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Research Interests

Areas of Interest

Virus capsids

Capsids are roughly spherical protein shells surrounding the DNA or RNA of many viruses and are responsible for transporting it to infect new hosts and cells.  Capsids contain many copies of 1 or more proteins arranged with icosahedral symmetry.  Our studies of viral assemblies are directed towards visualizing the interactions that target a virus to particular host cells, and that lead to its recognition and neutralization by the host's immune system.

Adenoassociated virus (AAV) is a widely-used vector in experimental gene therapies being developed to cure genetic diseases such as cystic fibrosis, cancers, etc..  In 2002 we published the first atomic structure, the culmination of efforts to culture large quantities of the virus in human cells and to solve one of the largest ever crystal structures at ~ 1 million atoms.  AAV has prominent surface protrusions.  They are formed by intertwined loops from adjacent subunits that bring together different regions of the primary sequence which had previously been implicated genetically in cell receptor binding.  Calculations of the electrostatic potential from the atomic coordinates revealed that one side of each protrusion was positively charged and a candidate site for binding of the heparan sulfate proteoglycan receptor.  This general location has since been confirmed by mutagenesis in other laboratories.

We continue to study AAV-receptor interactions through electron microscopy of virus-heparan complexes (in collaboration with Ken Taylor) and crystallography of virus complexed with small heparan analogs.  These should give us complementary low resolution over-view and detailed visualizations of virus-receptor interactions.  We are also investigating virus-antibody interactions in three ways:  (1) electron microscopic imaging of complexes with selected monoclonal antibodies; (2) in vitro selection of neutralizing escape mutant viruses, to map sites of mutation to the structure; (3) structure determinations of other AAV serotypes (strains), to see how natural variants have evolved in response to immune challenge. 

Together, these basic structure-function studies will allow us and others to pursue a more rationale approach to the engineering of improved viral vectors for gene therapy.  We hope that our studies will lay the groundwork for the retargeting of AAV to the tissues of choice and for the delivery of gene therapies without immune interception.

Human rhinovirus 50 (HRV50):  We have recently completed a 2.0 Å structure determination of this common cold virus, complexed with a clinically-tested drug.  Serotype 50 was chosen as the most typical in response to drugs.  Serendipitously, the structure is at higher resolution than hitherto possible.  We are beginning analyses of the virus-drug interactions and comparisons to other serotypes. 

Enzymes

Arginine kinase is the arthropod homologue of creatine kinase that catalyzes a reaction which maintains the ATP concentration.  We use it as a model for understanding how bimolecular (two-substrate) enzyme reactions differ from the predominant unimolecular paradigms in their catalysis and specificity.  Our structure was the first of a bimolecular enzyme transition state analog complex, and it is this enzyme's amenability to high resolution crystallographic structure, NMR dynamics and biochemical kinetics that makes it such an appealing system.

Using structure-assisted mutagenesis and kinetics we have shown that the expected general base catalysis can account for only part of the catalytic enhancement.  Our refinement at 1.2 Å resolution gave an unprecedented view of precise substrate pre-alignment in a two-substrate enzyme - within 3º of optimal.  Structures with substrate analogs show that alignment is needed for reactivity.  We are now working towards a quantitative understanding of the various contributions to the catalytic effect through hybrid quantum mechanical / molecular mechanical calculations in collaboration with Jeff Evanseck. 

Our structure of the substrate-free enzyme showed that there were large substrate-induced changes in the protein structure, so the precise alignment must be the result of a dynamic process.  In collaboration with Jack Skalicky, we have completed an NMR backbone resonance assignment, and are beginning to measure exchange rate constants for the conformational changes of important residues.  We are planning to correlate the time-dependent structural transitions with the biochemical kinetics of the enzyme.

Computer Methods Development

Crystallographic model refinement.  Our methods development started with "real-space" refinement of the fit of atomic models into the experimentally-derived electron density.  Generally, this is a good prelude to a more conventional refinement against diffraction amplitudes, widening convergence and reducing over-fitting.  When the phases are of excellent quality, as in virus structure determination, real-space methods can out-perform the conventional methods. 

Hybrid electron microscopy (EM) / crystallographic structure refinement.  We are now adapting real-space refinement for the fitting of known crystallographic component structures into lower resolution EM images of assemblies.  In collaboration with Ken Taylor and Joachim Frank, we are applying these methods to understanding the conformational changes that occur during muscle contraction and protein synthesis at the ribosome.  One important result, highlighted in our Cell (2003) paper, is that ribosomal proteins are not just a passive structural scaffold for the RNA, but are the hinge points of conformational dynamics.

Solid-state NMR.  In collaboration with Mathematicians Richard Bertram & Jack Quine, and spectroscopist Tim Cross, we have derived objective functions with which to refine atomic models against ssNMR data by analogous methods.  This is facilitating the determination of membrane protein structures that are very challenging by other methods.

Stereochemical restraining force fields.  Common to our refinement efforts is the need to obtain accurate models, even when high resolution data are not available.  To reduce over-fitting, we have been investigating stereochemical restraints additional to those applied in high resolution refinements.  To date, we have considered hydrogen bonding and electrostatics, neither of which are usually restrained, because their prior treatments were usually deleterious.  By accounting for the partial covalent nature of hydrogen bonds, and by using a Poisson continuum description of the electrostatic potential, we have developed restraints that are beneficial.

By combining these approaches, we plan to support investigations of large assemblies at increasing detail.  Currently, elucidation of the conformational changes within domains generally requires crystallographic resolutions, but we plan to make it possible at the sub-atomic resolutions with which large complexes and membrane proteins can be visualized by EM, NMR and other biophysical techniques.

For further information see: Publications; Software distributed

Research-Training Environment

The research projects offer a variety of opportunities for training in structure-function for doctoral students in biochemistry or molecular biophysics and post-doctoral fellows.  Many group members are jointly mentored in collaborative projects, offering a broad experience in interdisciplinary science.  Facilities for cell culture and protein expression, x-ray diffraction, and physical biochemistry and computing  offer not only equipment, but training by their managers who hold Ph.D.s in their specialist areas.  Highlights include BL2 facilities with hoods and incubators for cell/virus culture, two x-ray crystallographic data collection systems, and access to synchrotron beam-time through our membership in the SERCAT consortium based at the Argonne National Laboratory.  Our research laboratories are located in the Kasha Laboratory of Biophysics which underwent a complete $7.1M renovation in 2002-3.

(c) Michael S. Chapman, Research Interests; Last updated 10/25/2005

Publications

PubMed Listing (with available abstracts / text)

1. Chapman, M. S., Smith, W. W., Suh, S. W., Cascio, D., Howard, A., Hamlin, R., Xuong, N. H. & Eisenberg, D. (1986). Structural studies of RuBisCO from tobacco. Phil. Trans. Roy. Soc. Lond. B313, 367-378.
2. Chapman, M., Suh, S. W., Cascio, D., Smith, W. W. & Eisenberg, D. (1987). Sliding-layer conformational change limited by quaternary structure in plant RuBisCO. Nature 329, 354-356.
3. Eisenberg, D., Almassy, R. J., Janson, C. A., Chapman, M. S., Suh, S. W., Cascio, D. & Smith, W. W. (1987). Some Evolutionary Relationships of the Primary Biological Catalysts Glutamine Synthetase and RuBisCO. Cold Spr. Har. Symp. Quant. Biol. LII, 483-90.
4. Eisenberg, D., Chapman, M. S., Suh, S. W., Cascio, D. & Smith, W. W. (1987). The Path of the Polypeptide Backbone of Ribulose-1,-5-bis-phosphate from Nicotiana tabacum. In International Workshop on Ribulose-1,-5-bis-phosphate carboxylase-oxygenase (Bohnert, H. J. & Jensen, R. G., eds.). University of Arizona Press, Tuscon, AZ.
5. Suh, S. W., Cascio, D., Chapman, M. S. & Eisenberg, D. S. (1987). A Crystal Form of Ribulose-1,-5-bis-phosphate Carboxylase--Oxygenase from Nicotiana tabacum in the Activated state. J. Mol. Biol. 197, 363-365.
6. Chapman, M. S., Suh, S. W., Curmi, P. M. G., Cascio, D., Smith, W. W. & Eisenberg, D. S. (1988). Tertiary Structure of Plant RuBisCO: Domains and their Contacts. Science 241, 71-74.
7. Hajdu, J., Clifton, I. J., Hadfield, A., Howell, P. L., Almo, S. C., Petsko, G. A., Greenhough, T. J., Shrive, A. K., Campbell, J. W., Parson, M., Harrison, S. C., Liddington, R. C., Rossmann, M. G. & Chapman, M. (1989). Daresbury Annal.
8. Kim, S., Smith, T. J., Chapman, M. S., Rossmann, M. G., Pevear, D. C., Dutko, F. J., Felock, P. J., Diana, G. D. & McKinlay, M. A. (1989). Crystal Structure of Human Rhinovirus Serotype 1A (HRV1A). J. Mol. Biol. 210, 91-111.
9. Chapman, M. S., Giranda, V. L. & Rossmann, M. G. (1990). The Structures of Human Rhinovirus and Mengo Virus: Relevance to Function and Drug Design. Sem. Virol. 1, 413-27.
10. Giranda, V. L., Chapman, M. S. & Rossmann, M. G. (1990). Modelling of the Human Intercellular Adhesion Molecule-1, the Human Rhinovirus Major Group Receptor. Proteins 7, 227-33.
11. Giranda, V. L., Chapman, M. S., Rossmann, M. G., Staunton, D. & Springer, T. A. (1990). Modelling of the C1 Intercellular Adhesion Molecule 1 (ICAM-1), the Human Rhinovirus Major Group Receptor. In International Symposium on Positive Strand RNA Viruses, Vienna, Austria.
12. Chapman, M. S., Minor, I., Rossmann, M. G., Diana, G. D. & Andries, K. (1991). Human rhinovirus 14 complexed with antiviral compound R 61837. J. Mol. Biol. 217, 455-63.
13. Tsao, J., Chapman, M. S., Agbandje, M., Keller, W., Smith, K., Wu, H., Luo, M., Smith, T. J., Rossmann, M. G., Compans, R. W. & Parrish, C. (1991). The Three-Dimensional Structure of Canine Parvovirus and its Functional Implications. Science 251, 1456-1464.
14. Chapman, M. S., Tsao, J. & Rossmann, M. G. (1992). Ab initio Phase Determination for Spherical Viruses: Parameter Determination for Spherical Shell Models. Acta Crystallogr. A48, 301-312.
15. Mallamo, J. P., Diana, G. D., Pevear, D. C., Dutko, F. J., Chapman, M. S., Kim, K. H., Minor, I., Oliveira, M. & Rossmann, M. G. (1992). Conformationally Restricted Analogues of Disoxaril: A comparison of the Activity against Human Rhinovirus Type 14 and 1A. J. Med. Chem. 35, 4690-4695.
16. Tsao, J., Chapman, M. S. & Rossmann, M. G. (1992). Ab initio Phase Determination for Viruses with High Symmetry: A Feasibility Study. Acta Crystallogr. A48, 293-301.
17. Tsao, J., Chapman, M. S., Wu, H., Agbandje, M., Keller, W. & Rossmann, M. G. (1992). Structure Determination of Monoclinic Canine Parvovirus. Acta Crystallogr. B48, 75-88.
18. Chapman, M. S. (1993). Mapping the Surface Properties of Macromolecules. Prot. Sci. 2, 459-469.
19. Chapman, M. S., Kim, K. H. & Rossmann, M. G. (1993). Structural Comparisons of Several Antiviral Agents Complexed with Human Rhinoviruses of Different Serotypes. Antiviral News 1, 53-53.
20. Chapman, M. S. & Rossmann, M. G. (1993). Structure, Sequence and Function Correlations among Parvoviruses. Virology 194, 491-508.
21. Chapman, M. S. & Rossmann, M. G. (1993). Comparison of Surface Properties of Picornaviruses: Strategies for hiding the Receptor Site form Immune Surveillance. Virology 195, 745-765.
22. Kim, K. H., Willingmann, P., Gong, Z. X., Kremer, M. J., Chapman, M. S., Minor, I., Oliviera, M. A., Rossmann, M. G., Andries, K., Diana, G. D., Dutko, F. J., McKinlay, M. A. & Pevear, D. C. (1993). A comparison of the anti-rhinoviral drug binding pocket in HRV14 and HRV1A. J. Mol. Biol. 230, 206-227.
23. Chapman, M. S. (1994). Sequence Similarity Scores and the Inference of Structure/Function Relationships. Computer Applications in the Biosciences (CABIOS) 10, 111-119.
24. Chapman, M. S. (1995). Restrained Real-Space Macromolecular Atomic Refinement using a New Resolution-Dependent Electron Density Function. Acta Crystallogr. A51, 69-80.
25. Chapman, M. S. & Rossmann, M. G. (1995). Single-stranded DNA-protein interactions in Canine Parvovirus. Structure 3, 151-62.
26. Hadfield, A., Hajdu, J., Chapman, M. S. & Rossmann, M. G. (1995). Laue Diffraction Studies of Human Rhinovirus 14 and Canine Parvovirus. Acta Crystallogr. D51, 859-70.
27. Chapman, M. S. (1996). Cross-validation R-factors and their use in comparing the qualities of refined models for the DNA-containing and empty capsids of canine parvovirus. Acta Crystallogr. D52, 140-2.
28. Chapman, M. S. & Rossmann, M. G. (1996). Structural Refinement of the DNA-containing Capsid of Canine Parvovirus using RSRef, a Resolution-Dependent Stereochemically Restrained Real-Space Refinement Method. Acta Crystallogr. D52, 129-42.
29. Xie, Q. & Chapman, M. S. (1996). Canine parvovirus capsid structure, analyzed at 2.9 Å resolution. J. Mol. Biol. 264, 497-520.
30. Zhou, G., Parthasarathy, G., Somasunduram, T., Ables, A., Roy, L., Strong, S. J., Ellington, W. R. & Chapman, M. S. (1997). Expression, Purification from Inclusion Bodies, and Crystal Characterization of Transition State Analog Complex of Arginine Kinase: a Model for Studying Phosphagen Kinases. Prot. Sci. 6, 444-9.
31. Blanc, E. & Chapman, M. S. (1997). RSRef: Interactive real-space refinement with stereochemical restraints for use during model-building. J. Appl. Cryst. 30: 566-7.
32. Chapman, M. S. & Blanc, E. (1997). Potential use of Real Space Refinement in Protein Structure Determination. Acta Crystallogr. D53, 203-6.
33. Chapman, M. S. (1998). Watching "One's" Ps and Qs: Promiscuity, Plasticity and Quasi-Equivalence in a T=1 virus. Biophys. J. 74: 639-44.
34. Chapman, M. S. (1998). Introduction to the use of non-crystallographic symmetry in phasing. In Direct Methods for Solving Macromolecular Structures (Fortier, S., ed.), pp. 99-108. Kluwer, Dortrecht, Netherlands.
35. Chapman, M. S., Blanc, E., Johnson, J. E., McKenna, R., Munshi, S., Rossmann, M. G. & Tsao, J. (1998). Use of non-crystallographic symmetry for ab initio phasing of virus structures. In Direct Methods for Solving Macromolecular Structures (Fortier, S., ed.), pp. 433-442. Kluwer, Dortrecht, Netherlands.
36. Blanc, E., Chen, Z. & Chapman, M. S. (1998). Real-Space Refinement Using RSRef. In Direct Methods for Solving Macromolecular Structures (Fortier, S., ed.), pp. 513-9. Kluwer, Dortrecht, Netherlands.
37. Zhou, G., Wang, J., Blanc, E. & Chapman, M. S. (1998). Determination of the Relative Precision of Atoms in a Macromolecular Structure. Acta Crystallographica D54, 391-9.
38. Zhou, G., Somasundaram, T., Blanc, E., Parthsarathy, G., Ellington, W. R. & Chapman, M. S. (1998). Transition state structure of arginine kinase: Implications for catalysis of bimolecular reactions. Proceedings of the National Academy of Sciences, USA 95, 8449-54.
39. Chen, Z., Blanc, E. & Chapman, M. S. (1998). Real Space Molecular Dynamics Refinement. Acta Crystallographica D55: 464-8.
40. Chen, Z., Blanc, E. & Chapman, M. S. (1999). Improved free R-factors for the cross-validation of structures. Acta Crystallographica D55: 219-224.
41. Zhou, G., Somasundaram, T., Blanc, E. & Chapman, M. S. (1999). Critical Initial Real Space Refinement in the Structure Determination of Arginine Kinase. Acta Crystallographica D55: 835-845
42. Zhou, G., Ellington, W.R. & Chapman, M.S. (2000). Induced Fit in Arginine Kinase. Biophys J 78: 1541-1550.
43. Bertram, R., J. R. Quine, M. S. Chapman and T. A. Cross (2000). “Atomic Refinement Using Orientational Restraints from Solid-State NMR.” J. Magnetic Resonance, 147: 9-16.
44. Blanc, E., G. Zhou, Z. Chen, Q. Xie, J. Tang, J. Wang, and M.S. Chapman. 2001. Electron Density Representation and Real Space Refinement (New tricks from an old dog). In: Watenpaugh, K.D., and P.E. Bourne, editors. Crystallographic Computing 7: Proceedings of the IUCr Macromolecular Computing School, 1996. Corby, UK: Oxford University Press..
45. Gerstein, M., F. Richards, M.S. Chapman, and M. Connolly. 2001. Protein surfaces and volumes: measurement and use. In: Rossmann, M.G., and E. Arnold, editors. International Tables for Crystallography. Crystallography of Biological Molecules. Dortrecht, Netherlands: Kluwer Academic Publishers. p 531-45 (Cpt. 22.1).
46. Chen, L.F., E. Blanc, M.S. Chapman, and K.A. Taylor. 2001. Real space refinement of acto-myosin structures from sectioned muscle. J Struct Biol 133:221-32.
47. Chen, Z., and M.S. Chapman. 2001. Conformational Disorder of Proteins Assessed by Real-Space Molecular Dynamics Refinement. Biophys J 80:1466-1472.
48. Korostelev, A., Bertram, R., and Chapman, M.S. 2002. Simulated Annealing Real-Space Refinement as a Tool in Model Building. Acta Crystallogr. D58: 761-767.
49. Bubb, M.R., Govindasamy, L., Yarmola, E.G., Vorobiev, S.M., Almo, S.C., Somasundaram, T., Chapman, M.S., Agbandje-McKenna, M., and McKenna, R. 2002. Polylysine induces an antiparallel actin dimer that nucleates filament assembly: crystal structure at 3.5-A resolution. J Biol Chem 277: 20999-21006.
50. Fabiola, F., Bertram, R., Korostelev, A., and Chapman, M.S. 2002. An improved hydrogen bond potential: impact on medium resolution protein structures. Protein Sci 11: 1415-1423.
51. Xie, Q., Bu, W., Bhatia, S., Hare, J., Somasundaram, T., Azzi, A., and Chapman, M.S. 2002. The atomic structure of adeno-associated virus (AAV-2), a vector for human gene therapy. Proc Natl Acad Sci U S A 99: 10405-10410.
52. Yousef, M.S., Fabiola, F., Gattis, J., Somasundaram, T., and Chapman, M.S. 2002. Refinement of Arginine Kinase Transition State Analogue Complex at 1.2 Å resolution; mechanistic insights. Acta Crystallogr. D. Biol. Crystallogr. 58: 2009-2017.
53. Yousef, M.S., Clark, S., Pruett, P.S., Somasundaram, T., Ellington, W.R., and Chapman, M.S. 2003. Induced Fit in Guanidino Kinases - Comparison of Substrate-free and Transition State Analog Structures of Arginine Kinase. Protein Sci.  12: 103-111.
54. Xie, Q., T. Somasundaram, S. Bhatia, W. Bu, and M.S. Chapman, Structure determination of adeno-associated virus 2: three complete virus particles per asymmetric unit. Acta Crystallogr D Biol Crystallogr, 2003. 59: 959-70.
55. Gao, H., J. Sengupta, M. Valle, A. Korostelev, N. Eswar, S.M. Stagg, P. VanRoey, R.K. Agrawal, S.C. Harvey, A. Sali, M. Chapman, and J. Frank, Study of the Structural Dynamics of the E. coli 70S Ribosome Using Real Space Refinement. Cell, 2003. 113: 789-801.
56. Chapman, M.S., and Liljas, L. 2003. Structural Folds of Viral Proteins. In Advances in Protein Chemistry. (eds. W. Chiu, and J.E. Johnson), 64: 125-196. Academic Press.
57. Pruett, P.S., A. Azzi, S.A. Clark, M. Yousef, J.L. Gattis, T. Somasundaram, W.R. Ellington, and M.S. Chapman, The putative catalytic bases have, at most, an accessory role in the mechanism of arginine kinase. J Biol Chem, 2003. 29: 26952-7.
58. Bertram, R., T. Asbury, F. Fabiola, J. R. Quine, T. A. Cross and M. S. Chapman (2003). "Atomic Refinement with Correlated Solid-State NMR Restraints." Journal of Magnetic Resonance, 2003. 163: 300-9.
59. Chen, J.Z, Furst, J., Chapman, M.S., Grigorieff, N. 2003.  Low Resolution Refinement in Electron Microscopy.  Journal of Structural Biology, 144: 144-151.
60. Azzi, A., Clark, S.A., Ellington, W.R., and Chapman, M.S. 2004. The Role of Phosphagen Specificity Loops in Arginine Kinase. Protein Sci. 13: 575-585.
61. Gattis, J. L., E. Ruben, Fenley, M.O., Ellington, W.R., and Chapman, M.S (2004). "The active site cysteine of arginine kinase - structural and functional analysis of partially active mutants." Biochemistry, 43: 8680-8689.
62. Xie, Q., Hare, J., Bu, W., Jackson, W., Turnigan, J., and Chapman, M. S. (2004) Large-scale Preparation, Purification and Crystallization of Wild-type Adeno-Associated Virus 2, Journal of Virological Methods, 122: 17-27
63. Korostelev, A., Fenley, M. O., and Chapman, M. S. (2004) Impact of a Poisson-Boltzmann Electrostatic Restraint on Protein Structures Refined at Medium Resolution, Acta Crystallographica D, Biological Crystallography, 60: 1786-1794.
64. Quine, J.R., Cross, T.A., Chapman, M.S. and Bertram, R., 2004. Mathematical Aspects of protein structure determination with NMR orientational restraints. Bull. Math. Biol. 66: 1705-1730.
65. 65. Fabiola, F. and Chapman, M.S. (2005) Fitting of High Resolution Structures into Electron Miscroscopy Reconstruction Images, Structure, 13: 389-400.
66. 69. Davulcu, O., S. A. Clark, M. S. Chapman and J. J. Skalicky (2005). "Main chain 1H, 13C, and 15N resonance assignments of the 42 kDa enzyme arginine kinase." Journal of Biological NMR, 32: 178.
67. Ruben, E. A., Evanseck, J. D., and Chapman, M. S. (2006) A theoretical study of N-phosphoryl-guanidinium tautomers - influences of hyperconjugation on N-P bond strength, Journal of the American Chemical Society, 127: 17789-17798.
68. Chapman, M.S., and Agbandje-McKenna, M. 2006. Atomic structure of viral particles. In Parvoviruses. (eds. M.E. Bloom, S.F. Cotmore, R.M. Linden, C.R. Parrish, and J.R. Kerr), pp107-123. Hodder Arnold, London.
69. Agbandje-McKenna, M., and Chapman, M.S. 2006. Structure-function relationships. In Parvoviruses. (eds. M.E. Bloom, S.F. Cotmore, R.M. Linden, C.R. Parrish, and J.R. Kerr), pp125-139. Hodder Arnold, London.
70. Chapman, M. S. (2006) The Structural Enzymology of Arginine Kinase and its Implications for Creatine Kinase, in Creatine kinase biochemistry, physiology, structure and function (Vial, C., Ed.), NovaScience, New York, in press.
71. Fabiola, F., Korostelev, A. & Chapman, M. S. Cross-validation with Over-sampled Structure Factors. Acta Crystallogr D Biol Crystallogr, accepted (2006).
72. Quine, J.R., Achuthan, S., Asbury, T., Bertram, R., Chapman, M.S., Hu, J. and Cross, T.A., 2006. Intensity and mosaic spread analysis from PISEMA tensors in solid state NMR. Journal of Magnetic Resonance, accepted.
73. Blanc, E., Giranda, V., Alexander, R.S., Pevear, D.C., Grorke, J., Gattis, J., and Chapman, M.S. 2004. The 2 Å Structure of Human Rhino Virus 50. Structure in preparation.

Last updated 12/22/05