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Biophysical Characterization of a Disabled Double Mutant of Soybean Lipoxygenase: The "Undoing" of Precise Substrate Positioning Relative to Metal Cofactor and an Identified Dynamical Network.

Hu S, Offenbacher AR, Thompson EM, Gee CL, Wilcoxen J, Carr CAM, Prigozhin DM, Yang V, Alber T, Britt RD, Fraser JS, Klinman JP.

J Am Chem Soc. 2019 Jan 30;141(4):1555-1567. doi: 10.1021/jacs.8b10992. Epub 2019 Jan 15.


Biophysical Characterization of the Tandem FHA Domain Regulatory Module from the Mycobacterium tuberculosis ABC Transporter Rv1747.

Heinkel F, Shen L, Richard-Greenblatt M, Okon M, Bui JM, Gee CL, Gay LM, Alber T, Av-Gay Y, Gsponer J, McIntosh LP.

Structure. 2018 Jul 3;26(7):972-986.e6. doi: 10.1016/j.str.2018.04.018. Epub 2018 May 31.


Structural and Biophysical Characterization of the Mycobacterium tuberculosis Protein Rv0577, a Protein Associated with Neutral Red Staining of Virulent Tuberculosis Strains and Homologue of the Streptomyces coelicolor Protein KbpA.

Buchko GW, Echols N, Flynn EM, Ng HL, Stephenson S, Kim HB, Myler PJ, Terwilliger TC, Alber T, Kim CY.

Biochemistry. 2017 Aug 1;56(30):4015-4027. doi: 10.1021/acs.biochem.7b00511. Epub 2017 Jul 25.


Hydrogen-Deuterium Exchange of Lipoxygenase Uncovers a Relationship between Distal, Solvent Exposed Protein Motions and the Thermal Activation Barrier for Catalytic Proton-Coupled Electron Tunneling.

Offenbacher AR, Hu S, Poss EM, Carr CAM, Scouras AD, Prigozhin DM, Iavarone AT, Palla A, Alber T, Fraser JS, Klinman JP.

ACS Cent Sci. 2017 Jun 28;3(6):570-579. doi: 10.1021/acscentsci.7b00142. Epub 2017 Jun 9.


Structural and Genetic Analyses of the Mycobacterium tuberculosis Protein Kinase B Sensor Domain Identify a Potential Ligand-binding Site.

Prigozhin DM, Papavinasasundaram KG, Baer CE, Murphy KC, Moskaleva A, Chen TY, Alber T, Sassetti CM.

J Biol Chem. 2016 Oct 28;291(44):22961-22969. Epub 2016 Sep 6.


The energy landscape of adenylate kinase during catalysis.

Kerns SJ, Agafonov RV, Cho YJ, Pontiggia F, Otten R, Pachov DV, Kutter S, Phung LA, Murphy PN, Thai V, Alber T, Hagan MF, Kern D.

Nat Struct Mol Biol. 2015 Feb;22(2):124-31. doi: 10.1038/nsmb.2941. Epub 2015 Jan 12.


Subfamily-specific adaptations in the structures of two penicillin-binding proteins from Mycobacterium tuberculosis.

Prigozhin DM, Krieger IV, Huizar JP, Mavrici D, Waldo GS, Hung LW, Sacchettini JC, Terwilliger TC, Alber T.

PLoS One. 2014 Dec 31;9(12):e116249. doi: 10.1371/journal.pone.0116249. eCollection 2014.


Extremely elevated room-temperature kinetic isotope effects quantify the critical role of barrier width in enzymatic C-H activation.

Hu S, Sharma SC, Scouras AD, Soudackov AV, Carr CA, Hammes-Schiffer S, Alber T, Klinman JP.

J Am Chem Soc. 2014 Jun 11;136(23):8157-60. doi: 10.1021/ja502726s. Epub 2014 Jun 2.


Mycobacterium tuberculosis FtsX extracellular domain activates the peptidoglycan hydrolase, RipC.

Mavrici D, Marakalala MJ, Holton JM, Prigozhin DM, Gee CL, Zhang YJ, Rubin EJ, Alber T.

Proc Natl Acad Sci U S A. 2014 Jun 3;111(22):8037-42. doi: 10.1073/pnas.1321812111. Epub 2014 May 19.


AFF4 binding to Tat-P-TEFb indirectly stimulates TAR recognition of super elongation complexes at the HIV promoter.

Schulze-Gahmen U, Lu H, Zhou Q, Alber T.

Elife. 2014 Apr 24;3:e02375. doi: 10.7554/eLife.02375.


Molecular profiling of Mycobacterium tuberculosis identifies tuberculosinyl nucleoside products of the virulence-associated enzyme Rv3378c.

Layre E, Lee HJ, Young DC, Martinot AJ, Buter J, Minnaard AJ, Annand JW, Fortune SM, Snider BB, Matsunaga I, Rubin EJ, Alber T, Moody DB.

Proc Natl Acad Sci U S A. 2014 Feb 25;111(8):2978-83. doi: 10.1073/pnas.1315883111. Epub 2014 Feb 10.


Mycobacterium tuberculosis RpfE crystal structure reveals a positively charged catalytic cleft.

Mavrici D, Prigozhin DM, Alber T.

Protein Sci. 2014 Apr;23(4):481-7. doi: 10.1002/pro.2431.


AFF1 is a ubiquitous P-TEFb partner to enable Tat extraction of P-TEFb from 7SK snRNP and formation of SECs for HIV transactivation.

Lu H, Li Z, Xue Y, Schulze-Gahmen U, Johnson JR, Krogan NJ, Alber T, Zhou Q.

Proc Natl Acad Sci U S A. 2014 Jan 7;111(1):E15-24. doi: 10.1073/pnas.1318503111. Epub 2013 Dec 23.


Protein structural ensembles are revealed by redefining X-ray electron density noise.

Lang PT, Holton JM, Fraser JS, Alber T.

Proc Natl Acad Sci U S A. 2014 Jan 7;111(1):237-42. doi: 10.1073/pnas.1302823110. Epub 2013 Dec 20.


Osmosensory signaling in Mycobacterium tuberculosis mediated by a eukaryotic-like Ser/Thr protein kinase.

Hatzios SK, Baer CE, Rustad TR, Siegrist MS, Pang JM, Ortega C, Alber T, Grundner C, Sherman DR, Bertozzi CR.

Proc Natl Acad Sci U S A. 2013 Dec 24;110(52):E5069-77. doi: 10.1073/pnas.1321205110. Epub 2013 Dec 5.


Structural and biochemical analyses of Mycobacterium tuberculosis N-acetylmuramyl-L-alanine amidase Rv3717 point to a role in peptidoglycan fragment recycling.

Prigozhin DM, Mavrici D, Huizar JP, Vansell HJ, Alber T.

J Biol Chem. 2013 Nov 1;288(44):31549-55. doi: 10.1074/jbc.M113.510792. Epub 2013 Sep 9.


The AFF4 scaffold binds human P-TEFb adjacent to HIV Tat.

Schulze-Gahmen U, Upton H, Birnberg A, Bao K, Chou S, Krogan NJ, Zhou Q, Alber T.

Elife. 2013 Mar 5;2:e00327. doi: 10.7554/eLife.00327.


Protein complexes and proteolytic activation of the cell wall hydrolase RipA regulate septal resolution in mycobacteria.

Chao MC, Kieser KJ, Minami S, Mavrici D, Aldridge BB, Fortune SM, Alber T, Rubin EJ.

PLoS Pathog. 2013 Feb;9(2):e1003197. doi: 10.1371/journal.ppat.1003197. Epub 2013 Feb 28.


tRNA binding, structure, and localization of the human interferon-induced protein IFIT5.

Katibah GE, Lee HJ, Huizar JP, Vogan JM, Alber T, Collins K.

Mol Cell. 2013 Feb 21;49(4):743-50. doi: 10.1016/j.molcel.2012.12.015. Epub 2013 Jan 11.


HIV-1 Tat recruits transcription elongation factors dispersed along a flexible AFF4 scaffold.

Chou S, Upton H, Bao K, Schulze-Gahmen U, Samelson AJ, He N, Nowak A, Lu H, Krogan NJ, Zhou Q, Alber T.

Proc Natl Acad Sci U S A. 2013 Jan 8;110(2):E123-31. doi: 10.1073/pnas.1216971110. Epub 2012 Dec 18.


Structural basis for group B streptococcus pilus 1 sortases C regulation and specificity.

Cozzi R, Prigozhin D, Rosini R, Abate F, Bottomley MJ, Grandi G, Telford JL, Rinaudo CD, Maione D, Alber T.

PLoS One. 2012;7(11):e49048. doi: 10.1371/journal.pone.0049048. Epub 2012 Nov 8.


Cyclic AMP regulation of protein lysine acetylation in Mycobacterium tuberculosis.

Lee HJ, Lang PT, Fortune SM, Sassetti CM, Alber T.

Nat Struct Mol Biol. 2012 Aug;19(8):811-8. doi: 10.1038/nsmb.2318. Epub 2012 Jul 8.


Structure of the sensor domain of Mycobacterium tuberculosis PknH receptor kinase reveals a conserved binding cleft.

Cavazos A, Prigozhin DM, Alber T.

J Mol Biol. 2012 Sep 28;422(4):488-94. doi: 10.1016/j.jmb.2012.06.011. Epub 2012 Jun 20.


Macro-to-micro structural proteomics: native source proteins for high-throughput crystallization.

Totir M, Echols N, Nanao M, Gee CL, Moskaleva A, Gradia S, Iavarone AT, Berger JM, May AP, Zubieta C, Alber T.

PLoS One. 2012;7(2):e32498. doi: 10.1371/journal.pone.0032498. Epub 2012 Feb 29.


Ferritin protein nanocage ion channels: gating by N-terminal extensions.

Tosha T, Behera RK, Ng HL, Bhattasali O, Alber T, Theil EC.

J Biol Chem. 2012 Apr 13;287(16):13016-25. doi: 10.1074/jbc.M111.332734. Epub 2012 Feb 23.


A phosphorylated pseudokinase complex controls cell wall synthesis in mycobacteria.

Gee CL, Papavinasasundaram KG, Blair SR, Baer CE, Falick AM, King DS, Griffin JE, Venghatakrishnan H, Zukauskas A, Wei JR, Dhiman RK, Crick DC, Rubin EJ, Sassetti CM, Alber T.

Sci Signal. 2012 Jan 24;5(208):ra7. doi: 10.1126/scisignal.2002525.


Global landscape of HIV-human protein complexes.

Jäger S, Cimermancic P, Gulbahce N, Johnson JR, McGovern KE, Clarke SC, Shales M, Mercenne G, Pache L, Li K, Hernandez H, Jang GM, Roth SL, Akiva E, Marlett J, Stephens M, D'Orso I, Fernandes J, Fahey M, Mahon C, O'Donoghue AJ, Todorovic A, Morris JH, Maltby DA, Alber T, Cagney G, Bushman FD, Young JA, Chanda SK, Sundquist WI, Kortemme T, Hernandez RD, Craik CS, Burlingame A, Sali A, Frankel AD, Krogan NJ.

Nature. 2011 Dec 21;481(7381):365-70. doi: 10.1038/nature10719.


Accessing protein conformational ensembles using room-temperature X-ray crystallography.

Fraser JS, van den Bedem H, Samelson AJ, Lang PT, Holton JM, Echols N, Alber T.

Proc Natl Acad Sci U S A. 2011 Sep 27;108(39):16247-52. doi: 10.1073/pnas.1111325108. Epub 2011 Sep 14.


Human Polymerase-Associated Factor complex (PAFc) connects the Super Elongation Complex (SEC) to RNA polymerase II on chromatin.

He N, Chan CK, Sobhian B, Chou S, Xue Y, Liu M, Alber T, Benkirane M, Zhou Q.

Proc Natl Acad Sci U S A. 2011 Sep 6;108(36):E636-45. doi: 10.1073/pnas.1107107108. Epub 2011 Aug 22.


Hyaloperonospora arabidopsidis ATR1 effector is a repeat protein with distributed recognition surfaces.

Chou S, Krasileva KV, Holton JM, Steinbrenner AD, Alber T, Staskawicz BJ.

Proc Natl Acad Sci U S A. 2011 Aug 9;108(32):13323-8. doi: 10.1073/pnas.1109791108. Epub 2011 Jul 25.


Depletion of antibiotic targets has widely varying effects on growth.

Wei JR, Krishnamoorthy V, Murphy K, Kim JH, Schnappinger D, Alber T, Sassetti CM, Rhee KY, Rubin EJ.

Proc Natl Acad Sci U S A. 2011 Mar 8;108(10):4176-81. doi: 10.1073/pnas.1018301108. Epub 2011 Feb 22.


Solution structure of the guanine nucleotide-binding STAS domain of SLC26-related SulP protein Rv1739c from Mycobacterium tuberculosis.

Sharma AK, Ye L, Baer CE, Shanmugasundaram K, Alber T, Alper SL, Rigby AC.

J Biol Chem. 2011 Mar 11;286(10):8534-44. doi: 10.1074/jbc.M110.165449. Epub 2010 Dec 29.


Allosteric activation mechanism of the Mycobacterium tuberculosis receptor Ser/Thr protein kinase, PknB.

Lombana TN, Echols N, Good MC, Thomsen ND, Ng HL, Greenstein AE, Falick AM, King DS, Alber T.

Structure. 2010 Dec 8;18(12):1667-77. doi: 10.1016/j.str.2010.09.019.


Moving metal ions through ferritin-protein nanocages from three-fold pores to catalytic sites.

Tosha T, Ng HL, Bhattasali O, Alber T, Theil EC.

J Am Chem Soc. 2010 Oct 20;132(41):14562-9. doi: 10.1021/ja105583d.


Purification and characterization of HIV-human protein complexes.

Jäger S, Gulbahce N, Cimermancic P, Kane J, He N, Chou S, D'Orso I, Fernandes J, Jang G, Frankel AD, Alber T, Zhou Q, Krogan NJ.

Methods. 2011 Jan;53(1):13-9. doi: 10.1016/j.ymeth.2010.08.007. Epub 2010 Aug 12. Review.


Diterpene production in Mycobacterium tuberculosis.

Prach L, Kirby J, Keasling JD, Alber T.

FEBS J. 2010 Sep;277(17):3588-95. doi: 10.1111/j.1742-4658.2010.07767.x. Epub 2010 Jul 31.


Automated electron-density sampling reveals widespread conformational polymorphism in proteins.

Lang PT, Ng HL, Fraser JS, Corn JE, Echols N, Sales M, Holton JM, Alber T.

Protein Sci. 2010 Jul;19(7):1420-31. doi: 10.1002/pro.423.


HIV-1 Tat and host AFF4 recruit two transcription elongation factors into a bifunctional complex for coordinated activation of HIV-1 transcription.

He N, Liu M, Hsu J, Xue Y, Chou S, Burlingame A, Krogan NJ, Alber T, Zhou Q.

Mol Cell. 2010 May 14;38(3):428-38. doi: 10.1016/j.molcel.2010.04.013.


The Trypanosoma brucei life cycle switch TbPTP1 is structurally conserved and dephosphorylates the nucleolar protein NOPP44/46.

Chou S, Jensen BC, Parsons M, Alber T, Grundner C.

J Biol Chem. 2010 Jul 16;285(29):22075-81. doi: 10.1074/jbc.M110.108860. Epub 2010 May 5.


Dynamic active-site protection by the M. tuberculosis protein tyrosine phosphatase PtpB lid domain.

Flynn EM, Hanson JA, Alber T, Yang H.

J Am Chem Soc. 2010 Apr 7;132(13):4772-80. doi: 10.1021/ja909968n.


Hidden alternative structures of proline isomerase essential for catalysis.

Fraser JS, Clarkson MW, Degnan SC, Erion R, Kern D, Alber T.

Nature. 2009 Dec 3;462(7273):669-73. doi: 10.1038/nature08615.


Autofluorescent proteins with excitation in the optical window for intravital imaging in mammals.

Lin MZ, McKeown MR, Ng HL, Aguilera TA, Shaner NC, Campbell RE, Adams SR, Gross LA, Ma W, Alber T, Tsien RY.

Chem Biol. 2009 Nov 25;16(11):1169-79. doi: 10.1016/j.chembiol.2009.10.009.


Signaling mechanisms of the Mycobacterium tuberculosis receptor Ser/Thr protein kinases.

Alber T.

Curr Opin Struct Biol. 2009 Dec;19(6):650-7. doi: 10.1016/ Epub 2009 Nov 14. Review.


Fragment-based discovery of selective inhibitors of the Mycobacterium tuberculosis protein tyrosine phosphatase PtpA.

Rawls KA, Lang PT, Takeuchi J, Imamura S, Baguley TD, Grundner C, Alber T, Ellman JA.

Bioorg Med Chem Lett. 2009 Dec 15;19(24):6851-4. doi: 10.1016/j.bmcl.2009.10.090. Epub 2009 Oct 25.



Alber T.

Ugeskr Laeger. 2009 Sep 14;171(38):2765; author reply 2765. Danish. No abstract available.


Interdomain communication in the Mycobacterium tuberculosis environmental phosphatase Rv1364c.

Greenstein AE, Hammel M, Cavazos A, Alber T.

J Biol Chem. 2009 Oct 23;284(43):29828-35. doi: 10.1074/jbc.M109.056168. Epub 2009 Aug 20.


Discretization error when using finite element models: analysis and evaluation of an underestimated problem.

Schmidt H, Alber T, Wehner T, Blakytny R, Wilke HJ.

J Biomech. 2009 Aug 25;42(12):1926-34. doi: 10.1016/j.jbiomech.2009.05.005. Epub 2009 Jun 5.


Auto-activation mechanism of the Mycobacterium tuberculosis PknB receptor Ser/Thr kinase.

Mieczkowski C, Iavarone AT, Alber T.

EMBO J. 2008 Dec 3;27(23):3186-97. doi: 10.1038/emboj.2008.236. Epub 2008 Nov 13.


Protein tyrosine phosphatase PtpA is not required for Mycobacterium tuberculosis growth in mice.

Grundner C, Cox JS, Alber T.

FEMS Microbiol Lett. 2008 Oct;287(2):181-4. doi: 10.1111/j.1574-6968.2008.01309.x. Epub 2008 Aug 22.

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