2000–2003

2003

The first structure of an RNA m5C methyltransferase, Fmu, provides insight into catalytic mechanism and specific binding of RNA substrate.
Foster P.G., Nunes C.R., Greene P., Moustakas D., Stroud R.M. (2003).
Structure (Camb) 11, 1609.
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Selectivity and conductance among the glycerol and water conducting aquaporin family of channels.
Stroud R.M., Savage D., Miercke L.J., Lee J.K., Khademi S., Harries W. (2003).
FEBS Lett 555, 79.
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The crystal structure of dihydrofolate reductase-thymidylate synthase from Cryptosporidium hominis reveals a novel architecture for the bifunctional enzyme.
O'Neil, R. H., Lilien, R. H., Donald, B. R., Stroud, R.M. and Anderson, A.C. (2003)
J Eukaryot Microbiol 50 Suppl p555-6.

Architecture and selectivity in aquaporins: 2.5Å x-ray structure of aquaporin Z.
Savage, D. F., Egea, P.F., Robles, Y.C., O’Connell III, J.D., and Stroud, R.M. (2003)
PLoS Biology 1 334-340 with cover, and Synopsis 1 302.
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Phylogenetic classification of protozoa based on the structure of the linker domain in the bifunctional enzyme, dihydrofolate reductase-thymidylate synthase.
O'Neil, R.H., Lilien, R.H., Donald, B.R., Stroud, R.M., and Anderson, A.C. (2003)
J Biol Chem 278 52980-7.
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Catalysis, specificity, and ACP docking site of Streptomyces coelicolor malonyl-CoA: ACP transacylase.
Keatinge-Clay, A.T., Shelat, A.A., Savage, D.F., Tsai, S.C., Miercke, L.J.W., O'Connell, J.D.3rd., Khosla, C., and Stroud, R.M. Structure 11, 147-154.
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Crystal Structure of tRNA pseudouridine synthase TruB and its RNA complex: RNA-protein recognition through a combination of rigid docking and induced fit.
Pan, H., Agarwalla, S., Moustakas, D.T., Finer-Moore, J.S., and Stroud, R.M. (2003)
Proc Nat. Acad. Sci 100, p12648-53.
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Crystal Structure of RumA, an Iron-Sulfur Cluster Containing E. coli Ribosomal RNA 5-Methyluridine Methyltransferase.
Lee, T.L., Agarwalla S., and Stroud, R.M. (2003)
Structure 12, 397-407.
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The crystal structure of dihydrofolate reductase-thymidylate synthase from Cryptosporidium hominis reveals a novel architecture for the bifunctional enzyme.
O’Neil, R. H., Lilien, R. H., Donald, B. R., Stroud, R.M. and Anderson, A.C. (2003)
J Eukaryot Microbiol 50 Suppl p555-6.

Crystal structure and molecular modeling of 17-DMAG in complex with human Hsp90.
Jez, J.M., Chen, J. C., Rastelli, G., Stroud, R.M., Santi, D.V. (2003)
Chem Biol 10, 361-368.
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Structure of Human Pro-Chymase: A Model for the Activating Transition of Granule Associated Proteases.
Reiling, K.K Krucinski, J. Miercke,L.J.W. Raymond, W.W., Caughey, G.H. Stroud, R.M. (2003)
Biochemistry 42, 2616-2624.
PDB accession No. 1NN6
Review abstract
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Glycerol facilitator GlpF and the associated aquaporin family of channels.
Stroud, R.M., Miercke, L.J.W., O'Connell, J., Khademi, S., Lee, J. K., Remis, J., Harries, W., Robles, Y., and Akhavan, D. (2003). Curr Opin Struct Biol 13, 424-431.
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The structural roles of conserved Pro-196, Pro-197 and His-199 in the mechanism of thymidylate synthase.
Gonzalez-Pacanowska, D., Ruiz-Perez, L.M., Carreras-Gomez, M. A., Costi, M.P., Stroud, R.M., Finer-Moore, J.S. and Santi, D.V. (2003) Protein Engineering 16, 229-240
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Mechanisms of Receptor Signalling Across Cell Membranes.
Stroud, R.M. and Wells, J.A. (2003)
Science Signal Transduction Knowledge Environment

Lessons and Conclusions from Dissecting the Mechanism of a Bi-substrate Enzyme: Thymidylate Synthase Mutagenesis, Function and Structure.
Finer-Moore, J.S., Santi, D.V., Stroud, R.M. (2003)
Biochemistry 42, 248-256 (web released Dec 17th 2002 Bi 020599a)

The Only Active Mutant of Thymidylate Synthase D169, a Residue Far from the Site of Methyl Transfer, Demonstrates the Exquisite Nature of Catalysis in Enzymology.
Birdsall, D.L., Bencal, J., Santi, D.V., Stroud, R.M., and Finer-Moore-J. (2003).
Protein Engineering 16, 229-240.
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Conformational Dynamics Along an Enzymatic Reaction Pathway: Thymidylate Synthase, ‘the Movie.’
Robert M. Stroud, Janet S. Finer-Moore (2003)
Biochemistry 42, 239-247. (web released Dec 17th 2002 Bi 020598i)
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2002

Crystal structure of the priming β-ketosynthase from the R1128 polyketide iosynthetic Pathway.
Pan, H., Tsai, S., Meadows, E.S., Miercke, L.J.W., Keatinge-Clay, A.T., O'Connell, J., Khosla, C., Stroud, R.M. (2002)
Structure 10: 1559-1568.
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Structural basis for mobility in the 1.1Å crystal structure of the NG domain of Thermus aquaticus Ffh. Ramirez U.D, Minasov G, Focia P.J, Stroud R.M, Walter P., Kuhn, P., Freymann, D. M. (2002)
J Mol Biol 320: 783-99.
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The glycerol facilitator GlpF, its aquaporin family of channels and their selectivity.
Stroud, R.M., Nollert,P., Miercke, L.M.J. (2002)
Advances in Protein Chemistry Membrane Proteins Editor Doug Rees
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Insights into channel architecture and substrate specificity from crystal structures of two macrocycle forming thioesterases of modular polyketide synthases.
Tsai, S-c., Lu, R., Khosla, C., Stroud, R.M., and Cane, D.E. (2002)
Biochemistry 41 12598-12606
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Conformational dynamics along an enzymatic reaction pathway: Thymidylate Synthase, ‘the Movie.’
Robert M. Stroud, Janet S. Finer-Moore (2002)
Biochemistry (web released Dec 17th 2002 Bi 020598i)
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Lessons and Conclusions from Dissecting the Mechanism of a Bi-substrate Enzyme: Thymidylate Synthase Mutagenesis, Function and Structure.
Finer-Moore, J.S., Santi, D.V., Stroud, R.M. (2002)
Biochemistry (web released Dec 17th 2002 Bi 020599a)

Structure-based studies on species-specific inhibition of thymidylate synthase.
Costi, M.P., Tondi, D., Rinaldi, M., Barlocco, D., Pecorari, P., Soragni, F., Venturelli, A., and Stroud, R.M. (2002) Biochem Biophys Acta 1587, 206-214
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Anisotropic Dynamics of the JE-2147-HIV Protease complex: Drug Resistance and Thermodynamic Binding Mode Examined in a 1.09Å Structure.
Reiling, K., Endres, N., Dauber, D., Craik, C., Stroud, R. (2002)
Biochemistry 41 No 14 4582 –4594.
PDB accession No. 1KZK
Review abstract
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Tryptophan 80 and leucine 143 are critical for the hydride transfer step of thymidylate synthase by controlling active site access.
Fritz TA, Liu L, Finer-Moore JS, Stroud RM. (2002).
Biochemistry 41: 7021
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Chemistry Characterization of the 23 S rRNA m5U1939 Methyltransferase from E. coli.
Agarwalla, S; Kealey, JT; Santi, DV; Stroud, RM (2002).
J. Biol. Chem. 277, 11 8835-40.
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Control of the Selectivity of the Aquaporin Water Channel Family by Global Orientational Tuning.
Tajkhorshid, E. Nollert, P. Jensen, M.O. Miercke, L.J.W. O’Connell, J. Robert M.Stroud, KlausSchulten (2002) Science 296 (5567): 525
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The structure of GlpF, a glycerol conducting channel.
Fu D, Libson A, Stroud R. (2002). Novartis Found Symp 245: 51
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2001

Approaches to solving the rigid receptor problem by identifying a minimal set of flexible residues during ligand docking.
Anderson, A.C., O'Neil, R.H., Surti, T.S., Stroud, R.M. Chemistry & Biology 8 (200) 445-457.
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Structure of Cry2Aa suggests an unexpected recetor binding epitope.
Morse, R.J., Yamamoto, T., Stroud, R.M. (2001) Structure 9 409-417.
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Enzyme-catalyzed therapeutic agent (ECTA) design: activation of the antitumor ECTA compound NB1011 by thymidylate synthase.
Lackey, D., Groziak, M., Sergeeva, M., Beryt, M., Boyer, C., Stroud, R.M., Sayre, P., Park, J., Johnston, P., Slamon, D., Shepard, M., Pegram, M. (2001) Biochemical Pharmacology 61: 179-189.
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The Signal Recognition Particle.
Keenan, R.J., Freymann, D.M., Stroud, R.M., and Walter, P. (2001).
Ann. Rev. of Biochemistry 70:755-75.
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Atomic structure of a glycerol channel and implications for substrate permeation in aqua(glyero)porins.
Nollert, P., Harries, W.E.C., Fu, Daxiong, Miercke, L.J.W., Stroud, R.M. (2001).
FEBS Letters 504(3):112-7.
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Multi-targeted antifolates aimed at avoiding drug resistance form covalent closed inhibitory complexes with human and Escherichia coli thymidylate synthase.
Sayre, P.H., Finer-Moore, J.S., Fritz, T.A., Biermann, D., Gates, S.B., MacKellar, W.C., Patel, V.F., Stroud, R.M. (2001).
Journal of Molecular Biology 313 4 813-829
Review abstract
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Predicting and harnessing protein flexibility in the design of species-specific inhibitors of thymidylate synthase.
Fritz, T.A., Tondi, D., Finer-Moore, J.S., Costi, M.P., and Stroud, R.M. (2001).
Chemistry & Biology 8 No. 10 981-995.
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Crystal structure of the macrocycle-forming thioesterase domain of the erythromycin polyketide synthases: Versatility from a unique substrate channel.
Tsai, S.-C., Miercke, L.J.W., Krucinski, J., Gokhale, R., Chen, Julian C.-H., Foster, P.G., Cane, D.E., Khosla, C., and Stroud, R.M. (2001).
PNAS 98 26 14808-14813.
Review abstract
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2000

Mesoscopic surfactant organization and membrane protein crystallization.
Wiener, M.C., Verkman, A., Stroud, R.M., Van Hoek, A.N. (2000)
Protein Science 9:1407-1409
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Site-directed ligand discovery.
Erlanson, D., Braisted, A., Raphael, D., Randal, M., Stroud, R.M., Gordon, E.M., Wells, J. (2000)
PNAS 97: 17 9347-9372
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The structural basis for tRNA recognition and pseudouridine formation by pseudouridine synthase I.
Foster PG, Huang L, Santi DV, Stroud RM. (2000)
Nat Struct Biol 7:1 23-7.
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Effects of subunit occupancy on partitioning of an intermediate in thymidylate synthase mutants.
Variath, P., Yaoquan Liu, Lee, T.T., Stroud, R.M., and Santi, D.V. (2000).
Biochemistry 39, no. 10, 2429-2435.
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Replacement set mutagenesis of the four phosphate-binding arginine residues of thymidylate synthase.
Kawase, S., Cho, S.W., Rozelle, J., Stroud, R.M., Finer-Moore, J., and Santi, D. (2000).
Protein Engineering 13 8. 557-563.
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The crystal structure of thymidylate synthase from Pneumocystis carinii reveals a fungal insert important for drug design.
Anderson, A.C., Perry, K.M., Freymann, D.M., and Stroud, R.M. (2000).
Journal of Molecular Biology 297(3): 645-657.
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Energetic contributions of four arginines to phosphate-binding in thymidylate synthase are more than additive and depend on optimization of effective charge balance.
Morse, R.J., Kawase, S., Santi, D.V., Finer-Moore, J., and Stroud, R. (2000).
Biochemistry 39: 1011-1020.
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Active site water molecules revealed in the 2.1Å resolution structure of a site-directed mutant of isocitrate dehydrogenase.
Cherbavaz, D.B., Lee, M.E., Stroud, R.M. and Koshland, D.E. Jr. (2000).
J. Mol. Biol. 295, 377-385.
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The structure of a glycerol conducting channel reveals the basis for its selectivity.
Fu, D., Libson, A., Miercke, L., Weitzman, C., Nollert, P., Krucinski, J., and Stroud, R. (2000).
Science 290: 481-486.
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Crystal structure of the HIV-1 integrase catalytic core and C-terminal domains presents a model for viral DNA binding.
Chen, J. C.-H., Krucinski, J., Miercke, L.J.W., Finer-Moore, J.S., Tang, A.H., Leavitt, A.D., and Stroud, R.M. (2000)
Proc. of Natl. Acad. Sci. 97, 15 8233-8238.
Review abstract
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Functional consequences of the Kaposi's Sarcoma-associated herpesviral protease structure: Regulation of activity and dimerization by conserved structural elements.
Reiling, K.K., Pray, T.R., Craik, C.S., and Stroud, R.M. (2000)
Biochemistry 39, 42 12796-803
Review abstract
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