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Thomas Alber

Research Profile

Concepts & Ideas

Genes & Molecular Sequences

Amino Acid Sequences

Procedures

X Ray Crystallography

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Publications

TOP 3
James S Fraser; James M Holton; P Therese Lang; Avi J Samelson; Henry van den Bedem; Nathaniel Echols; Thomas Alber
Accessing protein conformational ensembles using room-temperature X-ray crystallography.
Seemay Chou; James M Holton; Ksenia V Krasileva; Thomas Alber; Adam D Steinbrenner; Brian J Staskawicz
Hyaloperonospora arabidopsidis ATR1 effector is a repeat protein with distributed recognition surfaces.
T Noelle Lombana; Nathaniel Echols; Matthew C Good; Nathan D Thomsen; Ho Leung Ng; Andrew E Greenstein; Arnold M Falick; David S King; Thomas Alber
Allosteric activation mechanism of the Mycobacterium tuberculosis receptor Ser/Thr protein kinase, PknB.

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All Publications

2011: James S Fraser; James M Holton; P Therese Lang; Avi J Samelson; Henry van den Bedem; Nathaniel Echols; Thomas Alber
Accessing protein conformational ensembles using room-temperature X-ray crystallography.
Proceedings of the National Academy of Sciences of the United States of America 2011;108(39):16247-52.
2011: Seemay Chou; James M Holton; Ksenia V Krasileva; Thomas Alber; Adam D Steinbrenner; Brian J Staskawicz
Hyaloperonospora arabidopsidis ATR1 effector is a repeat protein with distributed recognition surfaces.
Proceedings of the National Academy of Sciences of the United States of America 2011;108(32):13323-8.
2010: T Noelle Lombana; Nathaniel Echols; Matthew C Good; Nathan D Thomsen; Ho Leung Ng; Andrew E Greenstein; Arnold M Falick; David S King; Thomas Alber
Allosteric activation mechanism of the Mycobacterium tuberculosis receptor Ser/Thr protein kinase, PknB.
Structure (London, England : 1993) 2010;18(12):1667-77.
2010: Takehiko Tosha; Ho-Leung Ng; Onita Bhattasali; Thomas Alber; Elizabeth C Theil
Moving metal ions through ferritin-protein nanocages from three-fold pores to catalytic sites.
Journal of the American Chemical Society 2010;132(41):14562-9.
2010: Seemay Chou; Bryan C Jensen; Marilyn Parsons; Thomas Alber; Christoph Grundner
The Trypanosoma brucei life cycle switch TbPTP1 is structurally conserved and dephosphorylates the nucleolar protein NOPP44/46.
The Journal of biological chemistry 2010;285(29):22075-81.
2010: P Therese Lang; Ho-Leung Ng; James S Fraser; Jacob E Corn; Nathaniel Echols; Mark Sales; James M Holton; Thomas Alber
Automated electron-density sampling reveals widespread conformational polymorphism in proteins.
Protein science : a publication of the Protein Society 2010;19(7):1420-31.
2009: Katherine A Rawls; P Therese Lang; Jun Takeuchi; Shinichi Imamura; Tyler D Baguley; Christoph Grundner; Thomas Alber; Jonathan A Ellman
Fragment-based discovery of selective inhibitors of the Mycobacterium tuberculosis protein tyrosine phosphatase PtpA.
Bioorganic & medicinal chemistry letters 2009;19(24):6851-4.
2009: James S Fraser; Michael W Clarkson; Sheena C Degnan; Renske Erion; Dorothee Kern; Thomas Alber
Hidden alternative structures of proline isomerase essential for catalysis.
Nature 2009;462(7273):669-73.
2009: Andrew E Greenstein; Michal Hammel; Alexandra Cavazos; Thomas Alber
Interdomain communication in the Mycobacterium tuberculosis environmental phosphatase Rv1364c.
The Journal of biological chemistry 2009;284(43):29828-35.
2008: Carl Mieczkowski; Anthony T Iavarone; Thomas Alber
Auto-activation mechanism of the Mycobacterium tuberculosis PknB receptor Ser/Thr kinase.
The EMBO journal 2008;27(23):3186-97.
2008: Patrick Barth; Allyn J Schoeffler; Thomas Alber
Targeting metastable coiled-coil domains by computational design.
Journal of the American Chemical Society 2008;130(36):12038-44.
2008: Aurelie Bertin; Michael A McMurray; Patricia Grob; Sang-Shin Park; Galo Garcia; Insiyyah Patanwala; Ho Leung Ng; Thomas Alber; Jeremy Thorner; Eva Nogales
Saccharomyces cerevisiae septins: supramolecular organization of heterooligomers and the mechanism of filament assembly.
Proceedings of the National Academy of Sciences of the United States of America 2008;105(24):8274-9.
2007: Mark Sales; Joseph J Plecs; James M Holton; Thomas Alber
Structure of a designed, right-handed coiled-coil tetramer containing all biological amino acids.
Protein science : a publication of the Protein Society 2007;16(10):2224-32.
2007: Matthew B Soellner; Katherine A Rawls; Christoph Grundner; Thomas Alber; Jonathan A Ellman
Fragment-based substrate activity screening method for the identification of potent inhibitors of the Mycobacterium tuberculosis phosphatase PtpB.
Journal of the American Chemical Society 2007;129(31):9613-5.
2007: James S Fraser; John P Merlie; Nathaniel Echols; Shellie R Weisfield; Tâm Mignot; David E Wemmer; David R Zusman; Thomas Alber
An atypical receiver domain controls the dynamic polar localization of the Myxococcus xanthus social motility protein FrzS.
Molecular microbiology 2007;65(2):319-32.
2007: A C Murillo; H Y Li; Thomas Alber; Edward N Baker; James M Berger; Leonid T Cherney; M M Cherney; Yoon Song Cho; David Eisenberg; Craig Garen; Celia W Goulding; Li-Wei Hung; Thomas R Ioerger; William R. Jacobs Jr.; Michael N G James; C Kim; I Krieger; J S Lott; R Sankaranarayanan; Brent W Segelke; Thomas C Terwilliger; F Wang; S Wang; James C Sacchettini
High throughput crystallography of TB drug targets.
Infectious disorders drug targets 2007;7(2):127-39.
2007: Jason Cellitti; Manuel Llinas; Nathaniel Echols; Elizabeth A Shank; Blake Gillespie; Ester Kwon; Scott M Crowder; Frederick W Dahlquist; Thomas Alber; Susan Marqusee
Exploring subdomain cooperativity in T4 lysozyme I: structural and energetic studies of a circular permutant and protein fragment.
Protein science : a publication of the Protein Society 2007;16(5):842-51.
2007: Andrew E Greenstein; Nathaniel Echols; T Noelle Lombana; David S King; Thomas Alber
Allosteric activation by dimerization of the PknD receptor Ser/Thr protein kinase from Mycobacterium tuberculosis.
The Journal of biological chemistry 2007;282(15):11427-35.
2007: Christoph Grundner; Dominique Perrin; Rob Hooft van Huijsduijnen; Dominique Swinnen; Jérome Gonzalez; Christine L Gee; Timothy Wells; Thomas Alber
Structural basis for selective inhibition of Mycobacterium tuberculosis protein tyrosine phosphatase PtpB.
Structure (London, England : 1993) 2007;15(4):499-509.
2007: Andrew E Greenstein; Jason A MacGurn; Christina E Baer; Arnold M Falick; Jeffery S Cox; Thomas Alber
M. tuberculosis Ser/Thr protein kinase D phosphorylates an anti-anti-sigma factor homolog.
PLoS pathogens 2007;3(4):e49.
2007: P Barth; Thomas Alber; Pehr B Harbury
Accurate, conformation-dependent predictions of solvent effects on protein ionization constants.
Proceedings of the National Academy of Sciences of the United States of America 2007;104(12):4898-903.
2006: Laurie M Gay; Ho Leung Ng; Thomas Alber
A conserved dimer and global conformational changes in the structure of apo-PknE Ser/Thr protein kinase from Mycobacterium tuberculosis.
Journal of molecular biology 2006;360(2):409-20.
2005: Christoph Grundner; Ho Leung Ng; Thomas Alber
Mycobacterium tuberculosis protein tyrosine phosphatase PtpB structure reveals a diverged fold and a buried active site.
Structure (London, England : 1993) 2005;13(11):1625-34.
2005: Christoph Grundner; Laurie M Gay; Thomas Alber
Mycobacterium tuberculosis serine/threonine kinases PknB, PknD, PknE, and PknF phosphorylate multiple FHA domains.
Protein science : a publication of the Protein Society 2005;14(7):1918-21.
2005: Andrew E Greenstein; Christoph Grundner; Nathaniel Echols; Laurie M Gay; T Noelle Lombana; Carl A Miecskowski; Kristi E Pullen; Pei-Yi Sung; Thomas Alber
Structure/function studies of Ser/Thr and Tyr protein phosphorylation in Mycobacterium tuberculosis.
Journal of molecular microbiology and biotechnology 2005;9(3-4):167-81.
2004: Kristi E Pullen; Ho Leung Ng; Pei-Yi Sung; Matthew C Good; Stephen M Smith; Thomas Alber
An alternate conformation and a third metal in PstP/Ppp, the M. tuberculosis PP2C-Family Ser/Thr protein phosphatase.
Structure (London, England : 1993) 2004;12(11):1947-54.
2004: Alastair A MacDowell; Richard S Celestre; Malcolm Howells; Wayne R Mckinney; James Krupnick; Daniella Cambie; Edward E Domning; Robert M Duarte; Nicholas Kelez; David W Plate; Carl Cork; Thomas N Earnest; Jeffery Dickert; George Meigs; Corie Ralston; James M Holton; Thomas Alber; James M Berger; David A Agard; Howard A Padmore
Suite of three protein crystallography beamlines with single superconducting bend magnet as the source.
Journal of synchrotron radiation 2004;11(Pt 6):447-55.
2004: Matthias Versele; Björn Gullbrand; Mark J Shulewitz; Víctor J Cid; Shirin Bahmanyar; Raymond E Chen; Patrick Barth; Thomas Alber; Jeremy Thorner
Protein-protein interactions governing septin heteropentamer assembly and septin filament organization in Saccharomyces cerevisiae.
Molecular biology of the cell 2004;15(10):4568-83.
2004: Joseph J Plecs; Pehr B Harbury; Peter S Kim; Thomas Alber
Structural test of the parameterized-backbone method for protein design.
Journal of molecular biology 2004;342(1):289-97.
2004: Robert B Rose; Kristi E Pullen; J Henri Bayle; Gerald R Crabtree; Thomas Alber
Biochemical and structural basis for partially redundant enzymatic and transcriptional functions of DCoH and DCoH2.
Biochemistry 2004;43(23):7345-55.
2004: Matthew C Good; Andrew E Greenstein; Tracy A Young; Ho Leung Ng; Thomas Alber
Sensor domain of the Mycobacterium tuberculosis receptor Ser/Thr protein kinase, PknD, forms a highly symmetric beta propeller.
Journal of molecular biology 2004;339(2):459-69.
2004: James Holton; Thomas Alber
Automated protein crystal structure determination using ELVES.
Proceedings of the National Academy of Sciences of the United States of America 2004;101(6):1537-42.
2003: Tracy A Young; Benedicte Delagoutte; James A Endrizzi; Arnold M Falick; Thomas Alber
Structure of Mycobacterium tuberculosis PknB supports a universal activation mechanism for Ser/Thr protein kinases.
Nature structural biology 2003;10(3):168-74.
2002: Katja M Arndt; Joelle N Pelletier; Kristian M Müller; Andreas Plückthun; Thomas Alber
Comparison of in vivo selection and rational design of heterodimeric coiled coils.
Structure (London, England : 1993) 2002;10(9):1235-48.
2002: Celia W Goulding; Marcin I Apostol; Daniel H Anderson; Harindarpal S Gill; Clare V Smith; Mack R Kuo; Jin Kuk Yang; Geoffrey S Waldo; Se Won Suh; Radha Chauhan; Avinash Kale; Nandita Bachhawat; Shekhar C Mande; Jodie M Johnston; J Shaun Lott; Edward N Baker; Vickery Arcus; David Leys; Kirsty J McLean; Andrew W Munro; Joel Berendzen; Vivek Sharma; Min S Park; David Eisenberg; James C Sacchettini; Thomas Alber; Bernhard Rupp; William R. Jacobs Jr.; Thomas C Terwilliger
The TB structural genomics consortium: providing a structural foundation for drug discovery.
Current drug targets. Infectious disorders 2002;2(2):121-41.
2001: K D Corbett; Thomas Alber
The many faces of Ras: recognition of small GTP-binding proteins.
Trends in biochemical sciences 2001;26(12):710-6.
2001: Scott M Crowder; James Holton; Thomas Alber
Covariance analysis of RNA recognition motifs identifies functionally linked amino acids.
Journal of molecular biology 2001;310(4):793-800.
2001: J C Lougheed; James M Holton; Thomas Alber; J. Fernando Bazan; Tracy M Handel
Structure of melanoma inhibitory activity protein, a member of a recently identified family of secreted proteins.
Proceedings of the National Academy of Sciences of the United States of America 2001;98(10):5515-20.
2000: Robert B Rose; James A Endrizzi; Jeff D Cronk; James Holton; Thomas Alber
High-resolution structure of the HNF-1alpha dimerization domain.
Biochemistry 2000;39(49):15062-70.
2000: Robert B Rose; J Henri Bayle; James A Endrizzi; Jeff D Cronk; Gerald R Crabtree; Thomas Alber
Structural basis of dimerization, coactivator recognition and MODY3 mutations in HNF-1alpha.
Nature structural biology 2000;7(9):744-8.
2000: C L Day; Thomas Alber
Crystal structure of the amino-terminal coiled-coil domain of the APC tumor suppressor.
Journal of molecular biology 2000;301(1):147-56.
2000: James A Endrizzi; Peter Beernink; Thomas Alber; Howard K Schachman
Binding of bisubstrate analog promotes large structural changes in the unregulated catalytic trimer of aspartate transcarbamoylase: implications for allosteric regulation.
Proceedings of the National Academy of Sciences of the United States of America 2000;97(10):5077-82.
2000: Katja M Arndt; Joelle N Pelletier; KM Müller; Thomas Alber; Stephen W Michnick; Andreas Plückthun
A heterodimeric coiled-coil peptide pair selected in vivo from a designed library-versus-library ensemble.
Journal of molecular biology 2000;295(3):627-39.
2000: K M Müller; Katja M Arndt; Thomas Alber
Protein fusions to coiled-coil domains.
Methods in enzymology 2000;328():261-82.
1999: Steven S Pullen; Mark E Labadia; Richard H Ingraham; SM McWhirter; D S Everdeen; Thomas Alber; James J Crute; Marilyn R Kehry
High-affinity interactions of tumor necrosis factor receptor-associated factors (TRAFs) and CD40 require TRAF trimerization and CD40 multimerization.
Biochemistry 1999;38(31):10168-77.
1999: P E Hershey; SM McWhirter; John D Gross; Gerhard Wagner; Thomas Alber; Alan B Sachs
The Cap-binding protein eIF4E promotes folding of a functional domain of yeast translation initiation factor eIF4G1.
The Journal of biological chemistry 1999;274(30):21297-304.
1999: SM McWhirter; Steven S Pullen; James M Holton; James J Crute; Marilyn R Kehry; Thomas Alber
Crystallographic analysis of CD40 recognition and signaling by human TRAF2.
Proceedings of the National Academy of Sciences of the United States of America 1999;96(15):8408-13.
1999: Peter Beernink; James A Endrizzi; Thomas Alber; Howard K Schachman
Assessment of the allosteric mechanism of aspartate transcarbamoylase based on the crystalline structure of the unregulated catalytic subunit.
Proceedings of the National Academy of Sciences of the United States of America 1999;96(10):5388-93.
1999: Scott M Crowder; R Kanaar; Donald C Rio; Thomas Alber
Absence of interdomain contacts in the crystal structure of the RNA recognition motifs of Sex-lethal.
Proceedings of the National Academy of Sciences of the United States of America 1999;96(9):4892-7.
1999: SM McWhirter; Steven S Pullen; Brian G Werneburg; Mark E Labadia; Richard H Ingraham; James J Crute; Marilyn R Kehry; Thomas Alber
Structural and biochemical analysis of signal transduction by the TRAF family of adapter proteins.
Cold Spring Harbor symposia on quantitative biology 1999;64():551-62.
1999: S Nautiyal; Thomas Alber
Crystal structure of a designed, thermostable, heterotrimeric coiled coil.
Protein science : a publication of the Protein Society 1999;8(1):84-90.
1998: Pehr B Harbury; Joseph J Plecs; Bruce Tidor; Thomas Alber; Peter S Kim
High-resolution protein design with backbone freedom.
Science (New York, N.Y.) 1998;282(5393):1462-7.
1998: V A Sharma; J Logan; David S King; Raymond White; Thomas Alber
Sequence-based design of a peptide probe for the APC tumor suppressor protein.
Current biology : CB 1998;8(14):823-30.
1996: L Gonzalez; D N Woolfson; Thomas Alber
Buried polar residues and structural specificity in the GCN4 leucine zipper.
Nature structural biology 1996;3(12):1011-8.
1996: L Gonzalez; R A Brown; D Richardson; Thomas Alber
Crystal structures of a single coiled-coil peptide in two oligomeric states reveal the basis for structural polymorphism.
Nature structural biology 1996;3(12):1002-9.
1996: J D Cronk; J A Endrizzi; Thomas Alber
High-resolution structures of the bifunctional enzyme and transcriptional coactivator DCoH and its complex with a product analogue.
Protein science : a publication of the Protein Society 1996;5(10):1963-72.
1996: L Gonzalez; J J Plecs; Thomas Alber
An engineered allosteric switch in leucine-zipper oligomerization.
Nature structural biology 1996;3(6):510-5.
1995: J M Petersen; J J Skalicky; L W Donaldson; Lawrence P McIntosh; Thomas Alber; Barbara J Graves
Modulation of transcription factor Ets-1 DNA binding: DNA-induced unfolding of an alpha helix.
Science (New York, N.Y.) 1995;269(5232):1866-9.
1995: S Nautiyal; D N Woolfson; David S King; Thomas Alber
A designed heterotrimeric coiled coil.
Biochemistry 1995;34(37):11645-51.
1995: D N Woolfson; Thomas Alber
Predicting oligomerization states of coiled coils.
Protein science : a publication of the Protein Society 1995;4(8):1596-607.
1995: J A Endrizzi; J D Cronk; W Wang; G R Crabtree; Thomas Alber
Crystal structure of DCoH, a bifunctional, protein-binding transcriptional coactivator.
Science (New York, N.Y.) 1995;268(5210):556-9.
1994: P B Harbury; Peter S Kim; Thomas Alber
Crystal structure of an isoleucine-zipper trimer.
Nature 1994;371(6492):80-3.
1994: T Zhang; E Bertelsen; Thomas Alber
Entropic effects of disulphide bonds on protein stability.
Nature structural biology 1994;1(7):434-8.
1993: G Joslyn; D S Richardson; Raymond White; Thomas Alber
Dimer formation by an N-terminal coiled coil in the APC protein.
Proceedings of the National Academy of Sciences of the United States of America 1993;90(23):11109-13.
1993: P B Harbury; T Zhang; Peter S Kim; Thomas Alber
A switch between two-, three-, and four-stranded coiled coils in GCN4 leucine zipper mutants.
Science (New York, N.Y.) 1993;262(5138):1401-7.
1993: T Zhang; E Bertelsen; D Benvegnu; Thomas Alber
Circular permutation of T4 lysozyme.
Biochemistry 1993;32(46):12311-8.
1993: Thomas Alber
Protein-DNA interactions: how GCN4 binds DNA.
Current biology : CB 1993;3(3):182-4.
1992: Thomas Alber
Structure of the leucine zipper.
Current opinion in genetics & development 1992;2(2):205-10.
1991: E K O'Shea; J D Klemm; P S Kim; Thomas Alber
X-ray structure of the GCN4 leucine zipper, a two-stranded, parallel coiled coil.
Science (New York, N.Y.) 1991;254(5031):539-44.
1991: S Daopin; Thomas Alber; Walter A Baase; J A Wozniak; Brian W Matthews
Structural and thermodynamic analysis of the packing of two alpha-helices in bacteriophage T4 lysozyme.
Journal of molecular biology 1991;221(2):647-67.
1991: R Rasmussen; D Benvegnu; E K O'Shea; P S Kim; Thomas Alber
X-ray scattering indicates that the leucine zipper is a coiled coil.
Proceedings of the National Academy of Sciences of the United States of America 1991;88(2):561-4.
1991: J D Klemm; J A Wozniak; Thomas Alber; David P Goldenberg
Correlation between mutational destabilization of phage T4 lysozyme and increased unfolding rates.
Biochemistry 1991;30(2):589-94.
1991: S A Kuby; G Fleming; Thomas Alber; D Richardson; H Takenaka; M Hamada
Studies on yeast nucleoside triphosphate-nucleoside diphosphate transphosphorylase (nucleoside diphosphokinase). IV. Steady-state kinetic properties with thymidine nucleotides (including 3'-azido-3'-deoxythymidine analogues).
Enzyme 1991;45(1-2):1-13.
1990: E Lolis; Thomas Alber; R C Davenport; D Rose; F C Hartman; Gregory A Petsko
Structure of yeast triosephosphate isomerase at 1.9-A resolution.
Biochemistry 1990;29(28):6609-18.
1989: Thomas Alber
Mutational effects on protein stability.
Annual review of biochemistry 1989;58():765-98.
1988: Thomas Alber; J A Bell; D P Sun; H Nicholson; J A Wozniak; S Cook; Brian W Matthews
Replacements of Pro86 in phage T4 lysozyme extend an alpha-helix but do not alter protein stability.
Science (New York, N.Y.) 1988;239(4840):631-5.
1987: Thomas Alber; D P Sun; K Wilson; J A Wozniak; S P Cook; Brian W Matthews
Contributions of hydrogen bonds of Thr 157 to the thermodynamic stability of phage T4 lysozyme.
Nature 1987;330(6143):41-6.
1987: Thomas Alber; D P Sun; J A Nye; D C Muchmore; Brian W Matthews
Temperature-sensitive mutations of bacteriophage T4 lysozyme occur at sites with low mobility and low solvent accessibility in the folded protein.
Biochemistry 1987;26(13):3754-8.
1987: D P Sun; Thomas Alber; J A Bell; Larry H Weaver; Brian W Matthews
Use of site-directed mutagenesis to obtain isomorphous heavy-atom derivatives for protein crystallography: cysteine-containing mutants of phage T4 lysozyme.
Protein engineering 1987;1(2):115-23.
1987: Thomas Alber; R C Davenport; D A Giammona; E Lolis; Gregory A Petsko; Dagmar Ringe
Crystallography and site-directed mutagenesis of yeast triosephosphate isomerase: what can we learn about catalysis from a "simple" enzyme?
Cold Spring Harbor symposia on quantitative biology 1987;52():603-13.
1985: Thomas Alber; J A Wozniak
A genetic screen for mutations that increase the thermal stability of phage T4 lysozyme.
Proceedings of the National Academy of Sciences of the United States of America 1985;82(3):747-50.
1981: Thomas Alber; F C Hartman; Robert M Johnson; G A Petsko; D Tsernoglou
Crystallization of yeast triose phosphate isomerase from polyethylene glycol. Protein crystal formation following phase separation.
The Journal of biological chemistry 1981;256(3):1356-61.