Publications

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Katherine A Rawls, P Therese Lang, Jun Takeuchi, Shinichi Imamura, Tyler D Baguley, Christoph Grundner, Tom Alber, Jonathan A Ellman
Fragment-based discovery of selective inhibitors of the Mycobacterium tuberculosis protein tyrosine phosphatase PtpA.
Bioorg. Med. Chem. Lett.: 2009, (1);
[PubMed:19889539] [DOI] ( )

Andrew E Greenstein, Michal Hammel, Alexandra Cavazos, Tom Alber
Interdomain communication in the Mycobacterium tuberculosis environmental phosphatase Rv1364c.
J. Biol. Chem.: 2009, 284(43);29828-35
[PubMed:19700407] [DOI] ( )

Carl Mieczkowski, Anthony T Iavarone, Tom Alber
Auto-activation mechanism of the Mycobacterium tuberculosis PknB receptor Ser/Thr kinase.
EMBO J.: 2008, 27(23);3186-97
[PubMed:19008858] [DOI] ( )

Christoph Grundner, Jeffery S Cox, Tom Alber
Protein tyrosine phosphatase PtpA is not required for Mycobacterium tuberculosis growth in mice.
FEMS Microbiol. Lett.: 2008, 287(2);181-4
[PubMed:18752626] [DOI] ( )

Patrick Barth, Allyn Schoeffler, Tom Alber
Targeting metastable coiled-coil domains by computational design.
J. Am. Chem. Soc.: 2008, 130(36);12038-44
[PubMed:18698842] [DOI] ( )

Aurelie Bertin, Michael A McMurray, Patricia Grob, Sang-Shin Park, Galo Garcia, Insiyyah Patanwala, Ho-Leung Ng, Tom Alber, Jeremy Thorner, Eva Nogales
Saccharomyces cerevisiae septins: supramolecular organization of heterooligomers and the mechanism of filament assembly.
Proc. Natl. Acad. Sci. U.S.A.: 2008, 105(24);8274-9
[PubMed:18550837] [DOI] ( )

A C Murillo, H Y Li, T Alber, E N Baker, J M Berger, L T Cherney, M M Cherney, Yoon Song Cho, D Eisenberg, C R Garen, C W Goulding, L W Hung, T R Ioerger, W R Jacobs, M N G James, C Kim, I Krieger, J S Lott, R Sankaranarayanan, B W Segelke, T C Terwilliger, F Wang, S Wang, J C Sacchettini
High throughput crystallography of TB drug targets.
Infect Disord Drug Targets: 2007, 7(2);127-39
[PubMed:17970224] ( )

Mark Sales, Joseph J Plecs, James M Holton, Tom Alber
Structure of a designed, right-handed coiled-coil tetramer containing all biological amino acids.
Protein Sci.: 2007, 16(10);2224-32
[PubMed:17766380] [DOI] ( )

Matthew B Soellner, Katherine A Rawls, Christoph Grundner, Tom Alber, Jonathan A Ellman
Fragment-based substrate activity screening method for the identification of potent inhibitors of the Mycobacterium tuberculosis phosphatase PtpB.
J. Am. Chem. Soc.: 2007, 129(31);9613-5
[PubMed:17636914] [DOI] ( )

James S Fraser, John P Merlie, Nathaniel Echols, Shellie R Weisfield, Tâm Mignot, David E Wemmer, David R Zusman, Tom Alber
An atypical receiver domain controls the dynamic polar localization of the Myxococcus xanthus social motility protein FrzS.
Mol. Microbiol.: 2007, 65(2);319-32
[PubMed:17573816] [DOI] ( )

Christoph Grundner, Dominique Perrin, Rob Hooft van Huijsduijnen, Dominique Swinnen, Jérome Gonzalez, Christine L Gee, Timothy N Wells, Tom Alber
Structural basis for selective inhibition of Mycobacterium tuberculosis protein tyrosine phosphatase PtpB.
Structure: 2007, 15(4);499-509
[PubMed:17437721] [DOI] ( )

Andrew E Greenstein, Jason A MacGurn, Christina E Baer, Arnold M Falick, Jeffery S Cox, Tom Alber
M. tuberculosis Ser/Thr protein kinase D phosphorylates an anti-anti-sigma factor homolog.
PLoS Pathog.: 2007, 3(4);e49
[PubMed:17411339] [DOI] ( )

Jason Cellitti, Manuel Llinas, Nathaniel Echols, Elizabeth A Shank, Blake Gillespie, Ester Kwon, Scott M Crowder, Frederick W Dahlquist, Tom Alber, Susan Marqusee
Exploring subdomain cooperativity in T4 lysozyme I: structural and energetic studies of a circular permutant and protein fragment.
Protein Sci.: 2007, 16(5);842-51
[PubMed:17400926] [DOI] ( )

P Barth, T Alber, P B Harbury
Accurate, conformation-dependent predictions of solvent effects on protein ionization constants.
Proc. Natl. Acad. Sci. U.S.A.: 2007, 104(12);4898-903
[PubMed:17360348] [DOI] ( )

Andrew E Greenstein, Nathaniel Echols, T Noelle Lombana, David S King, Tom Alber
Allosteric activation by dimerization of the PknD receptor Ser/Thr protein kinase from Mycobacterium tuberculosis.
J. Biol. Chem.: 2007, 282(15);11427-35
[PubMed:17242402] [DOI] ( )

Laurie M Gay, Ho-Leung Ng, Tom Alber
A conserved dimer and global conformational changes in the structure of apo-PknE Ser/Thr protein kinase from Mycobacterium tuberculosis.
J. Mol. Biol.: 2006, 360(2);409-20
[PubMed:16762364] [DOI] ( )

Andrew E Greenstein, Christoph Grundner, Nathaniel Echols, Laurie M Gay, T Noelle Lombana, Carl A Miecskowski, Kristi E Pullen, Pei-Yi Sung, Tom Alber
Structure/function studies of Ser/Thr and Tyr protein phosphorylation in Mycobacterium tuberculosis.
J. Mol. Microbiol. Biotechnol.: 2005, 9(3-4);167-81
[PubMed:16415590] [DOI] ( )

Christoph Grundner, Ho-Leung Ng, Tom Alber
Mycobacterium tuberculosis protein tyrosine phosphatase PtpB structure reveals a diverged fold and a buried active site.
Structure: 2005, 13(11);1625-34
[PubMed:16271885] [DOI] ( )

Christoph Grundner, Laurie M Gay, Tom Alber
Mycobacterium tuberculosis serine/threonine kinases PknB, PknD, PknE, and PknF phosphorylate multiple FHA domains.
Protein Sci.: 2005, 14(7);1918-21
[PubMed:15987910] [DOI] ( )

Kristi E Pullen, Ho-Leung Ng, Pei-Yi Sung, Matthew C Good, Stephen M Smith, Tom Alber
An alternate conformation and a third metal in PstP/Ppp, the M. tuberculosis PP2C-Family Ser/Thr protein phosphatase.
Structure: 2004, 12(11);1947-54
[PubMed:15530359] [DOI] ( )

Alastair A MacDowell, Rich S Celestre, Malcolm Howells, Wayne McKinney, James Krupnick, Daniella Cambie, Edward E Domning, Robert M Duarte, Nicholas Kelez, David W Plate, Carl W Cork, Thomas N Earnest, Jeffery Dickert, George Meigs, Corie Ralston, James M Holton, Tom Alber, James M Berger, David A Agard, Howard A Padmore
Suite of three protein crystallography beamlines with single superconducting bend magnet as the source.
J Synchrotron Radiat: 2004, 11(Pt 6);447-55
[PubMed:15496731] [DOI] ( )

Joseph J Plecs, Pehr B Harbury, Peter S Kim, Tom Alber
Structural test of the parameterized-backbone method for protein design.
J. Mol. Biol.: 2004, 342(1);289-97
[PubMed:15313624] [DOI] ( )

Matthias Versele, Björn Gullbrand, Mark J Shulewitz, Victor J Cid, Shirin Bahmanyar, Raymond E Chen, Patrick Barth, Tom Alber, Jeremy Thorner
Protein-protein interactions governing septin heteropentamer assembly and septin filament organization in Saccharomyces cerevisiae.
Mol. Biol. Cell: 2004, 15(10);4568-83
[PubMed:15282341] [DOI] ( )

Robert B Rose, Kristi E Pullen, J Henri Bayle, Gerald R Crabtree, Tom Alber
Biochemical and structural basis for partially redundant enzymatic and transcriptional functions of DCoH and DCoH2.
Biochemistry: 2004, 43(23);7345-55
[PubMed:15182178] [DOI] ( )

Matthew C Good, Andrew E Greenstein, Tracy A Young, Ho-Leung Ng, Tom Alber
Sensor domain of the Mycobacterium tuberculosis receptor Ser/Thr protein kinase, PknD, forms a highly symmetric beta propeller.
J. Mol. Biol.: 2004, 339(2);459-69
[PubMed:15136047] [DOI] ( )

James Holton, Tom Alber
Automated protein crystal structure determination using ELVES.
Proc. Natl. Acad. Sci. U.S.A.: 2004, 101(6);1537-42
[PubMed:14752198] [DOI] ( )

T C Terwilliger, M S Park, G S Waldo, J Berendzen, L-W Hung, C-Y Kim, C V Smith, J C Sacchettini, M Bellinzoni, R Bossi, E De Rossi, A Mattevi, A Milano, G Riccardi, M Rizzi, M M Roberts, A R Coker, G Fossati, P Mascagni, A R M Coates, S P Wood, C W Goulding, M I Apostol, D H Anderson, H S Gill, D S Eisenberg, B Taneja, S Mande, E Pohl, V Lamzin, P Tucker, M Wilmanns, C Colovos, W Meyer-Klaucke, A W Munro, K J McLean, K R Marshall, D Leys, J K Yang, H-J Yoon, B I Lee, M G Lee, J E Kwak, B W Han, J Y Lee, S-H Baek, S W Suh, M M Komen, V L Arcus, E N Baker, J S Lott, W Jacobs, T Alber, B Rupp
The TB structural genomics consortium: a resource for Mycobacterium tuberculosis biology.
Tuberculosis (Edinb): 2003, 83(4);223-49
[PubMed:12906835] ( )

Tracy A Young, Benedicte Delagoutte, James A Endrizzi, Arnold M Falick, Tom Alber
Structure of Mycobacterium tuberculosis PknB supports a universal activation mechanism for Ser/Thr protein kinases.
Nat. Struct. Biol.: 2003, 10(3);168-74
[PubMed:12548283] [DOI] ( )

Celia W Goulding, Marcin 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 L Arcus, David Leys, Kirsty J McLean, Andrew W Munro, Joel Berendzen, Vivek Sharma, Min S Park, David Eisenberg, James Sacchettini, Tom Alber, Bernhard Rupp, William Jacobs, Thomas C Terwilliger
The TB structural genomics consortium: providing a structural foundation for drug discovery.
Curr Drug Targets Infect Disord: 2002, 2(2);121-41
[PubMed:12462144] ( )

Katja M Arndt, Joelle N Pelletier, Kristian M Müller, Andreas Plückthun, Tom Alber
Comparison of in vivo selection and rational design of heterodimeric coiled coils.
Structure: 2002, 10(9);1235-48
[PubMed:12220495] ( )

K D Corbett, T Alber
The many faces of Ras: recognition of small GTP-binding proteins.
Trends Biochem. Sci.: 2001, 26(12);710-6
[PubMed:11738594] ( )

S Crowder, J Holton, T Alber
Covariance analysis of RNA recognition motifs identifies functionally linked amino acids.
J. Mol. Biol.: 2001, 310(4);793-800
[PubMed:11453688] [DOI] ( )

J C Lougheed, J M Holton, T Alber, J F Bazan, T M Handel
Structure of melanoma inhibitory activity protein, a member of a recently identified family of secreted proteins.
Proc. Natl. Acad. Sci. U.S.A.: 2001, 98(10);5515-20
[PubMed:11331761] [DOI] ( )

S M McWhirter, S S Pullen, B G Werneburg, M E Labadia, R H Ingraham, J J Crute, M R Kehry, T Alber
Structural and biochemical analysis of signal transduction by the TRAF family of adapter proteins.
Cold Spring Harb. Symp. Quant. Biol.: 1999, 64(1);551-62
[PubMed:11232332] ( )

R B Rose, J A Endrizzi, J D Cronk, J Holton, T Alber
High-resolution structure of the HNF-1alpha dimerization domain.
Biochemistry: 2000, 39(49);15062-70
[PubMed:11106484] ( )

K M Müller, K M Arndt, T Alber
Protein fusions to coiled-coil domains.
Meth. Enzymol.: 2000, 328(1);261-82
[PubMed:11075350] ( )

R B Rose, J H Bayle, J A Endrizzi, J D Cronk, G R Crabtree, T Alber
Structural basis of dimerization, coactivator recognition and MODY3 mutations in HNF-1alpha.
Nat. Struct. Biol.: 2000, 7(9);744-8
[PubMed:10966642] [DOI] ( )

C L Day, T Alber
Crystal structure of the amino-terminal coiled-coil domain of the APC tumor suppressor.
J. Mol. Biol.: 2000, 301(1);147-56
[PubMed:10926498] [DOI] ( )

J A Endrizzi, P T Beernink, T Alber, H K Schachman
Binding of bisubstrate analog promotes large structural changes in the unregulated catalytic trimer of aspartate transcarbamoylase: implications for allosteric regulation.
Proc. Natl. Acad. Sci. U.S.A.: 2000, 97(10);5077-82
[PubMed:10805770] [DOI] ( )

K M Arndt, J N Pelletier, K M Müller, T Alber, S W Michnick, A Plückthun
A heterodimeric coiled-coil peptide pair selected in vivo from a designed library-versus-library ensemble.
J. Mol. Biol.: 2000, 295(3);627-39
[PubMed:10623552] [DOI] ( )

S S Pullen, M E Labadia, R H Ingraham, S M McWhirter, D S Everdeen, T Alber, J J Crute, M 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
[PubMed:10433725] [DOI] ( )

S M McWhirter, S S Pullen, J M Holton, J J Crute, M R Kehry, T Alber
Crystallographic analysis of CD40 recognition and signaling by human TRAF2.
Proc. Natl. Acad. Sci. U.S.A.: 1999, 96(15);8408-13
[PubMed:10411888] ( )

P E Hershey, S M McWhirter, J D Gross, G Wagner, T Alber, A B Sachs
The Cap-binding protein eIF4E promotes folding of a functional domain of yeast translation initiation factor eIF4G1.
J. Biol. Chem.: 1999, 274(30);21297-304
[PubMed:10409688] ( )

P T Beernink, J A Endrizzi, T Alber, H K Schachman
Assessment of the allosteric mechanism of aspartate transcarbamoylase based on the crystalline structure of the unregulated catalytic subunit.
Proc. Natl. Acad. Sci. U.S.A.: 1999, 96(10);5388-93
[PubMed:10318893] ( )

S M Crowder, R Kanaar, D C Rio, T Alber
Absence of interdomain contacts in the crystal structure of the RNA recognition motifs of Sex-lethal.
Proc. Natl. Acad. Sci. U.S.A.: 1999, 96(9);4892-7
[PubMed:10220389] ( )

S Nautiyal, T Alber
Crystal structure of a designed, thermostable, heterotrimeric coiled coil.
Protein Sci.: 1999, 8(1);84-90
[PubMed:10210186] [DOI] ( )

P B Harbury, J J Plecs, B Tidor, T Alber, P S Kim
High-resolution protein design with backbone freedom.
Science: 1998, 282(5393);1462-7
[PubMed:9822371] ( )

V A Sharma, J Logan, D S King, R White, T Alber
Sequence-based design of a peptide probe for the APC tumor suppressor protein.
Curr. Biol.: 1998, 8(14);823-30
[PubMed:9663391] ( )

L Gonzalez, D N Woolfson, T Alber
Buried polar residues and structural specificity in the GCN4 leucine zipper.
Nat. Struct. Biol.: 1996, 3(12);1011-8
[PubMed:8946854] ( )

L Gonzalez, R A Brown, D Richardson, T Alber
Crystal structures of a single coiled-coil peptide in two oligomeric states reveal the basis for structural polymorphism.
Nat. Struct. Biol.: 1996, 3(12);1002-9
[PubMed:8946853] ( )

J D Cronk, J A Endrizzi, T Alber
High-resolution structures of the bifunctional enzyme and transcriptional coactivator DCoH and its complex with a product analogue.
Protein Sci.: 1996, 5(10);1963-72
[PubMed:8897596] [DOI] ( )

L Gonzalez, J J Plecs, T Alber
An engineered allosteric switch in leucine-zipper oligomerization.
Nat. Struct. Biol.: 1996, 3(6);510-5
[PubMed:8646536] ( )

J M Petersen, J J Skalicky, L W Donaldson, L P McIntosh, T Alber, B J Graves
Modulation of transcription factor Ets-1 DNA binding: DNA-induced unfolding of an alpha helix.
Science: 1995, 269(5232);1866-9
[PubMed:7569926] ( )

S Nautiyal, D N Woolfson, D S King, T Alber
A designed heterotrimeric coiled coil.
Biochemistry: 1995, 34(37);11645-51
[PubMed:7547896] ( )

D N Woolfson, T Alber
Predicting oligomerization states of coiled coils.
Protein Sci.: 1995, 4(8);1596-607
[PubMed:8520486] [DOI] ( )

J A Endrizzi, J D Cronk, W Wang, G R Crabtree, T Alber
Crystal structure of DCoH, a bifunctional, protein-binding transcriptional coactivator.
Science: 1995, 268(5210);556-9
[PubMed:7725101] ( )

P B Harbury, P S Kim, T Alber
Crystal structure of an isoleucine-zipper trimer.
Nature: 1994, 371(6492);80-3
[PubMed:8072533] [DOI] ( )

T Zhang, E Bertelsen, T Alber
Entropic effects of disulphide bonds on protein stability.
Nat. Struct. Biol.: 1994, 1(7);434-8
[PubMed:7664061] ( )

G Joslyn, D S Richardson, R White, T Alber
Dimer formation by an N-terminal coiled coil in the APC protein.
Proc. Natl. Acad. Sci. U.S.A.: 1993, 90(23);11109-13
[PubMed:8248216] ( )

P B Harbury, T Zhang, P S Kim, T Alber
A switch between two-, three-, and four-stranded coiled coils in GCN4 leucine zipper mutants.
Science: 1993, 262(5138);1401-7
[PubMed:8248779] ( )

T Zhang, E Bertelsen, D Benvegnu, T Alber
Circular permutation of T4 lysozyme.
Biochemistry: 1993, 32(46);12311-8
[PubMed:8241117] ( )

T Alber
Protein-DNA interactions: how GCN4 binds DNA.
Curr. Biol.: 1993, 3(3);182-4
[PubMed:15335794] ( )

T Alber
Structure of the leucine zipper.
Curr. Opin. Genet. Dev.: 1992, 2(2);205-10
[PubMed:1638114] ( )

E K O'Shea, J D Klemm, P S Kim, T Alber
X-ray structure of the GCN4 leucine zipper, a two-stranded, parallel coiled coil.
Science: 1991, 254(5031);539-44
[PubMed:1948029] ( )

S Daopin, T Alber, W A Baase, J A Wozniak, B W Matthews
Structural and thermodynamic analysis of the packing of two alpha-helices in bacteriophage T4 lysozyme.
J. Mol. Biol.: 1991, 221(2);647-67
[PubMed:1920439] ( )

R Rasmussen, D Benvegnu, E K O'Shea, P S Kim, T Alber
X-ray scattering indicates that the leucine zipper is a coiled coil.
Proc. Natl. Acad. Sci. U.S.A.: 1991, 88(2);561-4
[PubMed:1988953] ( )

J D Klemm, J A Wozniak, T Alber, D P Goldenberg
Correlation between mutational destabilization of phage T4 lysozyme and increased unfolding rates.
Biochemistry: 1991, 30(2);589-94
[PubMed:1988046] ( )

S A Kuby, G Fleming, T 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
[PubMed:1666874] ( )

E Lolis, T Alber, R C Davenport, D Rose, F C Hartman, G A Petsko
Structure of yeast triosephosphate isomerase at 1.9-A resolution.
Biochemistry: 1990, 29(28);6609-18
[PubMed:2204417] ( )

T Alber
Mutational effects on protein stability.
Annu. Rev. Biochem.: 1989, 58(1);765-98
[PubMed:2673021] [DOI] ( )

T Alber, J A Bell, D P Sun, H Nicholson, J A Wozniak, S Cook, B W Matthews
Replacements of Pro86 in phage T4 lysozyme extend an alpha-helix but do not alter protein stability.
Science: 1988, 239(4840);631-5
[PubMed:3277275] ( )

T Alber, D P Sun, K Wilson, J A Wozniak, S P Cook, B W Matthews
Contributions of hydrogen bonds of Thr 157 to the thermodynamic stability of phage T4 lysozyme.
Nature: 1987 Nov 5-11, 330(6143);41-6
[PubMed:3118211] [DOI] ( )

T Alber, D P Sun, J A Nye, D C Muchmore, B 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
[PubMed:3651410] ( )

D P Sun, T Alber, J A Bell, L H Weaver, B W Matthews
Use of site-directed mutagenesis to obtain isomorphous heavy-atom derivatives for protein crystallography: cysteine-containing mutants of phage T4 lysozyme.
Protein Eng.: 1987 Feb-Mar, 1(2);115-23
[PubMed:3507694] ( )

T C Alber, R C Davenport, D A Giammona, E Lolis, G A Petsko, D Ringe
Crystallography and site-directed mutagenesis of yeast triosephosphate isomerase: what can we learn about catalysis from a "simple" enzyme?
Cold Spring Harb. Symp. Quant. Biol.: 1987, 52(1);603-13
[PubMed:3331346] ( )

T Alber, B W Matthews
Structure and thermal stability of phage T4 lysozyme.
Meth. Enzymol.: 1987, 154(1);511-33
[PubMed:3323816] ( )

T Alber, J A Wozniak
A genetic screen for mutations that increase the thermal stability of phage T4 lysozyme.
Proc. Natl. Acad. Sci. U.S.A.: 1985, 82(3);747-50
[PubMed:3856227] ( )

T Alber, W A Gilbert, D R Ponzi, G A Petsko
The role of mobility in the substrate binding and catalytic machinery of enzymes.
Ciba Found. Symp.: 1983, 93(1);4-24
[PubMed:6551232] ( )

T Alber, G Kawasaki
Nucleotide sequence of the triose phosphate isomerase gene of Saccharomyces cerevisiae.
J. Mol. Appl. Genet.: 1982, 1(5);419-34
[PubMed:6759603] ( )

T Alber, D W Banner, A C Bloomer, G A Petsko, D Phillips, P S Rivers, I A Wilson
On the three-dimensional structure and catalytic mechanism of triose phosphate isomerase.
Philos. Trans. R. Soc. Lond., B, Biol. Sci.: 1981, 293(1063);159-71
[PubMed:6115415] ( )

T Alber, M Fahnestock, S L Mowbray, G A Petsko
Preliminary x-ray data for the galactose binding protein from Salmonella typhimurium.
J. Mol. Biol.: 1981, 147(3);471-4
[PubMed:7031261] ( )

T Alber, F C Hartman, R M Johnson, G A Petsko, D Tsernoglou
Crystallization of yeast triose phosphate isomerase from polyethylene glycol. Protein crystal formation following phase separation.
J. Biol. Chem.: 1981, 256(3);1356-61
[PubMed:7005233] ( )

T Alber, G A Petsko, D Tsernoglou
Crystal structure of elastase-substrate complex at -- 55 degrees C.
Nature: 1976, 263(5575);297-300
[PubMed:958484] ( )

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