Graduate student supervision:
Weber, P.C. , Howard, A., Xuong, Ng -h and Salemme, F.R. (1981) Crystallographic structure of Rhodospirillum molischianum ferricytrochrome c' at 2.5 Å resolution. J. Mol. Biol. 153: 399-424.
Hamlin, R.C., Cork, C. Howard, A. Nielsen, C., Vernon, W., Matthews, D., and Xuong, Ng.-h. (1981) Characteristics of a flat multiwire area detector for protein crystallography, J. Applied Crystallogr.14: 85-93.
Howard, A.J. (1982) Computing requirements for area detector data collection, in : Computational Crystallography (Sayre, D., ed.: Oxford, Clarendon Press), pp. 29-40.
Howard, A.J. Nielsen, C.P., Xuong, Ng.-h (1984) Software for a multiwire area detector. Methods in Enzymology114: 452-472.
Howard, A.J. Mitchell, C.E., Dutcher, J.S., Henderson, T.R. and McClellan, R.O. (1986) Binding of nitropyrenes and benzo[a]pyrene to mouse lung deoxyribonucleic acid after pretreatment with inducing agents. Biochemical Pharmacology35: 2129-2134.
Howard, A.J. Gilliland, G.L., Finzel, B.C. Poulos, T.L. Ohlendorf, D.H. and Salemme, F.R. (1987) Use of an imaging proportional counter in macromolecular crystallography. J. Applied Crystallogr.20: 383:387.
Poulos, T.L. and Howard, A.J. (1987) Crystal structures of metyrapone- and phenyimidazole-inhibited complexes of cytochrome P-450cam. Biochemistry26: 8165-8174.
Poulos, T.L., Sheriff, S., and Howard, A.J. (1987) Cocrystals of yeast cytochrome c peroxidase and horse heart cytochrome c. J. Biol. Chem.262: 13881-13884.
Poulos, T.L., Finzel, B.C. and Howard, A.J. (1987) High-resolution crystal structure of Cytochrome P-450cam. J. Mol. Biol.195: 687-700.
Gilliland, G.L., Howard, A.J., Winborne, E.L., Poulos, T.L, Stewart, D.B., and Durham, D.R. (1987) Crystallization and Preliminary X-ray Diffraction Studies of Subtilisin GX from Bacillus sp. GX6644. J. Biol. Chem.262: 4280-4283.
Whitlow, M., and Howard, A.J. (1989) 1.6Å Structures of xylose isomerase from Streptomyces rubiginosus with xylitol and xylose and their mechanistic implications. Trans. Amer. Crystallogr. Assoc.25: 105-126.
Whitlow, M., Howard, A.J. Finzel, B.C. Poulos, T.L. Winborne, E., and Gilliland, G.L. (1991) A metal-mediated hydride shift mechanism for xylose isomerase based on 1.6Å Streptomyces rubiginosus structures with xylitol and D-xylose. Proteins: Struct., Func., Genet.9: 153-173.
Achari, A., Hale, S.P. Howard, A.J. Clore, G.M. Gronenborn, A.M., Hardman, K.D., and Whitlow, M. (1992), the 1.67A X-ray Structure of the B2 Immunoglobulin-Binding Domain of Streptococcal Protein G and Comparison to the NMR Structure of the B1 Domain. Biochemistry 31: 10449-10457.
Howard, A.J. and Poulos, T.L., (1992) Methods in macromolecular crystallography. chapter in Advances in Biophysical Chemistry2: 1-36.
Essig, N.Z. Wood, J.F., Howard, A.J., Raag, R., and Whitlow, M. (1993) Crystallization of Single-Chain Fv Proteins. J. Mol. Biol.234: 897-901.
Whitlow, M., Howard, A.J., Wood, J.F., Voss, E.W., and Hardman, K.D. (1995) 1.85 Å Structure of anti-fluorescein 4-4-20 Fab. Protein Engineering8: 749-761.
Howard, A.J. (2000) Data processing in macromolecular crystallography. Chapter in: Crystallographic Computing 7: Proceedings from the Macromolecular Crystallographic Computing School, 1996. P.E. Bourne and K.D. Watenpaugh, eds. Oxford: Oxford University Press.
Whitlow, M., Howard, A.J., Stewart, D., Hardman, K., Kuyper, L.F., Baccanari, D.P., Tansik, R.L., and Fling, M. (1997) X-ray crystallographic studies of Candida albicans dihydrofolate reductase: high resolution structures of the holoenzyme and an inhibited ternary complex. J. Biol. Chem.272 30289-30298.
Thoden, J.B., Miran, S.G., Phillips, J.C., Howard, A.J., Raushel, F.M., Holden, H.M. (1998) Carbamoyl phosphate synthetase: Caught in the Act of Glutamine hydrolysis. Biochemistry 37: 8825-8831.
Raves, M. L., Giles, K., Schrag, J. D., Schmid, M. F., Phillips Jr., G. N., Wah, C., Howard, A. J., Silman, I., Sussman, J. L. (1998) Quaternary Structure of Tetrameric Acetylcholinesterase. In: Structure and Function of Cholinesterases and Related Proteins (Doctor, B.P., Quinn, D.M., Rotundo, R.L. & Taylor, P., eds.).
Howard, A. (1998) Participation of pharmaceutical companies in synchrotron radiation research. Nature Structural Biology 5: 623-626.
Eisenstein, E., Gilliland, G.L., Herzberg, O., Moult, J., Orban, J., Poljak, R.J., Banerjei, L., Richardson, D., and Howard, A.J. (2000) Biological function made crystal clear - annotation of hypothetical proteins via structural genomics. Current Opinions in Biotechnology 11: 25-30.
Mayhew, M.P., Holden, M.J., Howard, A.J., Gallagher, D.T., and Stover, C. (2000) Crystallization and 1.1-Å diffraction of chorismate lyase from Escherichia coli. J. Structural Biology129: 96-99.
Ladner, J.E., Reddy, P., Davis, A., Tordova, M., Howard, A.J., and Gilliland, G.L. (2000) The 1.30 Å resolution structure of the Bacillus subtilis chorismate mutase catalytic homotrimer. Acta CrystallographicaD56: 673-683.
Gallagher, D.T., Mayhew, M., Holden, M.J., Howard, A., Kim, K.J., and Vilker, V.L. (2001) The crystal structure of chorismate lyase shows a new fold and a tightly retained product. Proteins 44: 304-311.
Lim, K., Zhang, H., Tempczyk, A., Bonander, N., Toedt, J., Howard, A., Eisenstein, E., and Herzberg, O. (2001) Crystal structure of YecO from Haemophilus influenzae (HI0319) reveals a methyltransferase fold and a bound S-Adenosylhomocysteine. Proteins 45: 397-407.
Sanders, D.A.R., Moothoo, D.N., Raftery, J., Howard, A.J., Helliwell, J.R., and Naismith, J.H. (2001). The 1.2 Å resolution structure of the con A-dimannose complex. J. Mol. Biol. 310: 875-884.
Tereshko, V., Wilds, C.J., Minasov, G., Prakash, T.P., Maier, M.A., Howard, A.J., Wawrzak, Z. Manoharan, M., and Egli, M. (2001) Detection of alkali metal ions in DNA crystals using state-of-the-art X-ray diffraction experiments. Nucleic Acids Res. 29: 1208-1215.
Hanson,B.L., Harp,J.M., Kirschbaum,K., Parrish,D.A., Timm,D.E., Howard,A.J., Pinkerton,A.A., and Bunick,G.J. (2001) Macromolecular data collection with cryogenic helium. J. Cryst. Growth 232, 536-544.
Obmolova, G., Teplyakov, A., Bonander, N., Eisenstein, E., Howard, A.J., and Gilliland, G.L. (2001) Crystal structure of dephospho-coenzyme A kinase from Haemophilus influenzae. J. Structural Biol. 136:119-125.
Parsons, J.F., Jensen, P.Y., Pachikara, A.S., Howard, A.J., Eisenstein, E., and Ladner J.E. (2002) Structure of Escherichia coli aminodeoxychorismate synthase: architectural conservation and diversity in chorismate-utilizing enzymes. Biochemistry 41(7): 2198-2208.
Howard, Andrew J. (2002) Macromolecular crystallography at third-generation synchrotron radiation sources. Third-generation Hard X-ray Synchrotron Radiation Sources: Source Properties, Optics, and Experiment. D.M. Mills, ed.; John Wiley & Sons, pp. 311-344.
Hanson,B.L., Harp,J.T., Kirschbaum,K., Schall,C.A., DeWitt,K. Howard,A., Pinkerton,A.A., and Bunick,G.J. (2002) Experiments testing the abatement of radiation damage in D-xylose isomerase crystals with cryogenic helium. J. Synchrotron Rad. 9: 375-381.
Herzberg, O., Chen, C.C.H., Liu, S., Tempczyk, A., Howard, A., Wei, M., Ye, D., and Dunaway-Mariano, D. (2002) Pyruvate site of pyruvate phosphate dikinase: crystal structure of the enzyme-phosphonopyruvate complex, and mutant analysis. Biochemistry-US 41: 780-787.
Chen, C., Zhang, H., Kim, A., Howard, A., Sheldrick, G.A., Mariano-Dunaway, D., and Herzberg, O. (2002) Degradation pathway of the phosphonate ciliatine: Crystal structure of 2-aminoethylphosphonate transaminase. Biochemistry-US 41: (44) 13162-13169, (2002).
Lehmann, C., Lim, K., Toedt, J., Krajewski, W., Howard, A., Eisenstein, E., and Herzberg, O. (2002) Structure of 2C-methyl-D-erythrol-2,4-cyclodiphosphate synthase from Haemophilus influenzae: activation by conformational transition. Proteins: Structure, Func., and Genet. 49(1): 249-260.
Kim, K.-J. and Howard, A.J. (2002) Crystallization and preliminary X-ray diffraction analysis of the trigonal crystal form of Saccharomyces cerevisiae alcohol dehydrogenase I: evidence for the existence of Zn ions in the crystal. Acta Crystallogr. D58: 1332-1334.
Teplyakov, A., Obmolova, G., Tordova, M., Thanki, N., Bonander, N., Eisenstein, E. Howard, A.J., and Gilliland, G.L. (2002) Crystal structure of the YjeE protein from Haemophilus influenzae: A putative ATPase involved in cell wall synthesis. Proteins 48: 220-226.
Kim, K.J., Kim, Y., Park, K.W., Webster, D.A., and Howard, A.J. (2002) Purification, crystallization, and preliminary X-ray analysis of the soluble domain of the Na+ -pumping cytochrome bo quinol oxidase from Vitreoscilla. Acta Crystallogr.D.58: 1329-1331.
Willis,M.A., Krajewski,W., Chalamasetty, V.R., Reddy,P., Howard,A., Herzberg,O. (2002) Structure of HI1333 (YhbY), a putative RNA-binding protein from Haemophilus. Proteins 49: 423-426.
Lim, K., Tempczyk, A., Bonander, N., Toedt, J., Howard, A., Eisenstein, E., and Herzberg, O. (2003) A catalytic mechanism for D-Tyr-tRNATyr deacylase based on the crystal structure of Hemophilus influenzae HI0670. J. Biol. Chem. 278(15): 13496-13502.
Gilliland, G.L., Teplyakov, A., Obmolova, G., Tordova, M., Thanki, N., Ladner, J., Herzberg, O., Lim, K., Zhang, H., Huang, K., Li, Z., Tempczyk, A., Krajewski, W., Parsons, L., Yeh, D.C., Orban, J., Howard, A.J., Eisenstein, E., Parsons, J.F, Bonander, N., Fisher, K.E., Toedt, J., Reddy, P., Rao, C.V., Melamud, E., and Moult, J.(2003) Assisting functional assignment for hypothetical Haemophilus influenzae gene products through structural genomics. Current Drug Targets - Infectious Disorders 2:339-353.
Lehmann, C., Lim, K., Rao Chalamasetty, V., Krajewski, W., Melamud, E., Galkin, A., Howard, A., Kelman, Z., Reddy, P.T., Murzin, A.G., and Herzberg, O. (2003) The HI0073/HI0074 protein pair from Haemophilus influenzae is a member of a new nucleotidyltransferase family: Structure, sequence analyses, and solution studies. Proteins: Structure, Func., and Genet. 50(2):249-260.
Teplyakov, A., Obmolova, G., Khil, P. P., Howard, A. J., Camerini-Otero, R. D., Gilliland, G. L. (2003) Crystal Structure of the Escherichia Coli Ycdx Protein Reveals a Trinuclear Zinc Active Site. Proteins: Struct.,Funct.,Genet. 51:315-318.
Teplyakov, A., Obmolova, O., Chu, S.Y., Toedt, J., Eisenstein, E., Howard, A.J., and Gilliland, G.L. (2003) Crystal structure of YchF protein reveals binding sites for GTP and nucleic acid J. Bacteriol. 185(14):4031-4037.
Lim, K., Tempcyzk, A., Parsons, J. F., Bonander, N., Toedt, J., Kelman, Z., Howard, A., Eisenstein, E., Herzberg, O. (2003) Crystal structure of Ybab from Haemophilus influenzae (Hi0442), a protein of unknown function coexpressed with the recombinational DNA repair protein RecR. Proteins: Struct.,Funct.,Genet. 50(2):375-79.
Lim, K., Zhang, H., Tempczyk, A., Krajewski, W., Bonander, N., Toedt, J., Howard, A., Eisenstein, E., and Herzberg, O. (2003) Structure of the YibK methyltransferase from Haemophilus influenzae (HI0766): a cofactor bound at a site formed by a knot. Proteins: Struct., Func., Genet. 51:56-67.
Teplyakov,A., Oblmolova,G., Bir,N., Reddy,P., Howard,A.J., and Gilliland, G.L. (2003) Crystal structure of YajQ protein from Haemophilus influenzae reveals a tandem of RNP-like domains. J.Struct.Funct.Geno. 4: 1-9.
Hoang, Q., Sicheri, F., Howard,A., Yang,D. (2003) Bone recognition mechanism of porcine osteocalcin from crystal structure. Nature 425: (October) 977-980.
Obmolova, G., Teplyakov, A., Khil, P. P., Howard, A. J., Camerini-Otero, R. D., Gilliland, G. L. (2003) Crystal structure of the Escherichia coli Tas protein, an Nadp(H)-dependent aldo-keto reductase Proteins: Struct.,Funct.,Genet. 53: 323-325.
Park, K.-W., Webster, D.A., Stark, B.C., Howard, A.J., and Kim, K.-J. (2003) Fusion protein system designed to provide color to aid in the expression and purification of proteins in Escherichia coli. Plasmid 50: 169-175.
Ladner, J.E., Obmolova, G., Teplyakov, A., Howard, A.J., Khil, P.P., Camerini-Otero, R.D., and Gilliland, G.L. (2003) Crystal structure of Escherichia coli protein ybgl, a toroidal structure with a dinuclear metal site. BioMed Central Structural Biology 3: 7.
Lehmann, C., Doseeva, V., Pullalarevu, S., Krajewski, W., Howard, A., and Herzberg, O. (2004) YbdK is a carboxylate-amine ligase with a γ- glutamyl:cystein ligase activity: crystal structure and enzymatic assays. Proteins: Struct., Func., Bioinform. 56: 376-383.
Khil, P. P., Obmolova, G., Teplyakov, A., Howard, A. J., Gilliland, G. L., Camerini-Otero, R. D. (2004) Crystal structure of the Escherichia coli Yjia protein suggests a GTP-dependent regulatory function. Proteins: Struct., Funct., Bioinform. 54: 371-374.
Liu, S., Lu, Z., Han, Y., Jia, Y., Howard, A., Dunaway-Mariano, D., and Herzberg, O. (2004) Conformational flexibility of PEP Mutase. Biochemistry 43: 4447-4453.
Lim, K., Sarikaya, E., Galkin, A., Krajewski, W., Pullalarevu, S., Shin, J-H., Kelman, Z., Howard, A., and Herzberg, O. (2004) Novel structure and nucleotide binding properties of HI1480 from Haemophilus influenzae: A protein with no known sequence homologies. Proteins: Struct., Func., Bioinform. 56: 564-571.
Galkin, A., Sarikaya, E., Lehmann, C., Howard, A., and Herzberg, O. (2004) X-ray structure of HI0817 from Haemophilus influenzae: Protein of unknown function with a novel fold. Proteins: Struct., Func., Bioinform. 57, 874-877.
Teplyakov, A., Obmolova, G., Sarikaya, E., Pullalarevu, S., Krajewski, W., Galkin, A., Howard, A. J., Herzberg, O., Gilliland, G. L. (2004) Crystal structure of the Ygfz protein from Escherichia coli suggests a folate-dependent regulatory role in one-carbon metabolism. J. Bacteriol. 186: 7134-7140.
Schormann, N., Pal, B., Senkovich, O., Carson, M., Howard, A., Smith, C., Delucas, L., Chattopadhyay, D. (2005) Crystal Structure of Trypanosoma cruzi pteridine reductase 2 in complex with a substrate and an inhibitor. J.Struct.Biol. 152: 64-75.
Lim, K., Doseeva, V., Sarikaya Demirkan, E., Pullalarevu, S., Krajewski, W., Galkin, A., Howard, A., Herzberg, O. (2005) Crystal structure of the Ygfy from Escherichia coli, a protein that may be involved in transcriptional regulation. Proteins: Struct., Funct., Bioinform. 58 759-763.
Willis, M. A., Song, F., Zhuang, Z., Krajewski, W., Chalamasetty, V. R., Reddy, P., Howard, A., Dunaway-Mariano, D., Herzberg, O. (2005) Structure of Ycii from Haemophilus influenzae (Hi0828) reveals a ferredoxin-like alpha/beta-fold with a histidine/ aspartate centered catalytic site. Proteins: Struct., Func., Bioinform. 59::648-652.
Herzberg, O., Gilliland, G., Orban, J., Howard, A., and Moult, J. (2005) Chasing the function of hypothetical proteins. Acta Crystallographica A61: c25.
Jin, T., Howard, A.J., Golemis, E.A., Wang, Y., and Zhang, Y.-Z. (2005) Overproduction, purification, crystallization and preliminary X-ray diffraction studies of the human spliceosomal protein TXNL4B. Acta Crystallographica F61: 282-284.
Jin, T., Howard, A.J., Golemis, E.A., Wang, Y., and Zhang, Y.-Z. (2005) Overproduction, purification, crystallization and preliminary X-ray diffraction studies of the human transcription repressor ERH. Acta Crystallographica F61: 531-533.
Lehmann, C., Pullalarevu, S., Krajewski, W., Willis, M. A., Galkin, A., Howard, A., Herzberg, O. (2005) Structure of Hi0073 from Haemophilus influenzae, the nucleotide-binding domain of a two-protein nucleotidyl transferase. Proteins: Struct., Func., Bioinform. 60: 807-811.
Smith, N., Roitberg, A.E., Rivera, E., Howard,A., Holden,M.J., Mayhew, Mayhew,M., Kaistha,S., and Gallagher,D.T. (2006) Structural analysis of ligand binding and catalysis in chorismate lyase, Arch.Biochem.Biophys. 445:72-80.
Chen,C.C.H., Han,C. Niu,W., Kulakova,A., Howard,A., Quinn,J.P., Dunaway-Mariano,D., and Herzberg,O. (2006) Structure and Kinetics of Phosphonopyruvate Hydrolase from VorioVorax sp. Pal2: New Insight into the Divergence of Catalysis within the PEP Mutase/Isocitrate Lyase Superfamily Biochemistry 45: 11491-11504.
Kim, S.-K., Reddy, S.K., Nelson, B.C., Vasquez, G.B., Davis, A., Howard, A.J., Patterson, S., Gilliland, G.L., Ladner, J.E., and Reddy, P.T. (2006) Biochemical and Structural Characterization of the Secreted Chorismate Mutase (Rv1885c) from Mycobacterium tuberculosis H37Rv: an *AroQ Enzyme Not Regulated by the Aromatic Amino Acids J. Bacteriol. 188: 8638-8648.
Guo, F., Jin, T., Howard, A., and Zhang, Y.-Z. (2007) Purification, crystallization and initial crystallographic characterization of brazil-nut allergen Ber e 2. Acta Crystallographica F63: 976-979.
Teplyakov,A., Lim,K., Zhu,P.P., Kapadia,G., Chen,C.C.H., Schwartz,J., Howard,A., Reddy,P.T., Peterkofsky,A., and Herzberg,O. (2006) Structure of phosphorylated enzyme I, the phosphoenolpyruvate:sugar phosphotransferase system sugar translocation signal protein. Proc.Natl.Acad.Sci. 103: 16218-16223.
Jin, T., Howard, A., and Zhang, Y.-Z. (2007) Purification, crystallization and initial crystallographic characterization of peanut major allergen Ara h 3. Acta Crystallographica F63: 848-851.
Guo, F., Jin, T., Howard, A., and Zhang, Y.Z. (2007) Purification, crystallization and initial crystallographic characterization of brazil-nut allergen Ber e 2. Acta Crystallographica F63: 976-979.
Jin, T., Kim, S., Guo, F., Howard, A., and Zhang, Y.-Z. (2007) Purification and crystallization of recombinant human TNF-like ligand TL1A. Cytokine 40: 115-122.
Jin, T., Fu, T-J., Kothary, M.H., Howard, A., and Zhang, Y.-Z. (2007) Crystallization and initial crystallographic characterization of a vicilin-type seed storage protein from Pinus koraiensis. Acta Crystallographica F63: 1041-1043.
Jin, T., Guo, F., Kim, S., Howard, A., and Zhang, Y.-Z. (2007) X-ray crystal structure of TNF ligand family member TL1A at 2.1Å. Biochem.Biophys.Res.Comm. 364: 1-6.
Guo, F., Kothary, M.H., Wang, Y., Yu, X., Howard, A.J., Fu T.J., and Zhang Y.Z. (2009) Purification and crystallization of Cor a 9, a major hazelnut allergen. Acta Crystallogr. F 65: 42-46.
Chao K.L., Lim, K., Lehmann. C., Doseeva, V., Howard, A.J., Schwarz, F.P., and Herzberg, O. (2008) The Escherichia coli YdcF binds S-adenosyl-L-methionine and adopts an alpha/beta-fold characteristic of nucleotide-utilizing enzymes. Proteins: Struct., Func., Bioinform. 65: 42-46.
Fang, X., Osipiuk J., Chakravarthy S., Yuan M., Menzer W.M., Nissen D., Liang P., Raba D.A., Tuz K., Howard A.J., Joachimiak A., Minh D.D.L., Juárez O. (2019) Conserved residue His-257 of Vibrio cholerae flavin transferase ApbE plays a critical role in substrate binding and catalysis. J.Biol.Chem. 294 (37): 13800-13810.
Howard, A.J. (2019) Ideal bond lengths and angles in nucleic acid structures: an update for the 2020s. Acta Crystallogr. B 58: 50-51.
Howard, A.J. (2022) A recommendation on the teaching of Michaelis-Menten kinetics in biochemistry courses. Biochemistry and Molecular Biology Education, in press.
1A2Q,
1A9X,
1AI9,
1AK9,
1AOE,
1AQN,
1AU9,
1DBF,
1EEA,
1FL9,
1FLR,
1HTW,
1I2K,
1I2L,
1I3H,
1IA1,
1IA2,
1IA3,
1IA4,
1IN0,
1JJV,
1JOS,
1JOV,
1K0E,
1K0G,
1LQA,
1M65,
1M68,
1M78,
1M79,
1M7A,
1NIJ,
1NMO,
1NMP,
1NRK,
1PGX,
1PHC,
1PHD,
1PHE,
1PHF,
1PHG,
1Q8H,
1S01,
1TT8,
1XIS,
1XLR,
2CPP,
2F6L,
2NML,
2XIS,
3XIS,
4XIS,
3TM9,
3TM3