Chris Dealwis, Ph.D.
Phone: (216) 368-1652, 368-3337
Fax: (216) 368-1300
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
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
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
Knapperberger AJ, Ahmah Md. Faiz, Viswanathan R, Dealwis CG, Harris ME. Nucleotide analog triphosphate allosterically regulate human ribonucleotide reductase and identify chemical determinants that drive substrate specificity. Biochemistry. (2016) PMID:27634056
Misko TA, Wijerathna SR, Radivoyevitch T, Berdis AJ, Ahmad Md. Faiz, Harris ME, Dealwis CG. Inhibition of yeast ribonucleotide reductase by Sml1 depends on the allosteric state of the enzyme. FEBS.Lett. (2016), 590:1704-12 doi:10.1002/1873-3468.12207. PMID: 27155231 PMCI: PMC4925217
Ahmad MF, Huff SE, Pink J, Alam I, Zhang A, Perry K, Harris ME, Misko T, Porwal SK, Oleinick NL, Miyagi M, Viswanathan R, Dealwis CG. Identification of Non-nucleoside Human Ribonucleotide Reductase Modulators J. Med. Chem. 2015 Dec 24;58(24):9498-509. PMID: 26488902. PMCID: PMC4751996
Zhang Y, 1 Desai A, 1 Yang S Y, 1 Bae Ki Beom, 1 Monika I. Antczak, 2 Stephen P. Fink, 1 Shruti Tiwari,1,10Joseph E. Willis, 3,4,10 Noelle S. Williams, 2 Dawn M. Dawson,3,4 David Wald, 1 Wei-Dong Chen, 1 Zhenghe Wang, 1 Lakshmi Kasturi, 1 Gretchen A. Larusch, 1 Lucy He, 1 Fabio Cominelli, 1,10 Luca Di Martino, 1 Zora Djuric, 11 Ginger L. Milne, 6 Mark Chance, 7 Juan Sanabria, 1 Chris Dealwis, 9 Debra Mikkola, 1 Jacinth Naidoo, 2 Shuguang Wei, 2 Hsin-Hsiung Tai, 12 Stanton L. Gerson, 1,3,10* Joseph Ready, 2,13* Bruce Posner, 2,13* James K. V. Willson, 13* Sanford D. Markowitz 1 Science 348 (2015) aaa2340-1. Inhibition of the Prostaglandin Degrading Enzyme 15-PGDH Potentiates Tissue Regeneration.
Wan Q, Bennett BC, Wilson MA, Kovalevsky A, Langan P, Howell EE, Dealwis C. Toward resolving the catalytic mechanism of dihydrofolate reductase using neutron and ultrahigh-resolution X-ray crystallography. Proc. Natl. Acad. Sci. USA (PNAS). 2014 Dec 23;111(51):18225-30. PMID: 25453083; PMCID: PMC4280638.
Wan Q, Kovalevsky AY, Wilson MA, Bennett BC, Langan P, Dealwis C.
Preliminary joint X-ray and neutron protein crystallographic studies of ecDHFR complexed with folate and NADP+. Acta Crystallogr F Struct Biol Commun. 2014 Jun;70(Pt 6):814-8. PMID: 24915100; PMCID: PMC4051544.
Ahmad MF, Dealwis CG.
The structural basis for the allosteric regulation of ribonucleotide reductase. Prog Mol Biol Transl Sci. 2013;117:389-410.PMID:23663976; PMCID: PMC4059395.
Ahmad MF, Wan Q, Jha S, Motea E, Berdis A, Dealwis C. Evaluating the therapeutic potential of a non-natural nucleotide that inhibits human ribonucleotide reductase. Mol Cancer Ther. 2012 Oct;11(10):2077-86. PMID: 22933704; PMCID: PMC3569060.
Ahmad MF, Kaushal PS, Wan Q, Wijerathna SR, An X, Huang M, Dealwis CG.
Role of arginine 293 and glutamine 288 in communication between catalytic and allosteric sites in yeast ribonucleotide reductase. J Mol Biol. 2012 Jun 22;419(5):315-29. PMID: 22465672; PMCID: PMC3589814.
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.