Zhang X., W.A. Baase, and B.W. Matthews (2002) A helix initiation signal in T4 lysozyme identified by polyalanine mutagenesis. Biophys Chem 101-102(1):43-56.

Lowther W.T. and B.W. Matthews (2002) Metalloaminopeptidases: common functional themes in disparate structural surroundings. Chem Rev 2002 102(12):4581-608.

Ostheimer G.J., A. Barkan, and B.W. Matthews (2002) Crystal structure of E. coli YhbY: a representative of a novel class of RNA binding proteins. Structure (Camb) 10(11):1593-601.

Ryter J.M., C.Q. Doe, and B.W. Matthews (2002) Structure of the DNA binding region of prospero reveals a novel homeo-prospero domain. Structure (Camb) 10(11):1541-9.

Wei, B.Q., W.A. Baase, L.H. Weaver, B.W. Matthews, and B.K. Shoichet (2002) A model binding site for testing scoring functions in molecular docking. J Mol Biol 322(2):339-55.

Hausrath, A.C. and B.W. Matthews. (2002). Thermolysin in the absence of substrate has an open conformation. Acta Cryst. 58(Pt 6 Pt2):1002-7.

Lowther, W.T., H. Weissbach, F. Etienne, N. Brot, and B.W. Matthews. (2002). The mirrored methionine sulfoxide reductases of Neisseria gonorrhoeae pilB. Nat Struct Biol 9(5):348-52.

Sagermann, M. and B.W. Matthews. (2002). Crystal structures of a T4-lysozyme duplication-extension mutant demonstrate that the highly conserved beta-sheet region has low intrinsic folding propensity. J Mol Biol. 316(4):348-52.

Sagermann, M. L.G. Martensson, W.A. Baase, and B.W. Matthews. (2002). A test of proposed rules for helix capping: implications for protein design. Protein Sci. 11(3):516-21.

Quillin, M.L. and B.W. Matthews. (2002). Generation of noble-gas binding sites for crystallographic phasing using site-directed mutagenesis. Acta Cryst. 58(Pt 1):97-103.

Juers, D.H. T.D. Heightman, A. Vasella, J.D. McCarter, L. Mackenzie, S.G. Withers, and B.W. Matthews. (2001). A structural view of the action of Escherichia coli (lacZ) beta-galactosidase. Biochemistry 40(49):14781-94.

Weaver, L.H., K. Kwon, D. Beckett, and B.W. Matthews. (2001). Competing protein:protein interactions are proposed to control the biological swich of the E. coli biotin repressor. Protein Sci. 10(12):2618-22.

Hausrath, A.C., R.A. Capaldi, and B.W. Matthews. (2001). The conformation of the epsilon- and gamma-subunits within the Escherichia coli F(1) ATPase. J Biol Chem. 276(50):47227-32.

Juers, D.H. and B.W. Matthews. (2001). Reversible lattice repacking illustrates the temperature dependence of macromolecular interactions. J Mol Biol. 311(4):851-62.

Breyer, W.A. and B.W. Matthews. (2001). A structural basis for processivity. Protein Sci. 10(9):1699-711.

Sagermann, M., T.H. Stevens, and B.W. Matthews. (2001). Crystal structure of the regulatory subunit H of the V-type ATPase of Saccharomyces cerevisiae. PNAS 98(13):7134-9.

Weaver L.H., K. Kwon, D. Beckett, and B.W. Matthews. (2001). Corepressor-induced organization and assembly of the biotin repressor: a model for allosteric activation of a transcriptional regulator. PNAS 98(11):6045-50.

Xu, J. W.A. Baase, M.L. Quillin, E.P. Baldwin, and B.W. Matthews. (2001). Structural and thermodynamic analysis of the binding of solvent at internal sites in T4 lysozyme. Protein Sci 10(5):1067-78.

Su, A.I., D.M. Lorber, G.S. Weston, W.A. Baase, B.W. Matthews, and B.K. Shoichet. (2001) Docking molecules by families to increase the diversity of hits in database screens: Computational strategy and experimental evaluation. Proteins 42:279-93.

Yang, G., C. Cecconi, W.A. Baase, I.R. Vetter, W.A. Breyer, J.A. Haack, B.W. Matthews, F.W. Dahlquist, and C. Bustamante. (2000) Solid-state synthesis and mechanical unfolding of polymers of T4 lysozyme. PNAS 97:139-44.

Korndörfer, I.P., J. Salerno, D. Jing, and B.W. Matthews. (2000) Crystallization and preliminary X-ray analysis of a bacteriophage T4 primase fragment. Acta Cryst. D56:95-7.

Liu, R., W.A. Baase, and B.W. Matthews. (2000) The introduction of strain and its effects on the structure and stability of T4 lysozyme. J. Mol. Biol. 295:127-45.

Matthews, B.W. (2000) Obituary: Paul Sigler. Nature 403:848.

Sagermann, M. and B.W. Matthews. (2000) Cloning, expression and crystallization of VMA13p, an essential subunit of the vacuolar H+-ATPase of Saccharomyces cerevisiae. Acta Cryst. D56:475-7.

Rupert, P.B., A.K.M.M. Mollah, M.C. Mossing, and B.W. Matthews. (2000) The structural basis for enhanced stability and reduced DNA binding seen in engineered second-generation Cro monomers and dimers. J. Mol. Biol. 296:1079-90.

Lowther, W.T. and B.W. Matthews. (2000) Structure and function of the methionine aminopeptidases. Biochem. Biophys. Acta 1477:157-67.

Wray, J.W., W.A. Baase, G.J. Ostheimer, and B.W. Matthews. (2000) Use of a non-rigid region in T4 lysozyme to design an adaptable metal-binding site. Prot. Engin. 13:313-21.

Quillin, M.L. and B.W. Matthews. (2000) Accurate calculation of the density of proteins. Acta Cryst. 56:791-4.

Lowther, W.T., N. Brot, H. Weissbach, J.F. Honek, and B.W. Matthews. (2000) Thiol-disulfide exchange is involved in the catalytic mechanism of peptide methionine sulfoxide reductase. PNAS 97:6463-8.

Korndoerfer, I.P., W-D. Fessner, and B.W. Matthews. (2000) The structure of rhamnose isomerase from Escherichia coli and its relation with xylose isomerase illustrates a change between inter- and intra-subunit complementation during evolution. J. Mol. Biol. 300:917-33.

He, M.H., S.L. Clugston, J.F. Honek, and B.W. Matthews. (2000) Determination of the structure of Escherichia coli glyoxalase I suggests a structural basis for differential metal activation. Biochemistry 39:8719-27.

Juers, D.H., R.H. Jacobson, D. Wigley, X-J. Zhang, R.E. Huber, D.E. Tronrud, and B.W. Matthews. (2000) High resolution refinement of ß-galactosidase in a new crystal form reveals multiple metal-binding sites and provides a structural basis for a-complementation. Prot. Sci. 9:1685-99.

Quillin, M.L., W.A. Breyer, I.J. Griswold, and B.W. Matthews. (2000) Size versus polarizability in protein-ligand interactions: Binding of noble gases within engineered cavities in phage T4 lysozyme. J. Mol. Biol. 302:955-77.

Juers, D.H., R.E. Huber, and B.W. Matthews. (1999) Structural comparisons of TIM barrel proteins suggest functional and evolutionary relationships between beta-galactosidase and other glycohydrolases. Prot. Sci. 8:122-36.

Sagermann, M., W.A. Baase, and B.W. Matthews. (1999) Structural characterization of an engineered tandem repeat contrasts the importance of context and sequence in protein folding. PNAS 96:6078-83.

Lowther, W.T., A.M. Orville, D.T. Madden, S. Lim, D.H. Rich, and B.W. Matthews. (1999) Escherichia coli methionine aminopeptidase: Implications of crystallographic analyses of the native, mutant and inhibited enzymes for the mechanism of catalysis. Biochemistry 38:7678-88.

Kuroki, R., Weaver, L.H. and Matthews, B.W. (1999) Structural basis of the conversion of T4 lysozyme into a transglycosidase by re-engineering the active site. PNAS 96:8949-54.

Kovall, R.A. and B.W. Matthews. (1999) Type II restriction endonucleases: Structural, functional and evolutionary relationships. Curr. Opin. Chem. Biol. 3:578-83.

Wray, J.W, W.A. Baase, J.D. Lindstrom, L.H. Weaver, A.R. Poteete, and B.W. Matthews. (1999) Structural analysis of a non-contiguous second-site revertant in T4 lysozyme shows that increasing the rigidity of a protein can enhance its stability. J. Mol. Biol. 292:1111-20.

Gassner, N.C., W.A. Baase, J.D. Lindstrom, J. Lu, F.W. Dahlquist, and B.W. Matthews. (1999) Methionine and alanine substitutions show that the formation of wildtype-like structure in the carboxy-terminal domain of T4 lysozyme is the rate-limiting step in folding. Biochemistry 38:14451-60.

Lowther, W.T., Y. Zhang, P.B. Sampson, J.F. Honek, and B.W. Matthews. (1999) Insights into the mechanism of Escherichia coli methionine aminopeptidase from the structural analysis of reaction products and phosphorus-based transition-state analogues. Biochemistry 38:14810-9.

Gassner, N.C., W.A. Baase, A.C. Hausrath, and B.W. Matthews. (1999) Substitution with selenomethionine can enhance the stability of methionine-rich proteins. J. Mol. Biol. 294:17-20.

Gassner, N.C. and B.W. Matthews. (1999) Use of differentially substituted selenomethionine proteins in X-ray structure determination. Acta Cryst. D55:1967-70.

Hausrath, A.C., G. Grüber, B.W. Matthews, and R.A. Capaldi. (1999) Structural features of the g-subunit of the Escherichia coli F1 ATPase revealed by a 4.4Å resolution map obtained by X-ray crystallography. PNAS 96:13697-702.

DuBose, R.F., W.A. Baase, X-J. Zhang, J. Xu, and Matthews, B.W. (1999) Putative intermediates between T4 and P22 lysozymes show the importance of synergistic effects in protein evolution. In Perspectives in Structural Biology, A Volume in Honour of G.N. Ramachandran (M. Vijayan, N. Yathindra, A.S. Kolaskar, eds.), Indian Academy of Sciences and the Universities Press, Hyderbad, India, pp. 139-52.

Baase, W.A., N.C. Gassner, X-J. Zhang, R. Kuroki, L.H. Weaver, D.E. Tronrud, and B.W. Matthews. (1999) How much sequence variation can the functions of biological molecules tolerate? In Simplicity and Complexity in Proteins and Nucleic Acids, Dahlem Workshop (H. Frauenfelder, J. Deisenhofer & P.G. Wolynes, eds.), Dahlem University Press, Berlin, pp. 297-311.

Xu, J., W.A. Baase, E. Baldwin, and B.W. Matthews. (1998) The response of T4 lysozyme to large-to-small substitutions within the core and its relation to the hydrophobic effect. Prot. Sci. 7:158-77.

Lipscomb, L.A., N.C. Gassner, S.D. Snow, A.M. Eldridge, W.A. Baase, D.L. Drew, and B.W. Matthews. (1998) Context-dependent protein stabilization by methionine-to-leucine substitution shown in T4 lysozyme. Prot. Sci. 7:765-73. (Erratum p. 1481)

Albright, R.A. and B.W. Matthews. (1998) How Cro and lambda-repressor distinguish between operators: The structural basis underlying a genetic switch. PNAS 95:3431-6.

Baldwin, E., W.A. Baase, X-J. Zhang, V. Feher, and B.W. Matthews. (1998) Generation of ligand binding sites in T4 lysozyme by deficiency-creating substitutions. J. Mol. Biol. 277:467-85.

Rupert, P.B., G.W. Daughdrill, B. Bowerman, and B.W. Matthews. (1998) A new DNA-binding motif in the Skn-1 binding domain-DNA complex. Nature Struct. Biol. 5:484-91.

Ohlendorf, D.H., D.E. Tronrud, and B.W. Matthews. (1998) Refined structure of Cro repressor protein from bacteriophage lambda suggests both flexibility and plasticity. J. Mol. Biol. 280:129-36.

Albright, R.A. and B.W. Matthews. (1998) Crystal structure of lambda-Cro bound to a consensus operator at 3.0A resolution. J. Mol. Biol. 280:137-51.

Albright, R.A., M.C. Mossing, and B.W. Matthews. (1998) Crystal structure of an engineered Cro monomer bound nonspecifically to DNA: Possible implications for nonspecific binding by the wild-type protein. Prot. Sci. 7:1485-94.

Kovall, R.A. and B.W. Matthews. (1998) Structural, functional and evolutionary relationships between lambda-exonuclease and the type II restriction endonucleases. PNAS 95:7893-7.

Lowther, W.T., D.A. McMillen, A.M. Orville, and B.W. Matthews. (1998) The anti-angiogenic agent fumagillin covalently modifies a conserved active-site histidine in the Escherichia coli methionine aminopeptidase. PNAS 95:12153-7.