Harms Lab
Evolutionary biochemistry @UO
Values
Our goal is for the lab to be a place of human thriving.
In a research group, human thriving means doing excellent and
impactful science. It also means that each lab member is
healthy and growing as a person, that the work we do makes
the world a better place, and that we strive to make the
scientific enterprise more inclusive and diverse.
Details...
Details...
Projects
The Harms Lab studies protein evolution and biophysics using experimental and computational methods.
Current Members
Mike
Harms
Principal Investigator
Favorite part of job: trainees waving graphs in office.
Jon
Muyskens
Lab Manager
Developmental biologist turned evolutionary biochemist.
Michael
Shavlik
PhD student
Experimental studies of "might-have-been" evolutionary trajectories
Kona
Orlandi
PhD student
Early evolution of TLR4
Lauren
Lehmann
PhD student
How does S100A9 interact with TLR4?
Sophia
Phillips
PhD student
Evolution of S100A9 proinflammatory activity
Jose
Sanchez-Borbon
PhD student
How did the CD14 LPS binding site evolve?
Previous Members
(in reverse order of when each left)
Luis
Perez
PhD student
Studies of protein sequence space
JJ
Yin
Undergrad researcher
Evolution of S100A9 proinflammatory activity
Anneliese
Morrison
PhD, 2021
Research scientist with Absci
Hannah
Murawsky
Undergrad, 2021
Biochemistry (honors thesis), med student at UNLV
Daria
Wonderlick
Undergrad, 2021
Biochemistry (honors thesis), PhD student at Stanford
Joseph
Harman
PhD, 2020
Postdoc with David Baker, U Washington
Patrick
Connor
Undergrad
Biochemistry, med student at Iowa
Gus
Warren
Undergrad
Biochemistry, research tech at OHSU
Nick
Frantz
Masters, 2020
Biochemistry
Jeremy
Anderson
Postdoc
Data scientist, Travelers Insurance
Genevieve
Dorrell
Undergrad
Marine Biology
Leander
Goldbach
Visiting Masters Student
Andrea
Loes
PhD, 2018
Lab manager, Bloom Lab, Fred Hutch
Zach
Sailer
PhD, 2018
Software developer, Apple
Caitlyn
Wong
Undergrad
Biochemistry (honors thesis), med student at OHSU
Luke
Wheeler
PhD, 2017
Postdoc with Stacey Smith, UC Boulder
Ran
Shi
Undergrad
Biochemistry, PhD student at U. Georgia
Bram
Rickett
Undergrad
Biochemistry (honors thesis)
Hiranmayi
Duvvuri
Undergrad
Biochemistry
Maureen
Heaphy
Undergrad
Marine Biology
Jaclyn
Smith
Undergrad
Biology
Publications
preprint
An experimental demonstration of ensemble epistasis in the lac repressor
bioRxiv
An experimental demonstration of ensemble epistasis in the lac repressor
bioRxiv
in press
Disentangling contact and ensemble epistasis in a riboswitch
Biophysical Journal
Disentangling contact and ensemble epistasis in a riboswitch
Biophysical Journal
2022
Higher-order interactions shape microbial interactions as microbial community complexity increases
Scientific Reports 12: 22640
Higher-order interactions shape microbial interactions as microbial community complexity increases
Scientific Reports 12: 22640
2022
Topiary: pruning the manual labor from ancestral sequence reconstruction
Protein Science
Topiary: pruning the manual labor from ancestral sequence reconstruction
Protein Science
2022
Evolution avoids a pathological stabilizing interaction in the immune protein S100A9
PNAS 119 (41) e2208029119
Evolution avoids a pathological stabilizing interaction in the immune protein S100A9
PNAS 119 (41) e2208029119
2021
Ensemble epistasis: thermodynamic origins of non-additivity between mutations
Genetics 219(1):iyab105
Ensemble epistasis: thermodynamic origins of non-additivity between mutations
Genetics 219(1):iyab105
2021
A conserved folding nucleus sculpts the free energy landscape of bacterial and archaeal orthologs from a divergent TIM barrel family
PNAS 118(17):e2019571118
A conserved folding nucleus sculpts the free energy landscape of bacterial and archaeal orthologs from a divergent TIM barrel family
PNAS 118(17):e2019571118
2021
Evolutionary conservation of structural and functional coupling between the BRM AT-hook and bromodomain
Journal of Molecular Biology 166845
Evolutionary conservation of structural and functional coupling between the BRM AT-hook and bromodomain
Journal of Molecular Biology 166845
2021
Exploring the evolutionary history of kinetic stability in the alpha-lytic protease family
Biochemistry 60(3):170–181
Exploring the evolutionary history of kinetic stability in the alpha-lytic protease family
Biochemistry 60(3):170–181
2021
Were ancestral proteins less specific?
Molecular Biology and Evolution msab019
Were ancestral proteins less specific?
Molecular Biology and Evolution msab019
2021
Identification and characterization of zebrafish Tlr4 co-receptor Md-2
Journal of Immunology 206(5):1046-1057
Identification and characterization of zebrafish Tlr4 co-receptor Md-2
Journal of Immunology 206(5):1046-1057
2020
Learning Peptide Recognition Rules for a Low Specificity Protein
Protein Science 29:2259 –2273
Learning Peptide Recognition Rules for a Low Specificity Protein
Protein Science 29:2259 –2273
2020
Inferring a complete genotype-phenotype map from a small number of measured phenotypes
PLOS Computational Biology e1008243
Inferring a complete genotype-phenotype map from a small number of measured phenotypes
PLOS Computational Biology e1008243
2020
Evolution of multifunctionality through a pleiotropic substitution in the innate immune protein S100A9
eLife 9:e54100
Evolution of multifunctionality through a pleiotropic substitution in the innate immune protein S100A9
eLife 9:e54100
preprint
Zinc-independent activation of Toll-like receptor 4 by S100A9
bioRxiv
Zinc-independent activation of Toll-like receptor 4 by S100A9
bioRxiv
preprint
Skeletal geometry and nice transitions restore organ size and shape during zebrafish fin regeneration
bioRxiv
Skeletal geometry and nice transitions restore organ size and shape during zebrafish fin regeneration
bioRxiv
2019
Tracing the evolution of novel features of human Toll-like receptor 4
Protein Science 28(7):1350-1358
Tracing the evolution of novel features of human Toll-like receptor 4
Protein Science 28(7):1350-1358
2018
pytc: open source python software for global analyses of isothermal titration calorimetry data
Biochemistry 57(18):2578–2583
pytc: open source python software for global analyses of isothermal titration calorimetry data
Biochemistry 57(18):2578–2583
2018
Coevolution of the Toll-Like Receptor 4 complex with calgranulins and lipopolysaccharide
Frontiers in Immunology
Coevolution of the Toll-Like Receptor 4 complex with calgranulins and lipopolysaccharide
Frontiers in Immunology
2018
Conservation of specificity in two low-specificity proteins
Biochemistry 57(5):684-695
Conservation of specificity in two low-specificity proteins
Biochemistry 57(5):684-695
2018
Enzymes emerge by upcycling [News & Views]
Nature Chemical Biology 14:526-527
Enzymes emerge by upcycling [News & Views]
Nature Chemical Biology 14:526-527
2017
Ca2+ and Cu2+ bind independently to human S100A5
BMC Biophysics 10:8
Ca2+ and Cu2+ bind independently to human S100A5
BMC Biophysics 10:8
2017
Molecular ensembles make evolution unpredictable
PNAS 114(45):11938-11943
Molecular ensembles make evolution unpredictable
PNAS 114(45):11938-11943
2017
High-order epistasis shapes evolutionary trajectories
PLOS Computational Biology
High-order epistasis shapes evolutionary trajectories
PLOS Computational Biology
2017
Detecting high-order epistasis in nonlinear genotype-phenotype maps
Genetics 205(3):1079-1088
Detecting high-order epistasis in nonlinear genotype-phenotype maps
Genetics 205(3):1079-1088
2017
Robustness of reconstructed ancestral protein functions to statistical uncertainty
Molecular Biology and Evolution 34 (2):247-261
Robustness of reconstructed ancestral protein functions to statistical uncertainty
Molecular Biology and Evolution 34 (2):247-261
2016
Multiple evolutionary origins of ubiquitous Cu2+ and Zn2+ binding in the S100 protein family
PLOS ONE 11(10): e0164740
Multiple evolutionary origins of ubiquitous Cu2+ and Zn2+ binding in the S100 protein family
PLOS ONE 11(10): e0164740
2016
Following the folding trajectory of RNases H over evolutionary time: a trend towards kinetic stability
PNAS 113(46):13045-13050
Following the folding trajectory of RNases H over evolutionary time: a trend towards kinetic stability
PNAS 113(46):13045-13050
2016
Ancient protein thermostability and specificity [Invited Review]
Current Opinions in Structural Biology 38:37-43
Ancient protein thermostability and specificity [Invited Review]
Current Opinions in Structural Biology 38:37-43
2014
Thermodynamic system drift in the evolution of protein thermostability
PLOS Biology 12(11):e1001994
Thermodynamic system drift in the evolution of protein thermostability
PLOS Biology 12(11):e1001994
2014
Biophysical basis for historical contingency in glucocorticoid receptor evolution
Nature 512:203-207
Biophysical basis for historical contingency in glucocorticoid receptor evolution
Nature 512:203-207
2013
Biophysical mechanisms for large-effect mutations in the evolution of steroid hormone receptors
PNAS 110(28):11475-11480
Biophysical mechanisms for large-effect mutations in the evolution of steroid hormone receptors
PNAS 110(28):11475-11480
2013
Evolutionary biochemistry: Revealing the historical and physical causes of protein function
Nature Reviews Genetics 14(8):559-571
Evolutionary biochemistry: Revealing the historical and physical causes of protein function
Nature Reviews Genetics 14(8):559-571
2013
Resurrection of an Urbilaterian U1A/U2B''/SNF protein
Journal of Molecular Biology 425(20):3846–3862
Resurrection of an Urbilaterian U1A/U2B''/SNF protein
Journal of Molecular Biology 425(20):3846–3862
2012
Evolution of minimal specificity in the steroid receptors
PLOS Genetics 8(11):e1003072
Evolution of minimal specificity in the steroid receptors
PLOS Genetics 8(11):e1003072
2011
Arginine is ionized at internal positions in a protein
PNAS 108(47):18954-9
Arginine is ionized at internal positions in a protein
PNAS 108(47):18954-9
2010
Protein evolution by molecular tinkering: diversification of the nuclear receptor superfamily from a ligand-dependent ancestor
PLOS Biology 8(10):e1000497
Protein evolution by molecular tinkering: diversification of the nuclear receptor superfamily from a ligand-dependent ancestor
PLOS Biology 8(10):e1000497
2010
Analyzing protein structure and function using ancestral gene reconstruction
Current Opinions in Structural Biology 20(3):360-366
Analyzing protein structure and function using ancestral gene reconstruction
Current Opinions in Structural Biology 20(3):360-366
2009
The pKa values of acidic and basic residues buried at the same internal location in a protein are governed by different factors
Journal of Molecular Biology 389:34-47
The pKa values of acidic and basic residues buried at the same internal location in a protein are governed by different factors
Journal of Molecular Biology 389:34-47
2008
A buried lysine that titrates with a normal pKa: Role of conformational flexibility at the protein–water interface as a determinant of pKa values
Protein Science 17:833-845
A buried lysine that titrates with a normal pKa: Role of conformational flexibility at the protein–water interface as a determinant of pKa values
Protein Science 17:833-845
2005
How sequence defines structure: a crystallographic map of DNA structure and conformation
PNAS 102(20):7157-7162
How sequence defines structure: a crystallographic map of DNA structure and conformation
PNAS 102(20):7157-7162
2003
Laser light-scattering evidence for an altered association of βB1-crystallin deamidated in the connecting peptide
Protein Science 13:678-686
Laser light-scattering evidence for an altered association of βB1-crystallin deamidated in the connecting peptide
Protein Science 13:678-686
Location
Location on campus
Mike's office: Willamette 340A
Lab: Willamette 340, 342
Address
Harms Lab
Institute for Molecular Biology
1229 University of Oregon
Eugene, OR 97403-1229
Phone
541-346-9003