department of pharmacology

Chris Dealwis, Ph.D.

Dealwis

 
Associate Professor

Phone: (216) 368-1652, 368-3337
Fax: (216) 368-1300
E-mail: chris.dealwis@case.edu
W333

Research:

Nearly every major process in a cell is carried out by a complex assembly of several proteins. The main focus of the lab involves understanding the structural organization requirements by multiple protein assemblies to facilitate biological function. Our approach is to use a multidisciplinary cycle to study the structure-function relationship of proteins. We also use structure-based drug and protein design to develop novel therapeutics against cancer, Alzheimer’s disease and microbial infections. Biophysical tools such as x-ray & neutron crystallography, molecular modeling, CD, MS, fluorescence spectroscopy and ultracentrifugation are the techniques used in our lab.

Specifically, my research focuses on three areas of interest. They are: (1) the structure-function and regulation of  ribonucleotide reductase (RNR) by small molecule effectors and its protein inhibitor, the Suppressor of Mec 1 Lethality 1 (Sml1), (2) the structure-function of pathogenic amyloid forming proteins, and (3) the investigation of enzyme catalytic mechanisms, dynamics and solvent structure of macromoleculesusing neutron and ultra-high resolution x-ray diffraction.

RNR

We study the structure-function and regulation of the anti-cancer target ribonucleotide reductase (RNR). RNR converts nucleotides to deoxynucleotides (dNTPs), the rate-limiting step in de novo DNA synthesis. Control of the dNTP pool is essential; an excess of deoxynucleotides causes mutations, while scarcity can lead to cell death due to improper cell division. RNR is highly regulated transcriptionally, allosterically, by subunit compartmentalization and, in S. cerevesiae, by its protein inhibitor Sml1. Recently, we solved the structure of the first eukaryotic Rnr1 from S. cerevisiae (see Figure below). Our structures provide a molecular basis for how RNR selects for specific nucleotide diphosphate substrates based on exquisite loop rearrangements induced by effector binding at a selectivity site, and balance cellular nucleotide pools.


Amyloids

Soluble proteins and peptides can sometimes aggregate into insoluble, self-assembled filamentous aggregates including amyloid and amyloid-like structures. Current interest in amyloid fibrils and related aggregates arises from their involvement in diseases such as Alzheimer’s disease (AD), type 2 diabetes, prion diseases, and other protein misfolding disorders. Since aggregates of the amyloid-beta (Aβ) peptide have been implicated in the molecular mechanism of Alzheimer’s disease (AD), reversing or preventing Aβ aggregation is an important prospective approach to AD therapy. We have solved the first three-dimensional x-ray structure of the immunodominant N-terminus of Aβ in complex with the Fab fragment of the mAb PFA1 (see Figure below). Our structures provide a molecular basis for Fab-Aβ(N-terminus) interactions. The crucial interactions are made between the WWDDD motif from CDRH2 with an EFRH motif of Aβ. We have also shown that the N-terminus directed mAbs have the potential to cross-react with EFRH-like sequences that are found within proteins found in the brain. Our structures provide a basis for improving selectivity and potency towards Aβ.

Neutron diffraction and ultrahigh resolution x-ray diffraction

We use neutron and ultra-high resolution x-ray diffraction to solve controversial mechanistic questions. The contribution of hydrogen atoms in noncovalent interactions and enzymatic reactions underlies all aspects of biology at the molecular level, yet their “visualization” is quite difficult.  Neutron diffraction (ND) is well suited to such studies, as it is able to resolve the positions of hydrogen atoms in macromolecules. ND is coming of age with the advent of the Spallation Neutron Source (SNS) at Oak Ridge National Laboratory. Our lab is one of the first to use Spallation neutrons to solve macromolecular structure. Using DHFR as our test enzyme, we were able to use 0.3mm3 non-perdeuterated crystals to obtain 2.2Å resolution data at the Protein Crystallography station (PCS) at Los Alamos National Lab. The neutron crystallography cycle is depicted pictorially below. Our lab continues to work on other signaling molecules to unravel the mechanisms of proton-coupled signal transduction.

Lab Photo Gallery

Selected Publications:

Langan, P., Fisher, Z., Kovalevsky, A., Mustyakimov, A., Sutcliffe, V., Afonine, AV., Bennett, B., Dealwis, C and Schoenborn, B. (2008), J. Synch. Rad, 15, 215-218. Protein structures by Spallation neutron crystallography.

Bennett, B.C., Gardberg, A. S., Blair, M and Dealwis, C. (2008), Acta. Cryst. D. 64, 764-83. On the determinants of amide backbone exchange in proteins: a neutron crystallographic comparative study.

Xu, H., Fairman, J.W., Wijerathna., Kreischer, N.R., LaMacchia, J., Helmbrecht, E., Cooperman, B.S and Dealwis, C. (2008), J. Med Chem. 51, 5653-9. The Structural Basis for Peptidomimetic Inhibition of Eukaryotic Ribonucleotide Reductase: a Conformationally Flexible Pharmacophore.

Azizi, F., Wan, Q., Radivoyevitch, T., Dealwis, C and Mastrangelo, C, H.   (2008), 12th Micro Total Anal Syst. 1904-1906

Brad C. Bennett, Qun Wan, Md Faiz Ahmad, Paul Langan and Chris G. Dealwis, (2009), J. Struct. Biol. 166,162-171. X-ray structure of the ternary MTX•NADPH complex of the anthrax dihydrofolate reductase: a pharmacophore for dual-site inhibitor design.

Anna Gardberg, Lezlee Dice, Kathleen Pridgen, Jan Ko, Paul Patterson, Susan Ou, Ronald Wetzel, Chris Dealwis.  Biochemistry. (2009), Structures of Aβ-related peptide-monoclonal antibody complexes. 48, 5210-7.

Dianqing Sun, Hai Xu, Sanath, R. Wijerathna, Chris Dealwis*, and Richard E. Lee*. Chem. Med. Chem. (2009), Structure-based Design, Synthesis, and Evaluation of 2'-(2-Hydroxyethyl)-2'-Deoxyadenosine and Its 5'-Diphosphate as Novel Ribonucleotide Reductase Inhibitors, ChemMedChem, 4, 1649-56 (*joint corresponding authors)

Jaskiran Kaur, Shalini Jha, Chris Dealwis and Barry S. Cooperman. (2009), Design, synthesis and structure of peptidomimetic inhibitors of eukaryotic ribonucleotide reductase: A target for cancer chemotherapy.Proceedings of the 21st American Peptide Society, Pages 80-88

Minami, S.S., Sidahmed, E., Aid, S., Shimoji, M., Niikura, T., Mocchetti, I., Rebeck, G.W., Prendergast, J.S., Dealwis, C., Wetzel, R., et al. Therapeutic versus neuroinflammatory effects of passive immunization is dependent on Abeta/amyloid burden in a transgenic mouse model of Alzheimer's disease. J Neuroinflammation 7, 57. Miyagi, M., Wan, Q., Ahmad, M. F., Gokulrangan, G., Tomechko, S. E., Bennett, B. & Dealwis, C. (2011). Histidine hydrogen‐deuterium exchange mass spectrometry for probing the microenvironment of histidine residues in dihydrofolate reductase. PLoS One 6, e17055.

Fairman, J. W., Wijerathna, S. R., Ahmad, M. F., Xu, H., Nakano, R., Jha, S., Prendergast, J., Welin, R. M., Flodin, S., Roos, A., Nordlund, P., Li, Z., Walz, T. & Dealwis, C. G. (2011). Structural basis for allosteric regulation of human ribonucleotide reductase by nucleotide‐induced oligomerization. Nat Struct Mol Biol 18, 316‐22.

Wan, Q., Ahmad, M. F., Fairman, J., Gorzelle, B., de la Fuente, M., Dealwis, C. & Maguire, M. E. (2011). X‐Ray Crystallography and Isothermal Titration Calorimetry Studies of the Salmonella Zinc Transporter ZntB. Structure 19, 700‐10.

Anna S. Gardberg, Lezlee T. Dice, Elizabeth Helmbrecht, Jan Ko, Susan Ou, Paul H. Patterson, Rebecca Rich, David Myszka, Ronald Wetzel, and Chris Dealwis (2007). PNAS, 104(40): 15659-64. Molecular basis for passive immunotherapy of Alzheimer’s disease.

Brad Bennett, Hai Xu, Richard F. Simmerman, Richard E. Lee and Chris G. Dealwis (2007). J. Med Chem, 18: 4374-81. Crystal structure of the anthrax drug target,
Bacillus anthracis dihydrofolate reductase.

Brad Bennett, Paul Langan, Leighton Coates, Marat Mustyakimov, Benno Schoenborn, Elizabeth  Howell, and Chris Dealwis (2006). PNAS, 103: 18493-18496. Neutron diffraction studies of E. coli DHFR in complex with Methotrexate.

Hai Xu, Catherine Faber, Tomoaki Uchiki, James W. Fairman, Joseph Racca, and Chris Dealwis (2006). PNAS, 103: 4022-4027. Structures of eukaryotic ribonucleotide reductase I provide insights into dNTP regulation.

Hai Xu, Catherine Faber, Tomoaki Uchiki, Joseph Racca, and Chris Dealwis (2006). PNAS, 103: 4028-4033. Structures of eukaryotic ribonucleotide reductase I define gemcitabine diphosphate binding and subunit assembly.

Uchiki T, Dice LT, Hettich RL, and Chris Dealwis (2004). J. Biol. Chem., 279: 11293-303.Identification of phosphorylation sites on the yeast ribonucleotide reductase inhibitor Sml1.

Gupta V, Peterson CB, Dice LT, Uchiki T, Racca J, Guo JT, Xu Y, Hettich R, Zhao X, Rothstein R, and Chris Dealwis (2004). Biochemistry 43: 8568-8578. Sml1p Is a Dimer in Solution: Characterization of Denaturation and Renaturation of Recombinant Sml1p.

Wall, JS, Gupta V, Wilkerson M, Schell M, Loris R, Adams P, Solomon A, Stevens F, and Chris Dealwis (2004). J. Mol. Recognit. 17: 323-31. Structural basis of light chain amyloidogenicity: comparison of the thermodynamic properties, fibrillogenic potential and tertiary structural features of four Vλ6 proteins.

Chris Dealwis and Jon Wall (2004). Curr. Drug Targets 5: 159-71. Towards understanding the structure-function relationship of human amyloid disease.

Uchiki T, Hettich R, Gupta V, and Chris Dealwis (2002). Anal. Biochem., 301: 35-48. Characterization of monomeric and dimeric forms of recombinant Sml1p-histag protein by electrospray mass spectrometry.