Recent Publications from the Department of Pharmacology and Chemical Biology

Denaturant-specific effects on the structural energetics of a protein-denatured ensemble.
Moosa MM, Goodman AZ, Ferreon JC, Lee CW, Ferreon ACM, Deniz AA.
Eur Biophys J. 2017 Oct 27. doi: 10.1007/s00249-017-1260-4. [Epub ahead of print]
PMID: 29080139

Enhancing Structure Prediction and Design of Soluble and Membrane Proteins with Explicit Solvent-Protein Interactions.
Lai JK, Ambia J, Wang Y, Barth P.
Structure. 2017 Nov 7;25(11):1758-1770.e8. doi: 10.1016/j.str.2017.09.002. Epub 2017 Sep 28.
PMID: 28966016

Reversible Reaction-Based Fluorescent Probe for Real-Time Imaging of Glutathione Dynamics in Mitochondria.
Chen J, Jiang X, Zhang C, MacKenzie KR, Stossi F, Palzkill T, Wang MC, Wang J.
ACS Sens. 2017 Sep 22;2(9):1257-1261. doi: 10.1021/acssensors.7b00425. Epub 2017 Aug 18.
PMID: 28809477

Switching cyclic nucleotide-selective activation of PKA holoenzyme reveals distinct roles of tandem CNB domains.
He D, Lorenz R, Kim C, Herberg FW, Lim CJ.
ACS Chem Biol. 2017 Nov 7. doi: 10.1021/acschembio.7b00732. [Epub ahead of print]
PMID: 29111666

The N-Terminal Domain of ALS-Linked TDP-43 Assembles without Misfolding.
Tsoi PS, Choi KJ, Leonard PG, Sizovs A, Moosa MM, MacKenzie KR, Ferreon JCFerreon ACM.
Angew Chem Int Ed Engl. 2017 Aug 21. doi: 10.1002/anie.201706769. [Epub ahead of print]

Quantitative real-time imaging of glutathione.
Jiang X, Chen J, Bajic A, Zhang C, Song X, Carroll SL, Cai ZL, Tang M, Xue M, Cheng N, Schaaf CP, Li F, MacKenzie KR, Ferreon ACM, Xia F, Wang MC, Maletic-Savatic M, Wang J.
Nat Commun. 2017 Jul 13;8:16087. doi: 10.1038/ncomms16087.

Reversible Reaction-Based Fluorescent Probe for Real-Time Imaging of Glutathione Dynamics in Mitochondria.
Chen J, Jiang X, Zhang C, MacKenzie KR, Stossi F, Palzkill T, Wang MC, Wang J.
ACS Sens. 2017 Aug 18. doi: 10.1021/acssensors.7b00425. [Epub ahead of print]

Microbial Genetic Composition Tunes Host Longevity.
Han B, Sivaramakrishnan P, Lin CJ, Neve IAA, He J, Tay LWR, Sowa JN, Sizovs A, Du G, Wang J, Herman C, Wang MC.
Cell. 2017 Jun 15;169(7):1249-1262.e13. doi: 10.1016/j.cell.2017.05.036.

Targeting SRC Coactivators Blocks the Tumor-Initiating Capacity of Cancer Stem-like Cells.
Rohira AD, Yan F, Wang L, Wang J, Zhou S, Lu A, Yu Y, Xu J, Lonard DM, O'Malley BW.
Cancer Res. 2017 Aug 15;77(16):4293-4304. doi: 10.1158/0008-5472.CAN-16-2982. Epub 2017 Jun 13.

Structure activity relationship and modeling studies of inhibitors of lysine specific demethylase 1.
Zhou C, Wu F, Lu L, Wei L, Pai E, Yao Y, Song Y.
PLoS One. 2017 Feb 3;12(2):e0170301. doi: 10.1371/journal.pone.0170301. eCollection 2017.

Reprogramming cellular functions with engineered membrane proteins.
Arber C, Young M, Barth P.
Curr Opin Biotechnol. 2017 Jul 11;47:92-101. doi: 10.1016/j.copbio.2017.06.009. [Epub ahead of print] Review.

Computational design of ligand-binding membrane receptors with high selectivity.
Feng X, Ambia J, Chen KM, Young M, Barth P.
Nat Chem Biol. 2017 Jul;13(7):715-723. doi: 10.1038/nchembio.2371. Epub 2017 May 1.

Structural Basis of Analog Specificity in PKG I and II.
Campbell JC, Henning P, Franz E, Sankaran B, Herberg FW, Kim C.
ACS Chem Biol. 2017 Sep 15;12(9):2388-2398. doi: 10.1021/acschembio.7b00369. Epub 2017 Aug 22.
PMID: 28793191

Mutations of PKA cyclic nucleotide-binding domains reveal novel aspects of cyclic nucleotide selectivity.
Lorenz R, Moon EW, Kim JJ, Schmidt SH, Sankaran B, Pavlidis IV, Kim C, Herberg FW.
Biochem J. 2017 Jul 6;474(14):2389-2403. doi: 10.1042/BCJ20160969.

Reversible Reaction-Based Fluorescent Probe for Real-Time Imaging of Glutathione Dynamics in Mitochondria.
Chen J, Jiang X, Zhang C, MacKenzie KR, Stossi F, Palzkill T, Wang MC, Wang J.
ACS Sens. 2017 Aug 18. doi: 10.1021/acssensors.7b00425. [Epub ahead of print]

The Drug-Resistant Variant P167S Expands the Substrate Profile of CTX-M β-Lactamases for Oxyimino-Cephalosporin Antibiotics by Enlarging the Active Site upon Acylation.
Patel MP, Hu L, Stojanoski V, Sankaran B, Prasad BVV, Palzkill T.
Biochemistry. 2017 Jul 11;56(27):3443-3453. doi: 10.1021/acs.biochem.7b00176. Epub 2017 Jun 27.

Systematic substitutions at BLIP position 50 result in changes in binding specificity for class A β-lactamases.
Adamski CJ, Palzkill T.
BMC Biochem. 2017 Mar 6;18(1):2. doi: 10.1186/s12858-017-0077-1.

BLIP-II Employs Differential Hotspot Residues To Bind Structurally Similar Staphylococcus aureus PBP2a and Class A β-Lactamases.
Adamski CJ, Palzkill T.
Biochemistry. 2017 Feb 28;56(8):1075-1084. doi: 10.1021/acs.biochem.6b00978. Epub 2017 Feb 16.

Identification and Characterization of Single-Chain Antibodies that Specifically Bind GI Noroviruses.
Hurwitz AM, Huang W, Kou B, Estes MK, Atmar RL, Palzkill T.
PLoS One. 2017 Jan 17;12(1):e0170162. doi: 10.1371/journal.pone.0170162. eCollection 2017.

Deep sequencing of phage-displayed peptide libraries reveals sequence motif that detects norovirus.
Hurwitz AM, Huang W, Estes MK, Atmar RL, Palzkill T.
Protein Eng Des Sel. 2017 Feb;30(2):129-139. doi: 10.1093/protein/gzw074. Epub 2016 Dec 28. 

Crystal structure of PKG Iβ CNB-B:Rp-cGMPS complex reveals an apo-like, inactive conformation. 
Campbell JC, VanSchouwen B, Lorenz R, Sankaran B, Herberg FW, Melacini G, Kim C.
FEBS Lett. 2016 Dec 3. doi: 10.1002/1873-3468.12505. [Epub ahead of print]

AMPK and Endothelial Nitric Oxide Synthase Signaling Regulates K-Ras Plasma Membrane Interactions via Cyclic GMP-Dependent Protein Kinase 2.
Cho KJ, Casteel DE, Prakash P, Tan L, van der Hoeven D, Salim AA, Kim C, Capon RJ, Lacey E, Cunha SR, Gorfe AA, Hancock JF.
Mol Cell Biol. 2016 Nov 28;36(24):3086-3099.

Engineering specificity from broad to narrow: Design of a BLIP variant that exclusively binds and detects KPC β-lactamase
Chow DC, Rice K, Huang W, Atmar RL, Palzkill TG.
ACS Infect Dis. 2016 Oct 18. [Epub ahead of print]

DOT1L as a therapeutic target for the treatment of DNMT3A-mutant acute myeloid leukemia.
Rau RE, Rodriguez BA, Luo M, Jeong M, Rosen A, Rogers JH, Campbell CT, Daigle SR, Deng L, Song Y, Sweet S, Chevassut T, Andreeff M, Kornblau SM, Li W, Goodell MA.
Blood. 2016 Aug 18;128(7):971-81. doi: 10.1182/blood-2015-11-684225.

Structure of the catalytic domain of the colistin resistance enzyme MCR-1.
Stojanoski V, Sankaran B, Prasad BV, Poirel L, Nordmann P, Palzkill T.
BMC Biol. 2016 Sep 21;14(1):81.

Deep Sequencing of Random Mutant Libraries Reveals the Active Site of the Narrow Specificity CphA Metallo-β-Lactamase is Fragile to Mutations.
Sun Z, Mehta SC, Adamski CJ, Gibbs RA, Palzkill T.
Sci Rep. 2016 Sep 12;6:33195. doi: 10.1038/srep33195.

Comment on: Resistance gene naming and numbering: is it a new gene or not?
Jacoby GA, Bonomo RA, Bradford PA, Bush K, Doi Y, Feldgarden M, Haft D, Klimke W, Nordmann P, Palzkill T, Poirel L, Prasad A, Rossolini GM, Walsh T.
J Antimicrob Chemother. 2016 Sep;71(9):2677-8. doi: 10.1093/jac/dkw204. No abstract available.

Introduction of a polar core into the de novo designed protein Top7.
Basanta B, Chan KK, Barth P, King T, Sosnick TR, Hinshaw JR, Liu G, Everett JK, Xiao R, Montelione GT, Baker D.
Protein Sci. 2016 Jul;25(7):1299-307. doi: 10.1002/pro.2899.

Diversity-Oriented Synthesis as a Strategy for Fragment Evolution against GSK3β.
Wang Y, Wach JY, Sheehan P, Zhong C, Zhan C, Harris R, Almo SC, Bishop J, Haggarty SJ, Ramek A, Berry KN, O'Herin C, Koehler AN, Hung AW, Young DW.
ACS Med Chem Lett. 2016 Jul 14;7(9):852-6. doi: 10.1021/acsmedchemlett.6b00230.

Toward high-resolution computational design of the structure and function of helical membrane proteins.
Barth P, Senes A.
Nat Struct Mol Biol. 2016 Jun 7;23(6):475-80. doi: 10.1038/nsmb.3231.

Antiviral targets of human noroviruses.
Prasad BV, Shanker S, Muhaxhiri Z, Deng L, Choi JM, Estes MK, Song Y, Palzkill T, Atmar RL.
Curr Opin Virol. 2016 Jun;18:117-25. doi: 10.1016/j.coviro.2016.06.002. Review.

Targeting histone methylation for cancer therapy: enzymes, inhibitors, biological activity and perspectives.
Song Y, Wu F, Wu J.
J Hematol Oncol. 2016 Jun 17;9(1):49. doi: 10.1186/s13045-016-0279-9. Review.

Development of potent small-molecule inhibitors to drug the undruggable steroid receptor coactivator-3.
Song X, Chen J, Zhao M, Zhang C, Yu Y, Lonard DM, Chow DC, Palzkill T, Xu J, O'Malley BW, Wang J.
Proc Natl Acad Sci U S A. 2016 May 3;113(18):4970-5. doi: 10.1073/pnas.1604274113.

Removal of the Side Chain at the Active-Site Serine by a Glycine Substitution Increases the Stability of a Wide Range of Serine β-Lactamases by Relieving Steric Strain.
Stojanoski V, Adamski CJ, Hu L, Mehta SC, Sankaran B, Zwart P, Prasad BV, Palzkill T.
Biochemistry. 2016 May 3;55(17):2479-90. doi: 10.1021/acs.biochem.6b00056.

Crystal Structure of PKG I:cGMP Complex Reveals a cGMP-Mediated Dimeric Interface that Facilitates cGMP-Induced Activation.
Kim JJ, Lorenz R, Arold ST, Reger AS, Sankaran B, Casteel DE, Herberg FW, Kim C.
Structure. 2016 May 3;24(5):710-20. doi: 10.1016/j.str.2016.03.009.

Data on the purification and crystallization of the loss-of-function von Willebrand disease variant (p.Gly1324Ser) of the von Willebrand factor A1 domain.
Campbell JC, Tischer A, Machha V, Moon-Tasson L, Sankaran B, Kim C, Auton M.
Data Brief. 2016 May 10;7:1700-1706.

Clinical Validation of a Transcranial Doppler-Based Noninvasive Intracranial Pressure Meter: A Prospective Cross-Sectional Study.
Bershad EM, Anand A, DeSantis SM, Yang M, Tang RA, Calvillo E, Malkin-Gosdin L, Foroozan R, Damani R, Maldonado N, Gupta P, Tan B, Venkatasubba Rao CP, Suarez JI, Clark JB, Sutton JP, Donoviel DB.
World Neurosurg. 2016 May;89:647-653.e1. doi: 10.1016/j.wneu.2015.11.102.

Small-molecule inhibition of STAT3 in radioresistant head and neck squamous cell carcinoma.
Bharadwaj U, Eckols TK, Xu X, Kasembeli MM, Chen Y, Adachi M, Song Y, Mo Q, Lai SY, Tweardy DJ.
Oncotarget. 2016 May 3;7(18):26307-30. doi: 10.18632/oncotarget.8368.

A topological and conformational stability alphabet for multipass membrane proteins.
Feng X, Barth P.
Nat Chem Biol. 2016 Mar;12(3):167-73. doi: 10.1038/nchembio.2001.

Pharmacological inhibition of LSD1 for the treatment of MLL-rearranged leukemia.
Feng Z, Yao Y, Zhou C, Chen F, Wu F, Wei L, Liu W, Dong S, Redell M, Mo Q, Song Y.
J Hematol Oncol. 2016 Mar 12;9:24. doi: 10.1186/s13045-016-0252-7.

Recognition of the disordered p53 transactivation domain by the transcriptional adapter zinc finger domains of CREB-binding protein.
Krois AS, Ferreon JC, Martinez-Yamout MA, Dyson HJ, Wright PE.
Proc Natl Acad Sci U S A. 2016 Mar 29;113(13):E1853-62. doi: 10.1073/pnas.1602487113.

Structural Basis of Cyclic Nucleotide Selectivity in cGMP-dependent Protein Kinase II.
Campbell JC, Kim JJ, Li KY, Huang GY, Reger AS, Matsuda S, Sankaran B, Link TM, Yuasa K, Ladbury JE, Casteel DE, Kim C.
J Biol Chem. 2016 Mar 11;291(11):5623-33. doi: 10.1074/jbc.M115.691303.

Mutational Constraints on Local Unfolding Inhibit the Rheological Adaptation of von Willebrand Factor.
Tischer A, Campbell JC, Machha VR, Moon-Tasson L, Benson LM, Sankaran B, Kim C, Auton M.
J Biol Chem. 2016 Feb 19;291(8):3848-59. doi: 10.1074/jbc.M115.703850.

Chemical Potency and Degradation Products of Medications Stored Over 550 Earth Days at the International Space Station.
Wotring VE.
AAPS J. 2016 Jan;18(1):210-6. doi: 10.1208/s12248-015-9834-5.

3-(Piperidin-4-ylmethoxy)pyridine Containing Compounds Are Potent Inhibitors of Lysine Specific Demethylase 1.
Wu F, Zhou C, Yao Y, Wei L, Feng Z, Deng L, Song Y.
J Med Chem. 2016 Jan 14;59(1):253-63. doi: 10.1021/acs.jmedchem.5b01361.