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CHRONO preprint image.png

CHRONO participates in multi-modal repression of circadian transcriptional complexes.

Crosby P, Goularte NF, Sharma D, Chen E, Parico GCG, Philpott JM, Harold R, Gustafson CL, Partch CL


Isoform-specific C-terminal phosphorylation drives autoinhibition of Casein Kinase 1.

Harold R*, Tulsian NK*, Narasimamurthy R, Yaitanes N, Ayala Hernandez MG, Lee H-W, Virshup DM, Partch CL


Regulation of the circadian clock in C. elegans by clock gene homologs kin-20 and lin-42.

Lamberti ML, Spangler RK, Cerdeira V, Ares M, Rivollet L, Ashley GE, Ramos Coronado A, Tripathi S, Spiousas I, Ward JD, Partch CL, Bénard CY, Goya ME, Golombek DA


PDB coordinates for C. elegans LIN-42 PAS-B domain: 8GCI

Conformationally responsive dyes enable protein-adaptive differential scanning fluorimetry.

Wu T, Yu JC, Suresh A, Gale-Day ZJ, Alteen MG, Woo AS, Millbern Z, Johnson OT, Carroll EC, Partch CL, Fourches D, Vinueza NC, Vocadlo DJ, Gestwicki JE

Nature Biotechnology

(2024) ––In press, link coming soon!



Dimerization Rules of Mammalian PAS Proteins.

Rojas BL, Vazquez-Rivera E, Partch CL, Bradfield CA

J Mol Biol



PAS Dimerization at the Nexus of the Mammalian Circadian Clock.

Sharma D and Partch CL

J Mol Biol



The inner workings of an ancient biological clock.

Fang M, LiWang A, Golden SS, Partch CL

Trends in Biochemical Sciences



Cooperation between bHLH transcription factors and histones for DNA access.

Michael A*, Stoos L*, Crosby P, Eggers N, Nie XY, Makasheva K, Minnich M, Healy KH, Weiss J, Kempf G, Cavadini S, Kater L, Seebacher J, Vecchia L, Chakraborty D, Isbel L, Grand RS, Andersch F, Fribourgh JL, Schübeler D, Zuber J, Liu AC, Becker PB, Fierz B, Partch CL, Menet J, Thomä N


(2023) 619: 385-393

Featured in Murawska M, Ladumer, Margulies CE (2023) Pioneers conquer core histones at the chromatin frontier. Nat Struct Mol Biol 30: 1050-1053

PDB coordinates for CLOCK:BMAL1-nuc SHL+5.8 – 8OSK

        (EMD 1715417157, 17158)

PDB coordinates for CLOCK:BMAL1-nuc SHL-6.2 – 8OSJ

        (EMD 17155, 17156)

PDB coordinates for CLOCK:BMAL1-nuc native Por promoter – 8OSL

        (EMD 17160, 17161)

PDB coordinates for OCT4 and MYC:MAX-nuc – 8OTS

        (EMD 17183)

PDB coordinates for MYC:MAX-nuc SHL+5.8 – 8OTT

        (EMD 17184)

ChIP-Seq data of MYC-MAX and CLOCK-BMAL1 on in vitro reconstituted chromatin, GEO accession code GSE224589

Protocols for in vitro reconstitution of the cyanobacterial circadian clock. 

Chavan A, Heisler J, Chang Y-G, Golden SS, Partch CL, LiWang A



CK1_pFASP preprint image.png

PERIOD phosphorylation leads to feedback inhibition of CK1 activity to control circadian period.

Philpott JM, Freeberg AM, Park J, Lee K, Ricci CG, Hunt SR, Narasimamurthy R, Segal DH, Robles R, Cai YD, Tripathi S, McCammon JA, Virshup DM, Chiu JC, Lee C, Partch CL

Mol Cell​

(2023) 83(10):1677-1692


Meet the Authors: Jonathan Philpott and Carrie L. Partch

Mol Cell​

(2023) 83(10):1539-1541

PDB coordinates for CK1-human PER2 2p-FASP complex: 8D7M

PDB coordinates for CK1-human PER2 3p-FASP complex: 8D7N

PDB coordinates for CK1-human PER2 4p-FASP complex: 8D7O

PDB coordinates for CK1-Drosophila PER pShort complex: 8D7P

Chemical shift assignments for the human PER2 FASP region at BMRB

FEBS Letts image.png

How circadian clocks keep time––the discovery of slowness.

Partch CL and Brunner M

FEBS Letts

(2022) 596: 1613-1614

Swan Sandate et al 2021.png

Coupling of distant ATPase domains in the circadian clock protein KaiC.

Swan JA*, Sandate CR*, Chavan A, Freeberg AM, Etwaru D, Ernst DC, Palacios JG, Golden SS, LiWang A, Lander GC, Partch CL

Nat Struct Mol Biol 

(2022) 29: 759-766


PDB coordinates for KaiC daytime mimetic – 7S67 (EMD 24852)

PDB coordinates for KaiC nighttime (C6) mimetic – 7S66 (EMD 24851)

PDB coordinates for KaiC nighttime (C2) mimetic – 7S65 (EMD 24850)

Bagnall et al 2021.png

Quantification of circadian interactions and protein abundance defines a mechanism for operational stability of the circadian clock

Bagnall JS*, Koch AA*, Smyllie NJ, Begley N, Adamson A, Fribourgh JL, Spiller DG, Meng Q-J, Partch CL, Strimmer K, House, TA, Hastings MH, Loudon ASI


(2022) 11:e73976


Screen Shot 2022-01-23 at 12.01.20 PM.png

Cryptochrome proteins regulate the circadian intra-cellular behavior and localization of PER2 in mouse suprachiasmatic nucleus neurons.

Smyllie, N.J., Bagnall, J., Koch, A., Niranjan, D., Poliarova, L., Chesham, J.E., Partch, C.L., Chin, J.W., Loudon, A.S.I., Hastings, M.H. Proc Natl Acad Sci USA



NF-kB modifies the mammalian circadian clock through interaction with the core clock protein BMAL1

Shen Y, Wang W, Endale M, Francey LJ, Harold RH, Hammers DW, Huo Z, Partch CL, Hogenesch JB, Wu Z-H, Liu AC

PLoS Genetics




Reconstitution of an intact clock reveals mechanisms of circadian timekeeping

Chavan AG*, Swan JA*, Heisler J*, Sancar C, Ernst DC, Fang M, Palacios JG, Spangler RK, Bagshaw CR, Tripathi S, Crosby P, Golden SS, Partch CL, LiWang A


(2021) Vol. 374

PDB coordinates for SasA:KaiC CI domain – 6X61 

Featured in Rust, M.J. (2021) Biological rhythms: The suspended animation clock. Curr Biol 31: R1513-R1534

Ketogenesis impact on liver metabolism revealed by proteomics of lysine β-hydroxybutyrylation

Koronowski KB, Greco CM, Huang H, Kim, J-K, Fribourgh JL, Crosby P, Partch CL, Qiao F, Zhao Y, Sassone-Corsi P

Cell Reports

(2021) 36: 109487


CRY2 missense mutations suppress P53 and enhance cell growth

Chan AB, Parico GCG, Fribourgh JL, Ibrahim LH, Bollong MJ, Partch CL, Lamia KA

Proceedings of the National Academy of Science USA

(2021) 118:e2101416118


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Biochemical mechanisms of period control within the mammalian circadian clock.

Philpott JM, Torgrimson MR, Harold RL and Partch CL

Seminars in Cell and Developmental Biology

(2021) S1084-9521(21)00085-9

The tail of cryptochromes: an intrinsically disordered cog within the mammalian circadian clock

Parico GCG and Partch CL

Cell Communication & Signaling

(2020) 18:182


New insights into non-transcriptional regulation of mammalian core clock proteins.

Crosby P and Partch CL

Journal of Cell Science

(2020) 133:jcs241174

2019 JMB review_TTFL.png

Orchestration of circadian timing by macromolecular protein assemblies.

Partch CL

Journal of Molecular Biology

(2020) 432: 3426-3448

Special issue on Molecular mechanisms underlying circadian regulation

Eds. Eva Wolf and Achim Kramer

The CRY1 tail controls circadian timing by regulating its association with CLOCK:BMAL1.

Parico GCG, Perez I, Fribourgh JL, Hernandez BN, Lee HW, and Partch CL

Proceedings of the National Academy of Science USA

(2020) 117:27971-27979


Featured in:

Chemical shift assignments for the human CRY1 tail at BMRB

Dynamics at the serine loop underlie differential ability of cryptochromes for CLOCK:BMAL1 to control circadian timing.

Fribourgh JL*, Srivastava A*, Sandate CR*, Michael AK, Hsu PL, Rakers C, Nguyen LT, Torgrimson MR, Parico GCG, Tripathi S, Zheng N, Lander GC, Hirota T, Tama F, and Partch CL


(2020) 9:e55275


PDB coordinates for mouse CRY1 PHR:PER2 CBD structure – 6OF7
Coordinates for the PER2 CBD:CRY1 PHR:CLOCK PAS-B HADDOCK model available upon request.

Casein kinase 1 dynamics underlie substrate selectivity and the PER2 circadian phosphoswitch.

Philpott JM*, Narasimamurthy R*, Ricci CG*, Freeberg AM, Hunt SR, Yee LE, Pelofsky RS, Tripathi S, Virshup DM, and Partch CL


(2020) 9:e52343


Featured in:

PDB coordinates for CK1δ kinase domain structures:
wild-type in anion-free crystallization conditions – 6PXO
tau mutant (R178C) – 6PXN
anion-binding site 2 mutant (R171E) – 6PXP
Ceh-Pavia image.png

Regulating behavior with the flip of a translational switch.

Ceh-Pavia E and Partch CL

Proceedings of the National Academy of Science USA

(2018) 115: 13151-13153

Check out the fantastic paper outlining use of genetic code expansion and noncanonical amino acids to regulate protein expression and circadian behavior from the Hastings and Chin labs here

CK1d/e protein kinase primes the PER2 circadian phosphoswitch.

Narasimamurthy R, Hunt SR, Lu Y, Fustin J-M, Okamura H, Partch CL, 

Forger DB, Kim JK, Virhup DM

Proceedings of the National Academy of Science USA

(2018) 115: 5986-5991

Chemical shift assignments for mouse PER2 FASP peptide

Check out this great paper from the Okamura lab on a related topic!

Structure, function, and mechanism of the core circadian clock in cyanobacteria.

Swan JA, Golden SS, LiWang A, Partch CL

Journal of Biological Chemistry

(2018) 293: 5026-5034​

Structural dynamics of RbmA governs plasticity of Vibrio cholerae  biofilms.

Fong JC, Rogers A, Michael AK, Parsley NC, Cornell WC, Lin YC, Singh PK, Hartmann R, Drescher K, Vinogradov E, Dietrich LE, Partch CL, Yildiz FH


(2017) 6:e26163

Featured in: Biofilms: Flipping the switch

Pierrat X and Persat A


(2017) 6:e31082

A slow conformational switch in the BMAL1 transactivation domain modulates circadin rhythms.
Gustafson CL, Parsley NC, Asimgil H, Lee HW, Ahlbach C, Michael AK, Williams OL, Xu H, Davis TL, Liu AC and Partch CL
Molecular Cell
(2017) Vol. 66: 447-457
Featured in: A flick of the tail keeps the circadian clock in line. Narasimamurthy R and Virshup DM
Molecular Cell Vol. 66: 437-438
The assembly and function of bHLH-PAS heterodimers.
Fribourgh JL and Partch CL
Proceedings of the National Academy of Science USA
(2017) Vol. 114: 5330-5332
Commentary on: Structural hierarchy controlling dimerization and target DNA recognition in the AHR transcriptional complex. Soek SH, Lee W, Jiang L, Molugu K, Li Y, Park S, Bradfield CA, Xing Y.
Proceedings of the National Academy of Science USA
(2017) Vol. 114: 5431-5436
Structural basis of the day-night transition in a bacterial circadian clock.
Tseng R*, Goularte NF*, Chavan A*, Luu J, Cohen SE, Chang YG, Heisler J, Michael AK, Tripathi S, Golden SS, LiWang A, Partch CL
(2017) Vol. 355: 1174-80

PDB coordinates for Kai complex structures:
fold-switch KaiB:KaiC CI domain – 5JWO 
fold-switch KaiB:KaiC S431E hexamer (left) – 5JWQ
KaiA deltaN:fold-switch KaiB:KaiC CI domain – 5JWR
fold-switch KaiB:CikA PsR domain –  5JY5
Formation of a repressive complex in the mammalian circadian clock is mediated by the secondary pocket of CRY1.
Michael A, Fribourgh J, Chelliah Y, Sandate C, Hura G, Schneidman-Duhovny D, Tripathi SM, Takahashi JS, Partch CL 
Proceedings of the National Academy of Science USA
(2017) Vol. 114: 1560-65 
PDB coordinates for mouse CRY1 PHR structure – 5T5X
Coordinates for HADDOCK, MultiFoXS, and FoXSDocK models available upon request.
Animal Cryptochromes: Divergent roles in light perception, circadian timekeeping and beyond.
Michael A*, Fribourgh J*, Van Gelder RN, Partch CL 
Photochemistry and Photobiology 
(2017) Vol. 93: 128-40
Special issue in honor of Aziz Sancar, 2015 Nobel Laureate in Chemistry
Early doors (Edo) mutant mouse reveals the importance of period 2 (PER2) PAS domain structure for circadian pacemaking.
Militi S*, Maywood ES*, Sandate CR, Chesham JE, Barnard AR, Parsons MJ, Vibert JL, Joynson GM,Partch CL, Hastings MH, Nolan PM
Proceedings of the National Academy of Science USA 
(2016) Vol. 113: 2756-61
SAXS profiles for WTEdo PER2 PAS-AB domains on
Cytosolic BMAL1 moonlights as a translation factor.
Michael AK, Asimgil H, Partch CL
Trends in Biochemical Science 
(2015) Vol. 40: 489-90
Cryptochrome 1 regulates the circadian clock through dynamic interactions with the BMAL1 C-terminus
Xu H*, Gustafson CL*, Sammons PJ, Khan SK, Parsley NC, Ramanathan C, Lee HW, Liu AC, Partch CL
Nature Structural and Molecular Biology 
(2015) Vol. 22: 476-84
Featured in: Grab the wiggly tail: new insights into the dynamics of circadian clocks. Hui KY and Ripperger JA
Nature Structural and Molecular Biology (2015) Vol. 22: 435-36
Chemical shift assignments for BMAL1 and BMAL2 TADs
Cancer/Testis antigen PASD1 silences the circadian clock.
Michael AK, Harvey SL, Sammons PJ, Anderson AP, Kopalle HM, Banham AH, Partch CL
Molecular Cell 
(2015) Vol. 58: 743-54
Featured in:
Analysis of protein stability and ligand interactions by thermal shift assay.
Huynh K and Partch CL
Current Protocols in Protein Science 
(2015) Vol. 79: 28.9.1-14
Additional information on acquiring and processing thermal shift data available on Resources page
Coiled-coil coactivators play a structural role mediating interactions in hypoxia-inducible factor heterodimerization.
Guo Y, Scheuermann TH, Partch CL, Tomchick DR, Gardner KH
Journal of Biological Chemistry 
(2015) Vol. 290: 7707-21
Emerging models for the molecular basis of mammalian circadian timing.
Gustafson CL and Partch CL
(2015) Vol. 54: 134-49
Antibacterial membrane attack by a pore-forming intestinal C-type lectin.
Mukherjee S, Zheng H, Derebe MG, Callenberg KM, Partch CL, Rollins D, Propheter DC, Rizo J, Grabe M, Jiang QX, Hooper LV
(2014) Vol. 505: 103-7
Molecular architecture of the mammalian circadian clock.
Partch CL, Green CB, Takahashi JS
Trends in Cell Biology
(2014) Vol. 24: 90-9
An ImPERfect link to cancer?
Kopalle HM and Partch CL
Cell Cycle
(2013) Vol. 13: 507
Regulating the ARNT/TACC3 axis: multiple approaches to manipulating protein/protein interactions with small molecules.
Guo Y, Partch CL, Key J, Card PB, Pashkov V, Patel A, Bruick RK, Wurdak H, Gardner KH
ACS Chemical Biology
(2013) Vol. 8: 626-35
bHLH-PAS proteins: functional specification through modular domain architecture.
Michael AK and Partch CL
OA Biochemistry
(2013) Vol. 1: 16-21
Crystal structure of the heterodimeric CLOCK:BMAL1 transcriptional activator complex of the mammalian circadian clock.
Huang N*, Chelliah Y*, Taylor CA, Yoo SH, Shan Y, Partch CL, Green CB, Zhang H, Takahashi JS
(2012) Vol. 337: 189-94
PDB coordinates for CLOCK:BMAL1 structure: 4F3L
Publications prior to 2011:
Structure and function of animal cryptochromes.
Oztürk N, Song SH, Ozgür S, Selby CP, Morrison L, Partch CL, Zhong D, Sancar A
Cold Spring Symposium on Quantitative Biology (2008) Vol. 72: 119-131
Coactivators necessary for transcriptional output of the hypoxia-inducible factor, HIF, are directly recruited by ARNT PAS-B.
Partch CL and Gardner KH
Proceedings of the National Academy of Science USA (2011) Vol. 108: 7739-44
The three Rs of transcription: recruit, retain, recycle.
Motta-mena LB, Partch CL, Gardner KH
Molecular Cell (2010) Vol. 40: 855-8
Molecular basis of peptidoglycan recognition by a bactericidal lectin.
Lehotzky RE*, Partch CL*, Mukherjee S, Cash HL, Goldman WE, Gardner KH, Hooper LV
Proceedings of the National Academy of Science USA (2010) Vol. 107: 7722-7
Coactivator recruitment: a new role for PAS domains in transcriptional regulation by the bHLH-PAS family.
Partch CL and Gardner KH
Journal of Cellular Physiology (2010) Vol. 223: 553-7
Molecular basis of coiled-coil coactivator recruitment by the aryl hydrocarbon nuclear translocator (ARNT).
Partch CL, Card PB, Amezcua CA, Gardner KH
Journal of Biological Chemistry (2009) Vol. 284: 15184-92
Regulation of C-type lectin antimicrobial activity by a flexible N-terminal prosegment.
Mukherjee S*, Partch CL*, Lehotzky RE, Whitham CV, Chu H, Bevins CL, Gardner KH, Hooper LV.
Journal of Biological Chemistry (2009) Vol. 284: 4881-8
Purification and characterization of a type III photolyase from Caulobacter crescentus.
Oztürk N, Kao YT, Selby CP, Kavakli IH, Partch CL, Zhong D, Sancar A
Biochemistry (2008) Vol. 47: 10255-61
Crystal structure of cryptochrome 3 from Arabidopsis thaliana and its implications for photolyase activity.
Huang Y, Baxter R, Smith BS, Partch CL, Colbert CL, Deisenhofer J
Proceedings of the National Academy of Science USA (2006) Vol. 103: 17701-6
Posttranslational regulation of the mammalian circadian clock by cryptochrome and protein phosphatase 5.
Partch CL, Shields KF, Thompson CL, Selby CP, Sancar A
Proceedings of the National Academy of Science USA (2006) Vol. 103: 10467-72
Photochemistry and photobiology of cryptochrome blue-light photoreceptors: the search for a photocycle.
Partch CL and Sancar A
Photochemistry and Photobiology (2005) Vol. 81: 1291-304
Cryptochromes and circadian photoreception in animals.
Partch CL and Sancar A
Methods in Enzymology (2005) Vol. 393: 726-45
Role of structural plasticity in signal transduction by the cryptochrome blue-light photoreceptor.
Partch CL, Clarkson MW, Ozgür S, Lee AL, Sancar A
Biochemistry (2005) Vol. 44: 3795-805
Further evidence for the role of cryptochromes in retinohypothalamic photoreception / phototransduction.
Thompson CL, Selby CP, Partch CL, Plante DT, Thresher RJ, Araujo F, Sancar A
Brain Research: Molecular Brain Research (2004) Vol. 122: 158-66
Identification of sperm-specific proteins that interact with A-kinase anchoring proteins in a amnner similar to the type II regulatory subunit of PKA.
Carr DW, Fujita A, Stentz (Partch) CL, Liberty GA, Olson GE, Narumiya S
Journal of Biological Chemistry (2001) Vol. 276: 17332-8
Regulation of IL-15-stimulated TNF-alpha production by rolipram.
Kasyapa CS, Stentz (Partch) CL, Davey MP, Carr DW
Journal of Immunology (1999) Vol. 163: 2836-43
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