Alber Lab Publications

Lab publications:

Murillo AC, Li HY, Alber T, Baker EN, Berger JM, Cherney LT, Cherney MM, Cho YS, Eisenberg D, Garen CR, Goulding CW, Hung LW, Ioerger TR, Jacobs WR, James MN, Kim C, Krieger I, Lott JS, Sankaranarayanan R, Segelke BW, Terwilliger TC, Wang F, Wang S, Sacchettini JC (2007). High throughput crystallography of TB drug targets. Infect Disord Drug Targets. 7:127-39.
    Medline: 17970224.

Sales M, Plecs JJ, Holton JM, Alber T (2007). Structure of a designed, right-handed coiled-coil tetramer containing all biological amino acids. Protein Sci. 16:2224-32.
    Medline: 17766380. PDB: 2o6n.

Soellner MB, Rawls KA, Grundner C, Alber T, Ellman JA (2007). Fragment-based substrate activity screening method for the identification of potent inhibitors of the Mycobacterium tuberculosis phosphatase PtpB. J Am Chem Soc. 129:9613-5.
    Medline: 17636914.

Fraser JS, Merlie Jr. JP, Echols N, Weisfield SR, Mignot T, Wemmer DE, Zusman D, Alber T (2007). An atypical receiver domain controls the dynamic polar localization of the Myxococcus xanthus social motility protein FrzS. Mol. Micro. 65:319-32.
    Medline: 17573816>. PDB: 2gkg, 2nt3, 2nt4.

Grundner C, Perrin D, Hooft van Huijsduijnen R, Swinnen D, Gonzalez J, Gee CL, Wells TN, Alber T (2007). Structural basis for selective inhibition of Mycobacterium tuberculosis protein tyrosine phosphatase PtpB. Structure 15:499-509.
    Medline: 17437721. PDB: 2oz5.

Greenstein AE, Macgurn JA, Baer CE, Falick AM, Cox JS, Alber T (2007). M. tuberculosis Ser/Thr Protein Kinase D Phosphorylates an Anti-Anti-Sigma Factor Homolog. PLoS Pathogens 3:e49.
    Medline: 17411339.

Cellitti J, Llinas M, Echols N, Shank EA, Gillespie B, Kwon E, Crowder SM, Dahlquist FW, Alber T, Marqusee S (2007). Exploring subdomain cooperativity in T4 lysozyme I: structural and energetic studies of a circular permutant and protein fragment. Protein Sci. 16:842-51.
    Medline: 17400926. PDB: 2o4w 2o79 2o7a

Barth P, Alber T, Harbury PB (2007). Accurate, conformation-dependent predictions of solvent effects on protein ionization constants. Proc Natl Acad Sci USA 104:4898-4903.
    Medline: 17360348.

Greenstein AE, Echols N, Lombana TN, King DS, Alber T (2007). Allosteric activation by dimerization of the PknD receptor Ser/Thr protein kinase from Mycobacterium tuberculosis. J. Biol. Chem. 282:11427-35.
    Medline: 17242402

Gay LM, Ng HL, Alber T (2006). A conserved dimer and global conformational changes in the structure of apo-PknE Ser/Thr protein kinase from Mycobacterium tuberculosis. J. Mol. Biol. 360:409-420.
    Medline: 16762364. PDB: 2h34.

Greenstein AE, Grundner C, Echols N, Gay LM, Lombana TN, Miecskowski CA, Pullen KE, Sung PY, Alber T (2005). Structure/function studies of Ser/Thr and Tyr protein phosphorylation in Mycobacterium tuberculosis. J. Mol. Microbiol. Biotechnol. 9:167-181.
    Medline: 16415590.

Grundner C, Ng HL, Alber T (2005). Mycobacterium tuberculosis protein tyrosine phosphatase PtpB structure reveals a diverged fold and a buried active site. Structure 13:1625-34.
    Medline: 16271885. PDB: 1YWF.
Grundner C, Gay LM, Alber T (2005). Mycobacterium tuberculosis serine/threonine kinases PknB, PknD, PknE, and PknF phosphorylate multiple FHA domains. Protein Sci 14:1918-21.
    Medline: 15987910.

Pullen KE, Ng HL, Sung PY, Good MC, Smith SM, Alber T (2004). An alternate conformation and a third metal in PstP/Ppp, the M. tuberculosis PP2C-Family Ser/Thr protein phosphatase. Structure (Camb) 12:1947-54.
    Medline: 15530359. PDB: 1TX0

MacDowell AA, Celestre RS, Howells M, McKinney W, Krupnick J, Cambie D, Domning EE, Duarte RM, Kelez N, Plate DW, Cork CW, Earnest TN, Dickert J, Meigs G, Ralston C, Holton JM, Alber T, Berger JM, Agard DA, Padmore HA (2004). Suite of three protein crystallography beamlines with single superconducting bend magnet as the source. J Synchrotron Radiat 11:447-55.
    Medline: 15496731.

Plecs JJ, Harbury PB, Kim PS, Alber T (2004). Structural test of the parameterized-backbone method for protein design. J Mol Biol 342:289-97.
    Medline: 15313624. PDB: 1TGG

Versele M, Gullbrand B, Shulewitz MJ, Cid VJ, Bahmanyar S, Chen RE, Barth P, Alber T, Thorner J (2004). Protein-protein interactions governing septin heteropentamer assembly and septin filament organization in Saccharomyces cerevisiae. Mol Biol Cell 15:4568-83.
    Medline: 15282341.

Rose RB, Pullen KE, Bayle JH, Crabtree GR, Alber T (2004). Biochemical and structural basis for partially redundant enzymatic and transcriptional functions of DCoH and DCoH2. Biochemistry 43:7345-55.
    Medline: 15182178. PDB: 1RU0

Good MC, Greenstein AE, Young TA, Ng HL, Alber T (2004). Sensor domain of the Mycobacterium tuberculosis receptor Ser/Thr protein kinase, PknD, forms a highly symmetric beta propeller. J Mol Biol 339:459-69.
    Medline: 15136047. PDB: 1RWI 1RWL

Holton J, Alber T (2004). Automated protein crystal structure determination using ELVES. Proc Natl Acad Sci U S A 101:1537-42.
    Medline: 14752198. PDB: 1RB1 1RB4 1RB5 1RB6

Terwilliger TC, Park MS, Waldo GS, Berendzen J, Hung LW, Kim CY, Smith CV, Sacchettini JC, Bellinzoni M, Bossi R, De Rossi E, Mattevi A, Milano A, Riccardi G, Rizzi M, Roberts MM, Coker AR, Fossati G, Mascagni P, Coates AR, Wood SP, Goulding CW, Apostol MI, Anderson DH, Gill HS, Eisenberg DS, Taneja B, Mande S, Pohl E, Lamzin V, Tucker P, Wilmanns M, Colovos C, Meyer-Klaucke W, Munro AW, McLean KJ, Marshall KR, Leys D, Yang JK, Yoon HJ, Lee BI, Lee MG, Kwak JE, Han BW, Lee JY, Baek SH, Suh SW, Komen MM, Arcus VL, Baker EN, Lott JS, Jacobs W, Alber T, Rupp B (2003). The TB structural genomics consortium: a resource for Mycobacterium tuberculosis biology. Tuberculosis (Edinb) 83:223-49.
    Medline: 12906835. PDB: 1FOP 1HTO 1LM1 1LU4 1P3H

Young TA, Delagoutte B, Endrizzi JA, Falick AM, Alber T (2003). Structure of Mycobacterium tuberculosis PknB supports a universal activation mechanism for Ser/Thr protein kinases. Nat Struct Biol 10:168-74.
    Medline: 12548283. PDB: 1MRU

Goulding CW, Apostol M, Anderson DH, Gill HS, Smith CV, Kuo MR, Yang JK, Waldo GS, Suh SW, Chauhan R, Kale A, Bachhawat N, Mande SC, Johnston JM, Lott JS, Baker EN, Arcus VL, Leys D, McLean KJ, Munro AW, Berendzen J, Sharma V, Park MS, Eisenberg D, Sacchettini J, Alber T, Rupp B, Jacobs W, Terwilliger TC (2002). The TB structural genomics consortium: providing a structural foundation for drug discovery. Curr Drug Targets Infect Disord 2:121-41.
    Medline: 12462144. PDB: 1FOP 1KP9 1KPG 1KPH 1KPI 1L1E

Arndt KM, Pelletier JN, Müller KM, Plückthun A, Alber T (2002). Comparison of in vivo selection and rational design of heterodimeric coiled coils. Structure (Camb) 10:1235-48.
    Medline: 12220495.

Corbett KD, Alber T (2001). The many faces of Ras: recognition of small GTP-binding proteins. Trends Biochem Sci 26:710-6.
    Medline: 11738594.

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

Lougheed JC, Holton JM, Alber T, Bazan JF, Handel TM (2001). Structure of melanoma inhibitory activity protein, a member of a recently identified family of secreted proteins. Proc Natl Acad Sci U S A 98:5515-20.
    Medline: 11331761. PDB: 1I1J

McWhirter SM, Pullen SS, Werneburg BG, Labadia ME, Ingraham RH, Crute JJ, Kehry MR, Alber T (1999). Structural and biochemical analysis of signal transduction by the TRAF family of adapter proteins. Cold Spring Harb Symp Quant Biol 64:551-62.
    Medline: 11232332.

Rose RB, Endrizzi JA, Cronk JD, Holton J, Alber T (2000). High-resolution structure of the HNF-1alpha dimerization domain. Biochemistry 39:15062-70.
    Medline: 11106484. PDB: 1G2Y 1G2Z 1G39

Müller KM, Arndt KM, Alber T (2000). Protein fusions to coiled-coil domains. Methods Enzymol 328:261-82.
    Medline: 11075350.

Rose RB, Bayle JH, Endrizzi JA, Cronk JD, Crabtree GR, Alber T (2000). Structural basis of dimerization, coactivator recognition and MODY3 mutations in HNF-1alpha. Nat Struct Biol 7:744-8.
    Medline: 10966642. PDB: 1F93

Day CL, Alber T (2000). Crystal structure of the amino-terminal coiled-coil domain of the APC tumor suppressor. J Mol Biol 301:147-56.
    Medline: 10926498. PDB: 1DEB

Endrizzi JA, Beernink PT, Alber T, Schachman HK (2000). Binding of bisubstrate analog promotes large structural changes in the unregulated catalytic trimer of aspartate transcarbamoylase: implications for allosteric regulation induced cell migration. Proc Natl Acad Sci U S A 97:5077-82.
    Medline: 10805770. PDB: 1EKX

Arndt KM, Pelletier JN, Müller KM, Alber T, Michnick SW, Plückthun A (2000). A heterodimeric coiled-coil peptide pair selected in vivo from a designed library-versus-library ensemble. J Mol Biol 295:627-39.
    Medline: 10623552.

Pullen SS, Labadia ME, Ingraham RH, McWhirter SM, Everdeen DS, Alber T, Crute JJ, Kehry MR (1999). High-affinity interactions of tumor necrosis factor receptor-associated factors (TRAFs) and CD40 require TRAF trimerization and CD40 multimerization. Biochemistry 38:10168-77.
    Medline: 10433725.

McWhirter SM, Pullen SS, Holton JM, Crute JJ, Kehry MR, Alber T (1999). Crystallographic analysis of CD40 recognition and signaling by human TRAF2. Proc Natl Acad Sci U S A 96:8408-13.
    Medline: 10411888. PDB: 1QSC

Hershey PE, McWhirter SM, Gross JD, Wagner G, Alber T, Sachs AB (1999). The Cap-binding protein eIF4E promotes folding of a functional domain of yeast translation initiation factor eIF4G1. J Biol Chem 274:21297-304.
    Medline: 10409688.

Beernink PT, Endrizzi JA, Alber T, Schachman HK (1999). 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 96:5388-93.
    Medline: 10318893.

Crowder SM, Kanaar R, Rio DC, Alber T (1999). Absence of interdomain contacts in the crystal structure of the RNA recognition motifs of Sex-lethal. Proc Natl Acad Sci U S A 96:4892-7.
    Medline: 10220389. PDB: 3SXL

Nautiyal S, Alber T (1999). Crystal structure of a designed, thermostable, heterotrimeric coiled coil. Protein Sci 8:84-90.
    Medline: 10210186. PDB: 1BB1

Harbury PB, Plecs JJ, Tidor B, Alber T, Kim PS (1998). High-resolution protein design with backbone freedom. Science 282:1462-7.
    Medline: 9822371. PDB: 1RH4

Sharma VA, Logan J, King DS, White R, Alber T (1998). Sequence-based design of a peptide probe for the APC tumor suppressor protein. Curr Biol 8:823-30.
    Medline: 9663391.

Gonzalez L, Woolfson DN, Alber T (1996). Buried polar residues and structural specificity in the GCN4 leucine zipper. Nat Struct Biol 3:1011-8.
    Medline: 8946854.

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

Cronk JD, Endrizzi JA, Alber T (1996). High-resolution structures of the bifunctional enzyme and transcriptional coactivator DCoH and its complex with a product analogue. Protein Sci 5:1963-72.
    Medline: 8897596.

Gonzalez L, Plecs JJ, Alber T (1996). An engineered allosteric switch in leucine-zipper oligomerization. Nat Struct Biol 3:510-5.
    Medline: 8646536.

Petersen JM, Skalicky JJ, Donaldson LW, McIntosh LP, Alber T, Graves BJ (1995). Modulation of transcription factor Ets-1 DNA binding: DNA-induced unfolding of an alpha helix. Science 269:1866-9.
    Medline: 7569926.

Nautiyal S, Woolfson DN, King DS, Alber T (1995). A designed heterotrimeric coiled coil. Biochemistry 34:11645-51.
    Medline: 7547896.

Woolfson DN, Alber T (1995). Predicting oligomerization states of coiled coils. Protein Sci 4:1596-607.
    Medline: 8520486.

Endrizzi JA, Cronk JD, Wang W, Crabtree GR, Alber T (1995). Crystal structure of DCoH, a bifunctional, protein-binding transcriptional coactivator. Science 268:556-9.
    Medline: 7725101. PDB: 1DCH

Harbury PB, Kim PS, Alber T (1994). Crystal structure of an isoleucine-zipper trimer. Nature 371:80-3.
    Medline: 8072533.

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