinants of structure and stability.

Kathuria SV, Chan YH, Nobrega RP, Özen A, Matthews CR.

Protein Sci. 2016 Mar;25(3):662-75. doi: 10.1002/pro.2860. Epub 2015 Dec 26.

2.

Design of symmetric TIM barrel proteins from first principles.

Nagarajan D, Deka G, Rao M.

BMC Biochem. 2015 Aug 12;16:18. doi: 10.1186/s12858-015-0047-4.

3.

Folding of the RNA recognition motif (RRM) domains of the amyotrophic lateral sclerosis (ALS)-linked protein TDP-43 reveals an intermediate state.

Mackness BC, Tran MT, McClain SP, Matthews CR, Zitzewitz JA.

J Biol Chem. 2014 Mar 21;289(12):8264-76. doi: 10.1074/jbc.M113.542779. Epub 2014 Feb 4.

4.

Octarellin VI: using rosetta to design a putative artificial (β/α)8 protein.

Figueroa M, Oliveira N, Lejeune A, Kaufmann KW, Dorr BM, Matagne A, Martial JA, Meiler J, Van de Weerdt C.

PLoS One. 2013 Aug 19;8(8):e71858. doi: 10.1371/journal.pone.0071858. eCollection 2013 Aug 19.

5.

Clusters of branched aliphatic side chains serve as cores of stability in the native state of the HisF TIM barrel protein.

Gangadhara BN, Laine JM, Kathuria SV, Massi F, Matthews CR.

J Mol Biol. 2013 Mar 25;425(6):1065-81. doi: 10.1016/j.jmb.2013.01.002. Epub 2013 Jan 16.

6.

Protein dynamics governed by interfaces of high polarity and low packing density.

Angarica VE, Sancho J.

PLoS One. 2012;7(10):e48212. doi: 10.1371/journal.pone.0048212. Epub 2012 Oct 26. Erratum in: PLoS One. 2013;8(5). doi:10.1371/annotation/ba19c84a-4f59-46de-88fb-04a5f8222585.

7.

CLIPS-1D: analysis of multiple sequence alignments to deduce for residue-positions a role in catalysis, ligand-binding, or protein structure.

Janda JO, Busch M, Kück F, Porfenenko M, Merkl R.

BMC Bioinformatics. 2012 Apr 5;13:55. doi: 10.1186/1471-2105-13-55.

8.

What lessons can be learned from studying the folding of homologous proteins?

Nickson AA, Clarke J.

Methods. 2010 Sep;52(1):38-50. doi: 10.1016/j.ymeth.2010.06.003. Epub 2010 Jun 4. Review.

9.

Topological frustration in beta alpha-repeat proteins: sequence diversity modulates the conserved folding mechanisms of alpha/beta/alpha sandwich proteins.

Hills RD Jr, Kathuria SV, Wallace LA, Day IJ, Brooks CL 3rd, Matthews CR.

J Mol Biol. 2010 Apr 30;398(2):332-50. doi: 10.1016/j.jmb.2010.03.001. Epub 2010 Mar 11.

10.

Betaalpha-hairpin clamps brace betaalphabeta modules and can make substantive contributions to the stability of TIM barrel proteins.

Yang X, Kathuria SV, Vadrevu R, Matthews CR.

PLoS One. 2009 Sep 29;4(9):e7179. doi: 10.1371/journal.pone.0007179.

11.

Relative stabilities of conserved and non-conserved structures in the OB-fold superfamily.

Guardino KM, Sheftic SR, Slattery RE, Alexandrescu AT.

Int J Mol Sci. 2009 May 22;10(5):2412-30. doi: 10.3390/ijms10052412.

12.

Steroid and protein ligand binding to cytochrome P450 46A1 as assessed by hydrogen-deuterium exchange and mass spectrometry.

Liao WL, Dodder NG, Mast N, Pikuleva IA, Turko IV.

Biochemistry. 2009 May 19;48(19):4150-8. doi: 10.1021/bi900168m.

13.
14.

The foldon substructure of staphylococcal nuclease.

Bédard S, Mayne LC, Peterson RW, Wand AJ, Englander SW.

J Mol Biol. 2008 Feb 29;376(4):1142-54. doi: 10.1016/j.jmb.2007.12.020. Epub 2007 Dec 15.

15.

Repeat-protein folding: new insights into origins of cooperativity, stability, and topology.

Kloss E, Courtemanche N, Barrick D.

Arch Biochem Biophys. 2008 Jan 1;469(1):83-99. Epub 2007 Sep 15. Review.

16.
17.

Partially folded states of staphylococcal nuclease highlight the conserved structural hierarchy of OB-fold proteins.

Watson E, Matousek WM, Irimies EL, Alexandrescu AT.

Biochemistry. 2007 Aug 21;46(33):9484-94. Epub 2007 Jul 28.

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