James’s Postdoc Publications

Kahne SC, Yoo JH, Chen J, Nakedi K, Iyer LM, Putzel G, Samhadaneh NM, Pironti A, Aravind L, Ekiert DC, Bhabha G, Rhee KY, Darwin KH^‡. Identification of a depupylation regulator for an essential enzyme in Mycobacterium tuberculosis. Proc Natl Acad Sci U S A, 2024. https://pubmed.ncbi.nlm.nih.gov/39585979/

Alexander LT^‡, Durairaj J, Kryshtafovych A, Abriata LA, Bayo Y, Bhabha G, Breyton C, Caulton SG, Chen J, Degroux S, Ekiert DC, Erlandsen BS, Freddolino PL, Gilzer D, Greening C, Grimes JM, Grinter R, Gurusaran M, Hartmann MD, Hitchman CJ, Keown JR, Kropp A, Kursula P, Lovering AL, Lemaitre B, Lia A, Liu S, Logotheti M, Lu S, Markússon S, Miller MD, Minasov G, Niemann HH, Opazo F, Phillips GN Jr, Davies OR, Rommelaere S, Rosas-Lemus M, Roversi P, Satchell K, Smith N, Wilson MA, Wu KL, Xia X, Xiao H, Zhang W, Zhou ZH, Fidelis K, Topf M, Moult J, Schwede T. Protein target highlights in CASP15: Analysis of models by structure providers. Proteins, 2023. https://pubmed.ncbi.nlm.nih.gov/37493353/

Chen J, Fruhauf A, Fan C, Ponce J, Ueberheide B, Bhabha G^‡, Ekiert DC^‡. Structure of an endogenous mycobacterial MCE lipid transporter. Nature, 2023. https://pubmed.ncbi.nlm.nih.gov/37495693/

Chen J, Ekiert DC^‡. A tale of two inhibitors: diarylquinolines and squaramides. EMBO J., 2023. https://pubmed.ncbi.nlm.nih.gov/37435707/

James’s Ph.D. Publications

Brewer J, Llewellyn E, Chen J, Campbell EA, Darst SA^‡. Structural basis for loading of Transcription Repair-Coupling factor Mfd onto stalled elongation complexes. bioRxiv, 2025. https://pubmed.ncbi.nlm.nih.gov/40949946/

Saecker RM, Mueller AU, Malone B, Chen J, Budell WC, Dandey VP, Maruthi K, Mendez JH, Molina N, Eng ET, Yen LY, Potter CS, Carragher B, Darst SA^‡. Early intermediates in bacterial RNA polymerase promoter melting visualized by time-resolved cryo-electron microscopy. Nat Struct Mol Biol, 2024. https://pubmed.ncbi.nlm.nih.gov/38951624/

Malone BF, Perry JK, Olinares PDB, Lee HW, Chen J, Appleby TC, Feng JY, Bilello JP, Ng H, Sotiris J, Ebrahim M, Chua EYD, Mendez JH, Eng ET, Landick R, Götte M, Chait BT, Campbell EA^‡, Darst SA^‡. Structural basis for substrate selection by the SARS-CoV-2 replicase. Nature, 2023. https://pubmed.ncbi.nlm.nih.gov/36725929/

Mueller AU*, Chen J*, Wu M, Chiu C, Nixon BT, Campbell EA, Darst SA^‡. A general mechanism for transcription bubble nucleation in bacteria. Proc Natl Acad Sci U S A, 2023. https://pubmed.ncbi.nlm.nih.gov/36972428/

Kang JY, Mishanina TV, Bao Y, Chen J, Llewellyn E, Liu J, Darst SA^‡, Landick R^‡. An ensemble of interconverting conformations of the elemental paused transcription complex creates regulatory options. Proc Natl Acad Sci U S A, 2023. https://pubmed.ncbi.nlm.nih.gov/36795753/

Cao X, Boyaci H, Chen J, Bao Y, Landick R^‡, Campbell EA^‡. Basis of narrow-spectrum activity of fidaxomicin on Clostridioides difficile. Nature, 2022. https://pubmed.ncbi.nlm.nih.gov/35388215/

Chen J*, Wang Q*, Malone B*, Llewellyn E, Pechersky Y, Maruthi K, Eng ET, Perry JK, Campbell EA, Shaw DE^‡, Darst SA^‡. Ensemble cryo-EM reveals conformational states of the nsp13 helicase in the SARS-CoV-2 helicase replication-transcription complex. Nat Struct Mol Biol, 2022. https://pubmed.ncbi.nlm.nih.gov/35260847/

Malone B*, Chen J*, Wang Q, Llewellyn E, Choi YJ, Olinares PDB, Cao X, Hernandez C, Eng ET, Chait BT, Shaw DE, Landick R, Darst SA^‡, Campbell EA^‡. Structural basis for backtracking by the SARS-CoV-2 replication-transcription complex. Proc Natl Acad Sci U S A, 2021. https://pubmed.ncbi.nlm.nih.gov/33883267/

Saecker RM, Chen J, Chiu CE, Malone B, Sotiris J, Ebrahim M, Yen LY, Eng ET, Darst SA^‡. Structural origins of Escherichia coli RNA polymerase open promoter complex stability. Proc Natl Acad Sci U S A, 2021. https://pubmed.ncbi.nlm.nih.gov/34599106/

Kang JY, Llewellyn E, Chen J, Olinares PDB, Brewer J, Chait BT, Campbell EA, Darst SA^‡. Structural basis for transcription complex disruption by the Mfd translocase. Elife, 2021. https://pubmed.ncbi.nlm.nih.gov/33480355/

Chen J, Boyaci H, Campbell EA^‡. Diverse and unified mechanisms of transcription initiation in bacteria. Nat Rev Microbiol, 2021. https://pubmed.ncbi.nlm.nih.gov/33122819/

Olinares PDB^‡, Kang JY, Llewellyn E, Chiu C, Chen J, Malone B, Saecker RM, Campbell EA, Darst SA, Chait BT^‡. Native Mass Spectrometry-Based Screening for Optimal Sample Preparation in Single-Particle Cryo-EM. Structure, 2021. https://pubmed.ncbi.nlm.nih.gov/33217329/

Lilic M, Chen J, Boyaci H, Braffman N, Hubin EA, Herrmann J, Müller R, Mooney R, Landick R, Darst SA, Campbell EA^‡. The antibiotic sorangicin A inhibits promoter DNA unwinding in a Mycobacterium tuberculosis rifampicin-resistant RNA polymerase. Proc Natl Acad Sci U S A, 2020. https://pubmed.ncbi.nlm.nih.gov/33199626/

Dandey VP, Budell WC, Wei H, Bobe D, Maruthi K, Kopylov M, Eng ET, Kahn PA, Hinshaw JE, Kundu N, Nimigean CM, Fan C, Sukomon N, Darst SA, Saecker RM, Chen J, Malone B, Potter CS, Carragher B^‡. Time-resolved cryo-EM using Spotiton. Nat Methods, 2020. https://pubmed.ncbi.nlm.nih.gov/32778833/

Chen J*, Malone B*, Llewellyn E, Grasso M, Shelton PMM, Olinares PDB, Maruthi K, Eng ET, Vatandaslar H, Chait BT, Kapoor TM, Darst SA^‡, Campbell EA^‡. Structural Basis for Helicase-Polymerase Coupling in the SARS-CoV-2 Replication-Transcription Complex. Cell, 2020. https://pubmed.ncbi.nlm.nih.gov/32783916/

Chen J, Chiu C, Gopalkrishnan S, Chen AY, Olinares PDB, Saecker RM, Winkelman JT, Maloney MF, Chait BT, Ross W, Gourse RL, Campbell EA, Darst SA^‡. Stepwise Promoter Melting by Bacterial RNA Polymerase. Mol Cell, 2020. https://pubmed.ncbi.nlm.nih.gov/32160514/ 

Chen J, Gopalkrishnan S, Chiu C, Chen AY, Campbell EA, Gourse RL, Ross W, Darst SA^‡. E. coli TraR allosterically regulates transcription initiation by altering RNA polymerase conformation. Elife, 2019. https://pubmed.ncbi.nlm.nih.gov/31841111/

Chen J*, Noble AJ*, Kang JY, Darst SA^‡. Eliminating effects of particle adsorption to the air/water interface in single-particle cryo-electron microscopy: Bacterial RNA polymerase and CHAPSO. J Struct Biol X, 2019. https://pubmed.ncbi.nlm.nih.gov/32285040/

Boyaci H, Chen J, Jansen R, Darst SA, Campbell EA^‡. Structures of an RNA polymerase promoter melting intermediate elucidate DNA unwinding. Nature, 2019. https://pubmed.ncbi.nlm.nih.gov/30626968/

Guo X, Myasnikov AG, Chen J, Crucifix C, Papai G, Takacs M, Schultz P, Weixlbaumer A^‡. Structural Basis for NusA Stabilized Transcriptional Pausing. Mol Cell, 2018. https://pubmed.ncbi.nlm.nih.gov/29499136/

Boyaci H*, Chen J*, Lilic M, Palka M, Mooney RA, Landick R, Darst SA^‡, Campbell EA^‡. Fidaxomicin jams Mycobacterium tuberculosis RNA polymerase motions needed for initiation via RbpA contacts. Elife, 2018. https://pubmed.ncbi.nlm.nih.gov/29480804/

Chen J, Wassarman KM, Feng S, Leon K, Feklistov A, Winkelman JT, Li Z, Walz T, Campbell EA^‡, Darst SA^‡. 6S RNA Mimics B-Form DNA to Regulate Escherichia coli RNA Polymerase. Mol Cell, 2017. https://pubmed.ncbi.nlm.nih.gov/28988932/

Kang JY, Olinares PD, Chen J, Campbell EA, Mustaev A, Chait BT, Gottesman ME, Darst SA^‡. Structural basis of transcription arrest by coliphage HK022 Nun in an Escherichia coli RNA polymerase elongation complex. Elife, 2017. https://pubmed.ncbi.nlm.nih.gov/28318486/

Garner AL, Rammohan J, Huynh JP, Onder LM, Chen J, Bae B, Jensen D, Weiss LA, Manzano AR, Darst SA, Campbell EA, Nickels BE, Galburt EA, Stallings CL^‡. Effects of Increasing the Affinity of CarD for RNA Polymerase on Mycobacterium tuberculosis Growth, rRNA Transcription, and Virulence. J Bacteriol, 2017. https://pubmed.ncbi.nlm.nih.gov/27920294/

Bae B, Chen J, Davis E, Leon K, Darst SA^‡, Campbell EA^‡. CarD uses a minor groove wedge mechanism to stabilize the RNA polymerase open promoter complex. Elife, 2015. https://pubmed.ncbi.nlm.nih.gov/26349034/

Davis E, Chen J, Leon K, Darst SA, Campbell EA^‡. Mycobacterial RNA polymerase forms unstable open promoter complexes that are stabilized by CarD. Nucleic Acids Res, 2015. https://pubmed.ncbi.nlm.nih.gov/25510492/ 

Gibb B, Gupta K, Ghosh K, Sharp R, Chen J, Van Duyne GD^‡. Requirements for catalysis in the Cre recombinase active site. Nucleic Acids Res, 2010. https://pubmed.ncbi.nlm.nih.gov/20462863/

* equal contribution

‡ corresponding author