Zucai Suo
| |
Associate Professor
Phone: 614-688-3706
Fax: 614-292-6773
email: suo.3@osu.edu
Webpage: Suo Homepage |
Research Interests:
The research in my laboratory has three major directions: one
is to elucidate kinetic mechanisms of enzymes involved in DNA/RNA replication,
repair, and lesion bypass; the second is to understand Hepatitis C (HCV)
replication and regulation of innate immunity; the third is to develop
antiviral and anti-cancer molecules based on rational drug design. In
kinetic studies, we use a variety of pre-steady state kinetic methods
including rapid chemical quench-flow and stopped-flow. These methods
allow us to quench reactions in milliseconds, and extract more kinetic
information than the traditional steady-state kinetic methods.We also
use site-directed mutagenesis and domain-swapping methods to study structure-function
relationship in these enzymes.Moreover, we are using the femtosecond-resolved
fluorescence up-conversion techniques to study the enzyme-substrate
interactions in the collaboration with the group of Dr. Dongping Zhong
at Dept. of Physics.These studies will allow us to develop new methods
and also push enzymology to an unprecedented territory.Our goals are
to understand the elementary steps of reactions occurred at the active
sites of enzymes. Then, these mechanisms will aid our rational drug
design. The designed enzyme inhibitors will be synthesized and tested in
vitro and in vivo.We are currently investigating several
systems described below. Pre-Steady State Kinetic Studies of DNA
Lesion Bypass Polymerases : DNA lesions often block DNA replication,
so cells possess specific, often error-prone, DNA polymerases to bypass
such lesions and promote replication of damaged DNA. A large number
of DNA lesion bypass polymerases have been discovered in the last two
years.These polymerases which share sequence similarity and catalyze
DNA polymerization with low fidelity and poor processivity are classified
into a new Family, the Y-family.Human polymerases eta (h),iota (i),
and zeta (z)are examples of those repairing enzymes.Polymerase
(Pol) h, encoded by hRAD30A, bypasses cis-syn thymine-thymine
dimmer efficiently and accurately.Mutations in hRAD30A inactivate
hPol h and lead to UV-induced mutagenesis and skin cancer.My laboratory
is using the pre-steady state kinetic methods to decipher the detailed
mechanisms of incorporations of correct and incorrect nucleotides opposite
undamaged or damaged DNA templates by Dpo4, a thermostable polymerase
from Sulfolobus solfataricus strain P2.Our studies will establish
a general kinetic mechanism for DNA translesion synthesis.
Kinetic and Protein-Protein Interaction Studies of Human DNA Polymerases:
The DNA in every cell of the human body is spontaneously damaged more
than 10,000 times every day.DNA repair plays a major role to maintain
genome integrity in cells.Two human DNA polymeraseslandmdiscovered recently
share sequence similarity with the well-known DNA repair polymeraseb and
are thereby believed to catalyze base-excision repair.My group has purified
the two polymerases and is characterizing them kinetically.In addition,
the two enzymes have N-terminal BRCT domain which supposedly interacts
with cell-cycle checking proteins, such as the tumor suppressor p53.We
are trying to identify these interacting proteins by employing immuno-precipitation
assay and mass spectroscopy analysis.Moreover, we are trying to crystallize
both lambda and mu in the presence of DNA and dNTP substrates in the
collaboration with the Todd Yeates’s group at UCLA.
Mechanistic Studies of Vaccinia Virus DNA Polymerases and Design/Synthesis
of Novel Nucleoside Analog Inhibitors:
Concerns about the possible release of smallpox by bioterrorists have
led to intensive hunt to find an effective molecule to inhibit viral
infection which does not exist yet. Since smallpox virus (variola virus)
and the smallpox vaccine (vaccinia virus) are highly homologous, the
latter has been used as a very good surrogate model. For example, vaccinia
virus DNA polymerase is about 99% identical to its counterpart in smallpox
virus. In my laboratory, we are using pre-steady state kinetic methods
to investigate the elementary steps of nucleotide incorporation catalyzed
by vaccinia virus DNA polymerase. In addition, we are testing more than
140 nucleotide analogs in order to find potent inhibitors which may
be effective as anti-smallpox agents.
Mechanistic Studies of HCV RNA Polymerases and Design/Synthesis
of Novel Nucleoside Analog Inhibitors:
Hepatitis C has infected about 2-3% of human population.Viral genome
replication is crucial for viral life cycles and has been studied intensively.NS5B,
the RNA-dependant RNA polymerase, which is at the center of viral replication,
is one of major antiviral drug targets. Although there are extensive
biochemical and steady-state kinetic studies on this polymerase, the
elementary steps of nucleotide incorporation catalyzed by NS5B are still
undefined. Using pre-steady state kinetic methods, we are studying the
kinetic mechanism, processivity, fidelity, drug susceptibility, and
drug resistance. The knowledge gained from these studies has severed
as the basis for our rational design of nucleoside inhibitors. Currently,
we are testing more than 140 nucleoside analogs which we have synthesized
or obtained through collaboration in our cell-based assays.
Developing Anti-HCV Peptide-Based Inhibitors:
The non-structural proteins NS3, NS4A, NS4B, NS5A, and NS5B of HCV
are processed from viral polyprotein precursor C-E1-E2-p7-NS2-NS3-NS4A-NS4B-NS5A-NS5B
by viral protease complex NS3/NS4A.NS3 has an N-terminal protease domain
and a C-terminal helicase domain.The crystal structure of the NS3 protease
domain shows that the N-terminus 28 residues are unfolded.In the complex
with NS4A, the NS3 N-terminus folds into a beta sheet and an alpha helix,
and the active site residues are slightly rearranged to form a catalytically
favorable conformation.The NS3 protease is 995-fold more active in the
presence than in the absence of NS4A.We are using the Stopped-Flow technology
to study these conformational changes in NS3 after NS4A binding.We are
also searching for tighter binding peptides to inhibit NS4A binding
to NS3.The peptide inhibitors are then tested in the liver cell-line
Huh 7-based HCV replicon assay.The inhibitory mechanism of the best
peptide inhibitors will be studied further use confocal and multiphoton
imaging and microscopy.
Effects of HCV Protease NS3/4A on Human Kinases Involved in Immune
Response:
Virus infection signals antiviral response through transcription factors,
nuclear factor k-B (NFkB) and interferon regulatory factors (IRFs).Current
treatment includes interferon-a (IFN-a) based therapy that amplifies
host antiviral response. In contrast, HCV has evolved unknown mechanisms
to disrupt the host response to IFN-a. To examine the effect of HCV
protease NS3/4A on these pathways, we are collaborating with Dr. T.
Maniatis at Harvard University to elucidate these novel pathways.
Publications
Selected publications from the last 5 years:
Brown JA, Duym WW, Fowler JD, Suo, Z.. (2007) "Single-turnover Kinetic Analysis of the Mutagenic Potential of 8-Oxo-7,8-dihydro-2'-deoxyguanosine during Gap-filling Synthesis Catalyzed by Human DNA Polymerases lambda and beta." J Mol Biol. [Epub ahead of print]
Suo, Z., Abdullah MA. (2007) "Unique Composite Active Site of the Hepatitis C Virus NS2-3 Protease: a New Opportunity for Antiviral Drug Design." ChemMedChem. 2(3), 283-284.
Fiala KA, Suo, Z.. (2007) "Sloppy bypass of an abasic lesion catalyzed by a Y-family DNA polymerase." J Biol Chem. [Epub ahead of print]
Fiala KA, Hypes CD, Suo, Z.. (2007) "Mechanism of abasic lesion bypass catalyzed by a Y-family DNA polymerase." J Biol Chem. [Epub ahead of print]
Fiala KA, Brown JA, Ling H, Kshetry AK, Zhang J, Taylor JS, Yang W, Suo, Z.. (2007) "Mechanism of template-independent nucleotide incorporation catalyzed by a template-dependent DNA polymerase." J Mol Biol. 365(3), 590-602.
Duym WW, Fiala KA, Bhatt N, Suo, Z.. (2006) "Kinetic effect of a downstream strand and its 5'-terminal moieties on single nucleotide gap-filling synthesis catalyzed by human DNA polymerase lambda." J Biol Chem. 281(47), 35649-55.
Fowler JD, Suo, Z.. (2006) "Biochemical, structural, and physiological characterization of terminal deoxynucleotidyl transferase." Chem Rev. 106(6), 2092-110.
Fiala KA, Duym WW, Zhang J, Suo, Z.. (2006) "Up-regulation of the fidelity of human DNA polymerase lambda by its non-enzymatic proline-rich domain." J Biol Chem. 281(28), 19038- 44.
Suo Z. (2005) "Thioesterase portability and peptidyl carrier
protein swapping in yersiniabactin synthetase from Yersinia pestis.", Biochemistry
44(12), 4926-38.
Roettger MP, Fiala KA, Sompalli S, Dong Y, Suo
Z. (2004) "Pre-steady-state
kinetic studies of the fidelity of human DNA polymerase mu",
Biochemistry 43(43), 13827-38.
Fiala KA, Abdel-Gawad W, Suo Z. (2004) "Pre-steady-state kinetic
studies of the fidelity and mechanism of polymerization catalyzed by
truncated human DNA polymerase lambda.", Biochemistry
43(21), 6751-62.
Fiala, K. A & Suo Z.* (2004) Pre-Steady State Kinetic Studies of
the Fidelity of Sulfolobus solfataricus P2 DNA Polymerase IV.Biochemistry 43,
2106-2115
Fiala, K. A & Suo Z.* (2004) Mechanism of DNA Polymerization Catalyzed
by Sulfolobus solfataricus P2 DNA Polymerase IV. Biochemistry 43,
2116-2125
Zhang G. & Suo Z.* (2004) A Mild and Convenient Synthetic Method
for Arylhydrazones of Methyl Benzoate. Synthetic Communications 34(4), 673-678.
Fiala, K. A, Abdel-Gawad, W. & Suo
Z.* (2004) Pre-Steady-State
Kinetic Studies of the Fidelity and Mechanism of Polymerization Catalyzed
by Truncated Human DNA Polymerase Lambda.Biochemistry, accepted
and in press.
Allison, A. J., Ray, A., Suo Z.., Colacino, J. M., Andeson, K. S.,
Johnson, K.A. (2001) “Toxicity of Antiviral Nucleoside Analogs and the
Human Mitochondrial DNA Polymerase", J. Biol. Chem. 276,
40847-40857.
Suo Z.. & Walsh, C. T. (2001) “Thioesterase Portability and Peptidyl
Carrier Protein Swapping in Yersiniabactin Synthetase from Yersinia
pestis”, Biochemistry, submitted.
Suo Z.., Tseng, C., & Walsh, C. T. (2001) “Purification, Priming,
and Catalytic Acylation of Carrier Protein Domains in the Polyketide
Synthase and Nonribosomal Peptidyl Synthetase Modules of the HMWP1 Subunit
of Yersiniabactin Synthetase”, Proc. Natl. Acad. Sci. U.S.A. 98,
99-104.
