Structure & Dynamics of Enzymes

Structure & Dynamics of Enzymes

Principal Investigator
Nozomi Ando, PhD
Assistant Professor of Chemistry & Chemical Biology
PhD, Physics, Cornell University
BS, Physics, MIT
Room: PSB 297
Phone: (607) 255-9454
ORCID: 0000-0001-7062-1644
[ info ] [ CV ]
Bio: Nozomi was born in Denver, CO and grew up in the suburbs of Boston, MA. She received her BS from MIT where she was a physics major and music performance minor. She was drawn to the spaceship-like feel of the Cornell High Energy Synchrotron Source (CHESS) and went to Cornell University for her PhD in physics. As a graduate student in Sol Gruner’s lab, she made her own diamond cells for high-pressure X-ray scattering studies. She then went on to work as a postdoctoral fellow in Cathy Drennan’s lab at MIT, where she developed a fascination with metalloenzymes. In 2014, she was appointed Assistant Professor of Chemistry at Princeton University and started a research program that combines X-ray physics and structural enzymology. In 2018, the Ando lab moved to Cornell University when she joined the faculty in Chemistry & Chemical Biology.

Interests outside of the lab: Nozomi is a classically trained soprano, so her serious hobby is music. She also enjoys observing and naming wild woodland animals. The kitchen is her lab outside of lab. Her various fermentation experiments include making bread (yeast), natto (Bacillus subtilis), miso (Aspergillus oryzae), and various Japanese tsukemono. Her current tools of choice are Japanese donabe pots made of ancient clay. The clay is sourced from regions that used to form the bed of Lake Biwa in prehistoric times and is thought to contain lots of fossilized microbes.

Nozomi's recommendations:

Books (especially for new members): “Unix and Linux: Visual QuickStart Guide” by Deborah Ray and Eric Ray, “Gene Machine” by Venki Ramakrishnan
Music: Renee Fleming’s Night Songs is perfect for grant-writing, paper-writing, and rainy evenings.

Postdoctoral Researchers
John Paul Bacik, PhD
Research Associate
PhD, Macromolecular Crystallography, University of Alberta
BSc, Biology, University of Winnipeg
Room: PSB G47
Phone: (607) 255-4064
ORCID: 0000-0001-9315-5332
[ info ]
Bio: John is from Winnipeg, Manitoba. He received his PhD from the University of Alberta in Macromolecular Crystallography, and has since worked at the University of Toronto, University of Manitoba, and Los Alamos National Laboratory. He joined the Ando group at Princeton University as an Associate Research Scholar in 2016 and moved with the lab to Cornell in 2018. He has extensive experience in protein crystallography and guiding functional studies to test structure-based hypotheses. His work has included studies of proteins from a wide range of sources including mammals, bacteria and viruses - providing insight into catalytic mechanism, structure-based inhibitor design, protein engineering and conformational dynamics.

Scientific Interests: Protein crystallography, structural biology, enzyme kinetics, biochemistry, molecular biology, microbiology, evolutionary biology.

Lab responsibilities: John helps with purchasing and crystallography training.

Interests outside the lab: Outside of the lab, John enjoys spending time with his family and exploring the many things to do around Ithaca.

John's recommendations:
Book: “Gene Machine: The Race to Decipher the Secrets of the Ribosome” by Venki Ramakrishnan
Place: Ithaca Sciencenter
Groceries: Aldi

Amanda Byer, PhD
Postdoctoral Associate
PhD, Chemistry & Biochemistry, Montana State University
BS, Chemistry, Montana State University
Room: PSB G47
Phone: (607) 255-4064
[ info ]
Bio: Amanda grew up in rural Pennsylvania and the San Francisco/Bay Area. While getting her undergraduate degree from UC San Diego, she investigated genes responsible for temperature and light sensing in Arabidopsis thaliana in Prof. Joanne Chory's lab at the Salk Institute. For her graduate work in Prof. Joan Broderick's lab at Montana State University, she worked primarily on two metalloenzyme projects: 1) [FeFe]-Hydrogenase H-cluster maturation with a focus on in vivo cluster maturation on HydF, and 2) radical SAM enzyme mechanism determination using several enzymes and spectroscopic techniques, including a little EPR spectroscopy.

Scientific interests: A true enzymologist, Amanda is fascinated by the mechanisms, structures, functions, and potential for alternate functionalization of metalloenzymes. She also loves spectroscopy (any and all).

Lab responsibilities: Amanda is on the lab-ops team and maintains the glove boxes.

Interests outside of the lab: Amanda enjoys drawing, biking, flat-skiing, reading, and observing plants and insects! When not in lab, she can be found exploring outside (by bike, ski, or foot) or inside (reading or drawing). She recently discovered senposai (a cross between lettuce and Japanese komatsuna) at Ithaca Farmer’s Market.

Amanda's recommendations:
Book: Steinbeck's “Log from the Sea of Cortez”
Movie: Miyazaki's “Nausicaä of the Valley of the Wind”

Steve Meisburger, PhD
Postdoctoral Associate
PhD, Applied Physics, Cornell University
BA, Physics, Carleton College
Room: PSB G47
Phone: (607) 255-4064
Personal website:
ORCID: 0000-0001-6577-8719
[ info ]
Bio: Steve grew up in sunny San José, California. He attended Carleton College in Northfield, Minnesota where he built robots, played bass in an award-winning funk band, met important people, and got a BA in physics. Afterward he earned a PhD in Applied Physics at Cornell University. There, he studied nucleic acid folding and electrostatics using solution X-ray scattering in the lab of Lois Pollack. Steve then joined the Ando Group, where he received an NIH postdoctoral fellowship (Ruth L. Kirschstein Postdoctoral Individual NRSA) to investigate the dynamics of metalloenzymes using advanced X-ray scattering methods, including diffuse scattering from crystals. When the lab moved back to Cornell, he tagged along.

Scientific interests: Protein motion, enzyme allostery, nucleic acid folding and electrostatics, experimental and computation methods for X-ray scattering

Lab responsibilities: Steve is the lab computer czar and maintains the lab GitHub. He's also a member of the lab-ops team.

Interests outside of the lab: Steve’s interests outside of lab are multitudinous and occasionally disjointed. They include gardening, backpacking, electronic noise-makers, furniture made of pine boards, electric cars, and the varieties of sea life found in tide pools. He is also the lab’s resident beer maven in terms of both production and consumption.

Steve's recommendations:
Sport: Hiking (some of) the Finger Lakes Trail
Book: "Numerical Recipes: the Art of Scientific Computing"
Food: Gimme coffee

Graduate Students
Will Thomas
Visiting Graduate Student, Cornell University
PhD Candidate in Chemistry, Princeton University
BA in Biochemistry, Chemistry and Biology, Oberlin College
Room: PSB G45
Email: |
Phone: (607) 255-4064
ORCID: 0000-0001-5490-4900
[ info ]
Bio: Will was born in New Orleans, LA and grew up in the suburbs of Cleveland, Ohio. He did his undergraduate studies at Oberlin College where he majored in biochemistry (and biology and chemistry). At Oberlin, he studied atmospheric environmental chemistry but was interested in finding physical chemistry research with a more biological slant in graduate school. Will went to Princeton in 2015 for his graduate studies to study protein function and structure using advanced X-ray techniques in the Ando lab, and he moved to Cornell with the group in 2018.

Scientific interests: As a biochemist, Will is interested in understanding the structural underpinnings of allosteric regulation using physical techniques. He considers himself an evolutionary biologist at heart, and his interests span from phylogenetics and molecular evolution to behavioral ecology and cognitive psychology.

Lab responsibilities: Will is the group meeting czar and lab safety officer. He's also a member of the lab-ops team.

Interests outside of the lab: Outside of lab, Will enjoys reading and learning about history, anthropology, zoology, and many other topics. He also reads plenty of fiction as long as it isn’t too realistic. Though tempered by his current habitation in a thin-walled apartment building, he also enjoys playing music and is known to write (bad) songs including such hits as "Let's Dimerize" and "Centrifugue". Finally he is an avid "world-builder", which mostly entails concocting unwarranted and unnoticed depth in the dungeons and dragons games he runs for friends.

Will's recommendations:
Food: Though no food is perfect (yet), Will has “scientifically” determined the baby carrot to optimally maximize healthiness, taste, price, and ease of preparation.
Music: Joe Hisaishi, composer for Studio Ghibli films, makes great music to pipette to.

Max Watkins
Visiting Graduate Student, Cornell University
PhD Candidate in Chemistry, Princeton University
BS Biochemistry, Lehigh University
Room: PSB G45
Email: |
Phone: (607) 255-4064
ORCID: 0000-0003-4559-2049
[ info ]
Bio: Max was born in Allentown, Pennsylvania and grew up in Emmaus, Pennsylvania. He received his undergraduate degree in Biochemistry from Lehigh University, where he studied membrane proteins involved in cell signaling in the group of Daniel Thévenin. He joined the Ando Group at Princeton University in 2015 and moved with the group in 2018. Max currently studies flexible enzymes primarily with solution scattering methods.

Scientific Interests: Protein dynamics, enzyme flexibility, Matlab, metalloenzymes, the heat death of the universe, knowing random facts like the economics of making a death star

Lab responsibilities: Max maintains the lab Globus account and the glove boxes. He is also on the lab-ops team.

Interests outside of the lab: Outside of lab, Max is an enthusiastic musician, actively playing both piano and cello. He currently performs in the Cornell University Orchestra and hopes to someday get back to practicing guitar as well. Max’s greatest achievement is that one time he got first at a local Smash Bros. tournament. Max also likes art and has contributed realistic drawings of fictional characters, e.g. Gollum and Appa, to Nozomi’s collection of student art.

Max's recommendation:
Music: A Mahler a day keeps the doctor away.

Audrey Burnim
PhD Candidate in Chemistry
BA, Chemistry, Bryn Mawr College
Room: PSB G45
Phone: (607) 255-9454
ORCID: 0000-0002-9962-1397
[ info ]
Bio: Audrey hails from Haverhill, Massachusetts. She received her bachelor's in chemistry at Bryn Mawr College and completed her first year of graduate study in chemistry at Princeton University. As an undergrad, Audrey studied the relationship between structure and function in hollow nanoparticles and organometallic photosensitizers. She is currently researching the function and evolution of protein allostery through the enzyme family of ribonucleotide reductase.

Scientific interests: Enzyme allostery, protein-protein/protein-ligand interactions, evolution of enzymes, drug design, metabolic pathways

Lab responsibilities: Audrey is the lab entropy-fighting sheriff and is on the lab-ops team.

Interests outside of the lab: Audrey is a fan of Netflix's modern renaissance of documentary-style cooking shows like Salt, Fat, Acid, Heat and Chef’s Table. She also enjoys being outdoors, either hiking in Ithaca or being at a beach whenever possible. The latter was easier in her hometown on the Northshore of Massachusetts but still possible on the shores of Lake Cayuga. She is newly interested in keeping succulents alive and crock-pot cooking (two as-of-yet unrelated endeavors).

Audrey's recommendations:
TV: The Great British Baking Show
Podcast: My Favorite Murder
Sport: The New England Patriots

Gabrielle Illava
Graduate Student in Chemistry
BS, Molecular Biology, Cornell University
Room: PSB G45
Phone: (607) 255-4064
ORCID: 0000-0002-5523-1960
[ info ]
Bio: Gabrielle is from upstate New York. She received her bachelor’s degree in molecular biology from Cornell University. As an undergraduate, Gabrielle gained experience with X-ray methods working at CHESS and with Prof. Sol Gruner on high-pressure SAXS and beamline technology development. She completed her first year of graduate study in chemistry at Princeton University before making her dramatic return to Cornell in 2018. She is currently applying her interests in X-ray method development to study metalloenzymes, making widely used techniques adaptable for use with oxygen sensitive proteins.

Scientific interests: Gabrielle loves developing new methods and technology and is happy to navigate a project start to finish, beginning with a goal and determining the best route to accomplish it. She is fascinated by the evolutionary perspective of molecular biology and pushing the boundaries of X-ray science.

Lab responsibilities: Gabrielle is in charge of maintaining the glove boxes.

Interests outside of lab: When she is not in lab, Gabrielle enjoys running on the beautiful Ithacan trails, swimming, and skiing. She also loves eating good food, traveling, and relaxing with her family. She can be frequently found teaching her son about some science way beyond his current grade level, though she admits that increasingly she’s the student and he’s the teacher.

Gabrielle's recommendations:
Food: Starbucks doubleshot espresso
Sport: Unashamedly cracking corny jokes

Mike Patterson
Graduate Student in Chemistry
BS, Chemistry, University of Tampa
Room: PSB G45
Phone: (607) 255-4064
ORCID: 0000-0001-9688-942X
[ info ]
Bio: Mike was born in Tampa, Florida. He served a 5 year enlistment in the U.S. Army infantry after he finished high school. When he separated, Mike completed his undergraduate degree in chemistry at the University of Tampa. As an undergraduate, Mike studied liquid-liquid rare-earth metal separations via carbamoylmethylphosphine oxide (CMPO) ligand design optimization in the lab of Dr. Eric Werner. He joined the Ando lab when he came to Cornell University in 2018.

Scientific interests: Mike is currently interested in using X-ray diffuse scattering to study protein dynamics and the use of crystalline synthetic materials as protein characterization scaffolds.

Lab responsibilities: Mike organizes XLG.

Interests outside of the lab: Mike spends his spare time with his family and his chainsaw (usually not at the same time). He has been married to his incredibly supportive wife, Alyssa, for 7 years, and they have two kids, Zandt and Fiona. Mike likes to mill up old logs he finds around town and build things in his garage wood shop. He also dabbles in yoga.

Mike's recommendations:
Music: Mike recommends giving Guns and Roses another try.
Food: Aldi brand Spaghetti-Os

Darren (Da) Xu
Graduate Student in Chemistry
BS, Chemistry, Nanjing University
Room: PSB G45
Phone: (607) 255-4064
ORCID: 0000-0002-3879-039X
[ info ]
Bio: Darren grew up in eastern China and obtained his bachelor’s degree in Chemistry from Nanjing University. As an undergrad, he worked on studying biomolecules with mechanical force. He joined the Ando lab at Cornell University in 2018. He is intrigued by the structural dynamics behind the operations of proteins and hopes to elucidate the complex mechanisms of them.

Scientific interests: Darren is interested in the structural dynamics behind enzyme function and allostery, and how these characteristics emerged during evolution.

Interests outside the lab: Darren enjoys running, though he is quite secretive of his favorite running spots. He also enjoys playing music, particularly traditional Chinese instruments. Although he started out by learning Dizi, he now likes the sound of Xiao more because it's less intrusive, an aspect that is particularly appealing to Darren. A lesser known fact about Darren is that he understands some Japanese and can sing at least one Japanese song.

Darren's recommendations:
Music: The New Age music of Pacific Moon.
Food: Darren recommends being completely food-neutral and eating anything that technically counts as edible.

Robert Miller
Graduate Student in Chemistry
MS, Chemistry, University of Minnesota
BS, Biochemistry and Molecular Biology, University of Minnesota
Room: PSB G45 / Wilson 309
ORCID: 0000-0002-0211-7515
[ info ]
Bio: Robby was born and raised in Bloomington, Minnesota. He received a BS in biochemistry and molecular biology from the University of Minnesota Duluth (UMD) and then stayed to complete his MS in chemistry. At UMD, Robby studied under Erin Sheets and Ahmed Heikal where he used integrated fluorescence spectroscopy to characterize a family of FRET sensors designed for measuring intracellular ionic strength. During this time, Robby realized his passion for using physical chemistry to study and answer relevant biological questions. As a result, he decided to attend Cornell University in 2019, where he is a graduate student in the Ando group. Starting in 2020, he'll also start a half-time appointment at CHESS working with Richard Gillilan. When not in lab, he’ll be at the new ID7A (formerly G1) at CHESS!

Scientific Interests: X-ray instrumentation and method development, high-pressure biology and deep-sea life, and protein allostery

Interests outside the lab: Robby loves landscape photography and finding new and amazing places to photograph. In fact, he likes to spend as much time outside as he can, no matter the season. As a high school student, Robby competed and placed nationally at freestyle snowboarding, one of his proudest achievements. He still loves making the most of winter and riding whenever he can. 

Rob’s Recommendations: 
Music: Trampled by Turtles

Jung-Un Park
Graduate Student in Chemistry (Kellogg-Ando Lab)
BS, Chemistry, Seoul National University
Room: Kellogg Lab
[ info ]
Bio: Jung-Un was born and raised in Seoul, South Korea. He did his undergraduate study at Seoul National University, where he received a BS in chemistry. At SNU, Jung-Un performed research jointly with Seokhee Kim and Chaok Seok studying mechanistic enzymology using both biochemical and computational methods. He came to Cornell in 2019 as a graduate student and has begun work as a joint student in the Ando group and the Kellogg group in the Department of Molecular Biology and Genetics, where Jung-Un combines his interests in X-ray scattering and cryo-electron microscopy to study protein structure and dynamics. When not in lab, he is either freezing grids or collecting EM data!

Research interests: Jung-Un is interested in understanding the underpinnings of protein dynamics. In particular, he is interested in developing methods to describe the full conformational space of proteins during important structural transitions, such as an enzyme's catalytic cycle.

Interests outside the lab:  When not in lab, Jung-Un loves to cook and enjoys serving his meals with beer from Ithaca's local breweries. He hopes to have sampled every beer from the area by the time he finishes his PhD (not counting homebrews of course).

Jung-Un's recommendations:
Swimming at the Teagle in the early morning, when it's still nice and quiet. There's nothing more refreshing, both physically and mentally.

Undergraduate Students
Marc Morizono
Chemistry Major, '20
Room: PSB G45
Phone: (607) 255-4064
[ info ]
Bio: Marc was born in Los Angeles and raised in Mission Viejo, California with two younger brothers. He is currently an undergrad at Cornell going into this fourth year and majoring in Chemistry. At Cornell, Marc has explored the beauty of upstate New York, joined a professional chemistry fraternity, and was a member of the Men’s Varsity Swim Team for his first and second years. He has previously worked on the immobilization of complex enzymatic systems and its applications in catalysis. Joining the Ando and Milner Labs in the summer of 2019, Marc continues to explore the many facets of protein dynamics and investigates new methods in crystallization.

Scientific interests: Marc is very interested in the dynamic structures of proteins and the methods of analyzing them, such as spectroscopy and X-ray diffraction. Additionally, he is intrigued by the prospect of using synthesized materials to facilitate the study of particular protein conformations.

Interests outside of the lab: During the sparse sunny days of Ithaca, you can usually find Marc exploring the Ithaca gorges, lounging around Lake Cayuga, or playing frisbee with friends. He also enjoys cooking and trying different kinds of foods.

Marc's recommendations:
Music: Blink-182’s newest album is fire
Sports: Swimming and rock climbing
Movies/TV: The Prestige, Game of Thrones, Marvel movies

Essential Personnel
Panda Pando
Essential Panda, Chemistry
[ info ]
Bio: Panda was born in Costco's and trained in Garnet Chan's lab at Princeton University. He moved to Cornell University with the Ando lab in 2018. Currently guarding the lab during the covid-19 shutdown, while continuing critical work.

Scientific interests: Theoretically, interested in new theories.

Interests outside of the lab: Hanging out with mini Totoro.