Ichiro Matsumura PhD

Department of Biochemistry
Associate Professor, Emeritus

(404) 727-2908
imatsum@emory.edu
Pubmed

Emory University School of Medicine
Department of Biochemistry
1510 Clifton Rd., Room 4017 RRC

Overview

My objective is to understand the adaptive evolution of protein structure and function. I recapitulate the evolutionary process in the laboratory, and identify the correlations between specific changes in tertiary structure and improvements in fitness. These experiments often yield proteins with enhanced industrial or pharmaceutical utility.

Academic Appointment

Associate Professor of Biochemistry, Emory University School of Medicine

Education

Degrees

M.B.A. from Goizueta Business School, Emory University
PhD from University of California
Bachelor of Science from Massachusetts Institute of Technology

Research

Focus

My objective is to understand the adaptive evolution of protein structure and function. I recapitulate the evolutionary process in the laboratory, and identify the correlations between specific changes in tertiary structure and improvements in fitness. These experiments often yield proteins with enhanced industrial or pharmaceutical utility.

Publications

Methylase-assisted subcloning for high throughput BioBrick assembly.
PeerJ Volume: 8 Page(s): e9841
01/01/2020 Authors: Matsumura I
Statistical noise from recombinant plasmids can be abated via complementation of a ribosomal protein gene deletion.
Protein Eng Des Sel Volume: 32 Page(s): 433 - 441
12/31/2019 Authors: Matsumura I; Chyong D
A GAL80 Collection To Inhibit GAL4 Transgenes in Drosophila Olfactory Sensory Neurons.
G3 (Bethesda) Volume: 8 Page(s): 3661 - 3668
11/06/2018 Authors: Eliason J; Afify A; Potter C; Matsumura I
Semi-automated Tip Snip cloning of restriction fragments into and out of plasmid polylinkers.
Biotechniques Volume: 62 Page(s): 99 - 106
03/01/2017 Authors: Matsumura I
Why Johnny can't clone: Common pitfalls and not so common solutions.
Biotechniques Volume: 59 Page(s): IV - XIII
09/01/2015 Authors: Matsumura I
Transformable facultative thermophile Geobacillus stearothermophilus NUB3621 as a host strain for metabolic engineering.
Appl Microbiol Biotechnol Volume: 98 Page(s): 6715 - 6723
08/01/2014 Authors: Blanchard K; Robic S; Matsumura I
Escherichia coli deletion mutants illuminate trade-offs between growth rate and flux through a foreign anabolic pathway.
PLoS One Volume: 9 Page(s): e88159
01/01/2014 Authors: Falls KC; Williams AL; Bryksin AV; Matsumura I
Substrate ambiguous enzymes within the Escherichia coli proteome offer different evolutionary solutions to the same problem.
Mol Biol Evol Volume: 30 Page(s): 2001 - 2012
09/01/2013 Authors: Yip SH-C; Matsumura I
A quarter century of reaping what we SOE.
Biotechniques Volume: 54 Page(s): 127 - 128
03/01/2013 Authors: Matsumura I
Directed evolution of aminoglycoside phosphotransferase (3') type IIIa variants that inactivate amikacin but impose significant fitness costs.
PLoS One Volume: 8 Page(s): e76687
01/01/2013 Authors: Kramer JR; Matsumura I
Overlap extension PCR cloning.
Methods Mol Biol Volume: 1073 Page(s): 31 - 42
01/01/2013 Authors: Bryksin A; Matsumura I
The adenosine deaminases of Plasmodium vivax and Plasmodium falciparum exhibit surprising differences in ligand specificity.
J Mol Graph Model Volume: 35 Page(s): 43 - 48
05/01/2012 Authors: Ivanov A; Matsumura I
Expression vectors for Acinetobacter baylyi ADP1.
Appl Environ Microbiol Volume: 78 Page(s): 280 - 283
01/01/2012 Authors: Murin CD; Segal K; Bryksin A; Matsumura I
Rational design of a plasmid origin that replicates efficiently in both gram-positive and gram-negative bacteria.
PLoS One Volume: 5 Page(s): e13244
10/08/2010 Authors: Bryksin AV; Matsumura I
Overlap extension PCR cloning: a simple and reliable way to create recombinant plasmids.
Biotechniques Volume: 48 Page(s): 463 - 465
06/01/2010 Authors: Bryksin AV; Matsumura I
How evolving enzymes can beat the heat and avoid defeat.
Nat Chem Biol Volume: 5 Page(s): 538 - 539
08/01/2009 Authors: Matsumura I; Ivanov AA
A study in molecular contingency: glutamine phosphoribosylpyrophosphate amidotransferase is a promiscuous and evolvable phosphoribosylanthranilate isomerase.
J Mol Biol Volume: 377 Page(s): 323 - 336
03/21/2008 Authors: Patrick WM; Matsumura I
Multicopy suppression underpins metabolic evolvability.
Mol Biol Evol Volume: 24 Page(s): 2716 - 2722
12/01/2007 Authors: Patrick WM; Quandt EM; Swartzlander DB; Matsumura I
Antibody-induced oligomerization and activation of an engineered reporter enzyme.
J Mol Biol Volume: 369 Page(s): 1052 - 1059
06/15/2007 Authors: Geddie ML; Matsumura I
Artificially evolved Synechococcus PCC6301 Rubisco variants exhibit improvements in folding and catalytic efficiency.
Biochem J Volume: 404 Page(s): 517 - 524
06/15/2007 Authors: Greene DN; Whitney SM; Matsumura I
Natural history as a predictor of protein evolvability.
Protein Eng Des Sel Volume: 19 Page(s): 439 - 442
10/01/2006 Authors: O'Loughlin TL; Patrick WM; Matsumura I
HIV protease-activated molecular switches based on beta-glucuronidase and alkaline phosphatase.
Comb Chem High Throughput Screen Volume: 9 Page(s): 313 - 320
05/01/2006 Authors: O'Loughlin TL; Matsumura I
Diversification and specialization of HIV protease function during in vitro evolution.
Mol Biol Evol Volume: 23 Page(s): 764 - 772
04/01/2006 Authors: O'Loughlin TL; Greene DN; Matsumura I
Directed evolution of RuBisCO hypermorphs through genetic selection in engineered E.coli.
Protein Eng Des Sel Volume: 19 Page(s): 113 - 119
03/01/2006 Authors: Parikh MR; Greene DN; Woods KK; Matsumura I
Pooling for improved screening of combinatorial libraries for directed evolution.
Volume: 22 Page(s): 961 - 967
01/01/2006 Authors: Polizzi KM; Parikh M; Spencer CU; Matsumura I; Lee JH; Realff MJ; Bommarius AS
Simulation modeling of pooling for combinatorial protein engineering.
J Biomol Screen Volume: 10 Page(s): 856 - 864
12/01/2005 Authors: Polizzi KM; Spencer CU; Dubey A; Matsumura I; Lee JH; Realff MJ; Bommarius AS
Rational design of p53, an intrinsically unstructured protein, for the fabrication of novel molecular sensors.
J Biol Chem Volume: 280 Page(s): 35641 - 35646
10/21/2005 Authors: Geddie ML; O'Loughlin TL; Woods KK; Matsumura I
Site-saturation mutagenesis is more efficient than DNA shuffling for the directed evolution of beta-fucosidase from beta-galactosidase.
J Mol Biol Volume: 352 Page(s): 621 - 628
09/23/2005 Authors: Parikh MR; Matsumura I
Whole plasmid mutagenic PCR for directed protein evolution.
Biomol Eng Volume: 22 Page(s): 73 - 79
06/01/2005 Authors: Matsumura I; Rowe LA
Pooling of mutants from directed evolution to improve throughput and quality of variants.
Volume: 229 Page(s): U185 - U185
03/13/2005 Authors: Polizzi KM; Spencer CU; Dubey A; Matsumura I; Lee JH; Realff MJ; Bommarius AS
Rapid evolution of beta-glucuronidase specificity by saturation mutagenesis of an active site loop.
J Biol Chem Volume: 279 Page(s): 26462 - 26468
06/18/2004 Authors: Geddie ML; Matsumura I
High throughput microplate screens for directed protein evolution.
Methods Enzymol Volume: 388 Page(s): 134 - 145
01/01/2004 Authors: Geddie ML; Rowe LA; Alexander OB; Matsumura I
A comparison of directed evolution approaches using the beta-glucuronidase model system.
J Mol Biol Volume: 332 Page(s): 851 - 860
09/26/2003 Authors: Rowe LA; Geddie ML; Alexander OB; Matsumura I
Mutagenic polymerase chain reaction of protein-coding genes for in vitro evolution.
Methods Mol Biol Volume: 182 Page(s): 259 - 267
01/01/2002 Authors: Matsumura I; Ellington AD
Optimization of heterologous gene expression for in vitro evolution.
Biotechniques Volume: 30 Page(s): 474 - 476
03/01/2001 Authors: Matsumura I; Olsen MJ; Ellington AD
In vitro evolution of beta-glucuronidase into a beta-galactosidase proceeds through non-specific intermediates.
J Mol Biol Volume: 305 Page(s): 331 - 339
01/12/2001 Authors: Matsumura I; Ellington AD
Directed evolution of the surface chemistry of the reporter enzyme beta-glucuronidase.
Nat Biotechnol Volume: 17 Page(s): 696 - 701
07/01/1999 Authors: Matsumura I; Wallingford JB; Surana NK; Vize PD; Ellington AD
In vitro evolution of thermostable p53 variants.
Protein Sci Volume: 8 Page(s): 731 - 740
04/01/1999 Authors: Matsumura I; Ellington AD
Aptamers as therapeutic and diagnostic reagents: problems and prospects.
Curr Opin Chem Biol Volume: 1 Page(s): 5 - 9
06/01/1997 Authors: Osborne SE; Matsumura I; Ellington AD
DNA shuffling brightens prospects for GFP.
Nat Biotechnol Volume: 14 Page(s): 366
03/01/1996 Authors: Matsumura I; Ellington AD
Synergistic contributions of asparagine 46 and aspartate 52 to the catalytic mechanism of chicken egg white lysozyme.
Biochemistry Volume: 35 Page(s): 1890 - 1896
02/13/1996 Authors: Matsumura I; Kirsch JF
Is aspartate 52 essential for catalysis by chicken egg white lysozyme? The role of natural substrate-assisted hydrolysis.
Biochemistry Volume: 35 Page(s): 1881 - 1889
02/13/1996 Authors: Matsumura I; Kirsch JF
Fluorine-19 nuclear magnetic resonance spectroscopic study of fluorophenylalanine- and fluorotryptophan-labeled avian egg white lysozymes.
Biochemistry Volume: 33 Page(s): 5238 - 5245
05/03/1994 Authors: Lian C; Le H; Montez B; Patterson J; Harrell S; Laws D; Matsumura I; Pearson J; Oldfield E
Evidence for a new family of evolutionarily conserved homeobox genes.
Nucleic Acids Res Volume: 18 Page(s): 1908
04/11/1990 Authors: Wedeen CJ; Kostriken RG; Matsumura I; Weisblat DA

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