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Items: 32

1.

Tracing the evolution of novel features of human Toll-like receptor 4.

Anderson JA, Loes AN, Waddell GL, Harms MJ.

Protein Sci. 2019 Jul;28(7):1350-1358. doi: 10.1002/pro.3644. Epub 2019 Jun 3.

PMID:
31075178
2.

Mature Human White Adipocytes Cultured under Membranes Maintain Identity, Function, and Can Transdifferentiate into Brown-like Adipocytes.

Harms MJ, Li Q, Lee S, Zhang C, Kull B, Hallen S, Thorell A, Alexandersson I, Hagberg CE, Peng XR, Mardinoglu A, Spalding KL, Boucher J.

Cell Rep. 2019 Apr 2;27(1):213-225.e5. doi: 10.1016/j.celrep.2019.03.026.

3.

Flow Cytometry of Mouse and Human Adipocytes for the Analysis of Browning and Cellular Heterogeneity.

Hagberg CE, Li Q, Kutschke M, Bhowmick D, Kiss E, Shabalina IG, Harms MJ, Shilkova O, Kozina V, Nedergaard J, Boucher J, Thorell A, Spalding KL.

Cell Rep. 2018 Sep 4;24(10):2746-2756.e5. doi: 10.1016/j.celrep.2018.08.006.

4.

Enzymes emerge by upcycling.

Harms MJ.

Nat Chem Biol. 2018 Jun;14(6):526-527. doi: 10.1038/s41589-018-0064-x. No abstract available.

PMID:
29769735
5.

pytc: Open-Source Python Software for Global Analyses of Isothermal Titration Calorimetry Data.

Duvvuri H, Wheeler LC, Harms MJ.

Biochemistry. 2018 May 8;57(18):2578-2583. doi: 10.1021/acs.biochem.7b01264. Epub 2018 Apr 18.

6.

Coevolution of the Toll-Like Receptor 4 Complex with Calgranulins and Lipopolysaccharide.

Loes AN, Bridgham JT, Harms MJ.

Front Immunol. 2018 Feb 21;9:304. doi: 10.3389/fimmu.2018.00304. eCollection 2018.

7.

Conservation of Specificity in Two Low-Specificity Proteins.

Wheeler LC, Anderson JA, Morrison AJ, Wong CE, Harms MJ.

Biochemistry. 2018 Feb 6;57(5):684-695. doi: 10.1021/acs.biochem.7b01086. Epub 2017 Dec 29.

8.

Human S100A5 binds Ca2+ and Cu2+ independently.

Wheeler LC, Harms MJ.

BMC Biophys. 2017 Nov 22;10:8. doi: 10.1186/s13628-017-0040-y. eCollection 2017.

9.

Molecular ensembles make evolution unpredictable.

Sailer ZR, Harms MJ.

Proc Natl Acad Sci U S A. 2017 Nov 7;114(45):11938-11943. doi: 10.1073/pnas.1711927114. Epub 2017 Oct 23.

10.

High-order epistasis shapes evolutionary trajectories.

Sailer ZR, Harms MJ.

PLoS Comput Biol. 2017 May 15;13(5):e1005541. doi: 10.1371/journal.pcbi.1005541. eCollection 2017 May.

11.

EBF2 transcriptionally regulates brown adipogenesis via the histone reader DPF3 and the BAF chromatin remodeling complex.

Shapira SN, Lim HW, Rajakumari S, Sakers AP, Ishibashi J, Harms MJ, Won KJ, Seale P.

Genes Dev. 2017 Apr 1;31(7):660-673. doi: 10.1101/gad.294405.116. Epub 2017 Apr 20.

12.

PRDM16 represses the type I interferon response in adipocytes to promote mitochondrial and thermogenic programing.

Kissig M, Ishibashi J, Harms MJ, Lim HW, Stine RR, Won KJ, Seale P.

EMBO J. 2017 Jun 1;36(11):1528-1542. doi: 10.15252/embj.201695588. Epub 2017 Apr 13.

13.

Detecting High-Order Epistasis in Nonlinear Genotype-Phenotype Maps.

Sailer ZR, Harms MJ.

Genetics. 2017 Mar;205(3):1079-1088. doi: 10.1534/genetics.116.195214. Epub 2017 Jan 18.

14.

Evolutionary trend toward kinetic stability in the folding trajectory of RNases H.

Lim SA, Hart KM, Harms MJ, Marqusee S.

Proc Natl Acad Sci U S A. 2016 Nov 15;113(46):13045-13050. Epub 2016 Oct 31.

15.

Robustness of Reconstructed Ancestral Protein Functions to Statistical Uncertainty.

Eick GN, Bridgham JT, Anderson DP, Harms MJ, Thornton JW.

Mol Biol Evol. 2017 Feb 1;34(2):247-261. doi: 10.1093/molbev/msw223.

16.

Multiple Evolutionary Origins of Ubiquitous Cu2+ and Zn2+ Binding in the S100 Protein Family.

Wheeler LC, Donor MT, Prell JS, Harms MJ.

PLoS One. 2016 Oct 20;11(10):e0164740. doi: 10.1371/journal.pone.0164740. eCollection 2016.

17.

The thermostability and specificity of ancient proteins.

Wheeler LC, Lim SA, Marqusee S, Harms MJ.

Curr Opin Struct Biol. 2016 Jun;38:37-43. doi: 10.1016/j.sbi.2016.05.015. Epub 2016 Jun 9. Review.

18.

PRDM16 binds MED1 and controls chromatin architecture to determine a brown fat transcriptional program.

Harms MJ, Lim HW, Ho Y, Shapira SN, Ishibashi J, Rajakumari S, Steger DJ, Lazar MA, Won KJ, Seale P.

Genes Dev. 2015 Feb 1;29(3):298-307. doi: 10.1101/gad.252734.114.

19.

Thermodynamic system drift in protein evolution.

Hart KM, Harms MJ, Schmidt BH, Elya C, Thornton JW, Marqusee S.

PLoS Biol. 2014 Nov 11;12(11):e1001994. doi: 10.1371/journal.pbio.1001994. eCollection 2014 Nov. Erratum in: PLoS Biol. 2015 Feb;13(2):e1002091.

20.

Historical contingency and its biophysical basis in glucocorticoid receptor evolution.

Harms MJ, Thornton JW.

Nature. 2014 Aug 14;512(7513):203-7. doi: 10.1038/nature13410. Epub 2014 Jun 15.

21.

Prdm16 is required for the maintenance of brown adipocyte identity and function in adult mice.

Harms MJ, Ishibashi J, Wang W, Lim HW, Goyama S, Sato T, Kurokawa M, Won KJ, Seale P.

Cell Metab. 2014 Apr 1;19(4):593-604. doi: 10.1016/j.cmet.2014.03.007.

22.

Evolutionary biochemistry: revealing the historical and physical causes of protein properties.

Harms MJ, Thornton JW.

Nat Rev Genet. 2013 Aug;14(8):559-71. doi: 10.1038/nrg3540. Review.

23.

Biophysical mechanisms for large-effect mutations in the evolution of steroid hormone receptors.

Harms MJ, Eick GN, Goswami D, Colucci JK, Griffin PR, Ortlund EA, Thornton JW.

Proc Natl Acad Sci U S A. 2013 Jul 9;110(28):11475-80. doi: 10.1073/pnas.1303930110. Epub 2013 Jun 24.

24.

Resurrection of an Urbilaterian U1A/U2B″/SNF protein.

Williams SG, Harms MJ, Hall KB.

J Mol Biol. 2013 Oct 23;425(20):3846-62. doi: 10.1016/j.jmb.2013.05.031. Epub 2013 Jun 22.

25.

Evolution of minimal specificity and promiscuity in steroid hormone receptors.

Eick GN, Colucci JK, Harms MJ, Ortlund EA, Thornton JW.

PLoS Genet. 2012;8(11):e1003072. doi: 10.1371/journal.pgen.1003072. Epub 2012 Nov 15.

26.

Arginine residues at internal positions in a protein are always charged.

Harms MJ, Schlessman JL, Sue GR, García-Moreno B.

Proc Natl Acad Sci U S A. 2011 Nov 22;108(47):18954-9. doi: 10.1073/pnas.1104808108. Epub 2011 Nov 11.

27.

ApoE suppresses atherosclerosis by reducing lipid accumulation in circulating monocytes and the expression of inflammatory molecules on monocytes and vascular endothelium.

Gaudreault N, Kumar N, Posada JM, Stephens KB, Reyes de Mochel NS, Eberlé D, Olivas VR, Kim RY, Harms MJ, Johnson S, Messina LM, Rapp JH, Raffai RL.

Arterioscler Thromb Vasc Biol. 2012 Feb;32(2):264-72. doi: 10.1161/ATVBAHA.111.238964. Epub 2011 Nov 3.

28.

Protein evolution by molecular tinkering: diversification of the nuclear receptor superfamily from a ligand-dependent ancestor.

Bridgham JT, Eick GN, Larroux C, Deshpande K, Harms MJ, Gauthier ME, Ortlund EA, Degnan BM, Thornton JW.

PLoS Biol. 2010 Oct 5;8(10). pii: e1000497. doi: 10.1371/journal.pbio.1000497.

29.

Analyzing protein structure and function using ancestral gene reconstruction.

Harms MJ, Thornton JW.

Curr Opin Struct Biol. 2010 Jun;20(3):360-6. doi: 10.1016/j.sbi.2010.03.005. Epub 2010 Apr 21. Review.

30.

The pK(a) values of acidic and basic residues buried at the same internal location in a protein are governed by different factors.

Harms MJ, Castañeda CA, Schlessman JL, Sue GR, Isom DG, Cannon BR, García-Moreno E B.

J Mol Biol. 2009 May 29;389(1):34-47. doi: 10.1016/j.jmb.2009.03.039. Epub 2009 Mar 24.

31.

A buried lysine that titrates with a normal pKa: role of conformational flexibility at the protein-water interface as a determinant of pKa values.

Harms MJ, Schlessman JL, Chimenti MS, Sue GR, Damjanović A, García-Moreno B.

Protein Sci. 2008 May;17(5):833-45. doi: 10.1110/ps.073397708. Epub 2008 Mar 27.

32.

Laser light-scattering evidence for an altered association of beta B1-crystallin deamidated in the connecting peptide.

Harms MJ, Wilmarth PA, Kapfer DM, Steel EA, David LL, Bächinger HP, Lampi KJ.

Protein Sci. 2004 Mar;13(3):678-86.

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