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Title: TrkA undergoes a tetramer-to-dimer conversion to open TrkH which enables changes in membrane potential

Abstract

TrkH is a bacterial ion channel implicated in K+ uptake and pH regulation. TrkH assembles with its regulatory protein, TrkA, which closes the channel when bound to ADP and opens it when bound to ATP. However, it is unknown how nucleotides control the gating of TrkH through TrkA. Here we report the structures of the TrkH-TrkA complex in the presence of ADP or ATP. TrkA forms a tetrameric ring when bound to ADP and constrains TrkH to a closed conformation. The TrkA ring splits into two TrkA dimers in the presence of ATP and releases the constraints on TrkH, resulting in an open channel conformation. Functional studies show that both the tetramer-to-dimer conversion of TrkA and the loss of constraints on TrkH are required for channel gating. In addition, deletion of TrkA in Escherichia coli depolarizes the cell, suggesting that the TrkH-TrkA complex couples changes in intracellular nucleotides to membrane potential.

Authors:
 [1];  [1]; ORCiD logo [1];  [2];  [2];  [1];  [1]; ORCiD logo [1]; ORCiD logo [1];  [2];  [3];  [1]
+ Show Author Affiliations
  1. Baylor College of Medicine, Houston, TX (United States)
  2. Texas A & M Univ., College Station, TX (United States)
  3. Stanford Univ., CA (United States)
Publication Date:
Research Org.:
Argonne National Laboratory (ANL), Argonne, IL (United States). Advanced Photon Source (APS)
Sponsoring Org.:
National Institutes of Health (NIH); Cancer Prevention and Research Institute of Texas (CPRIT); Robert Welch Foundation
OSTI Identifier:
1598012
Grant/Contract Number:  
HL086392; DK122784; P41GM103832; GM132436; R1223; Q-1279; Q-1967; A-1742; AC02-06CH11357
Resource Type:
Accepted Manuscript
Journal Name:
Nature Communications
Additional Journal Information:
Journal Volume: 11; Journal Issue: 1; Journal ID: ISSN 2041-1723
Publisher:
Nature Publishing Group
Country of Publication:
United States
Language:
ENGLISH
Subject:
36 MATERIALS SCIENCE; Cryoelectron microscopy; Permeation and transport; X-ray crystallography

Citation Formats

Zhang, Hanzhi, Pan, Yaping, Hu, Liya, Hudson, M. Ashley, Hofstetter, Katrina S., Xu, Zhichun, Rong, Mingqiang, Wang, Zhao, Prasad, B. V. Venkataram, Lockless, Steve W., Chiu, Wah, and Zhou, Ming. TrkA undergoes a tetramer-to-dimer conversion to open TrkH which enables changes in membrane potential. United States: N. p., 2020. Web. doi:10.1038/s41467-019-14240-9.
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Zhang, Hanzhi, Pan, Yaping, Hu, Liya, Hudson, M. Ashley, Hofstetter, Katrina S., Xu, Zhichun, Rong, Mingqiang, Wang, Zhao, Prasad, B. V. Venkataram, Lockless, Steve W., Chiu, Wah, & Zhou, Ming. TrkA undergoes a tetramer-to-dimer conversion to open TrkH which enables changes in membrane potential. United States. https://doi.org/10.1038/s41467-019-14240-9
Copy to clipboard
Zhang, Hanzhi, Pan, Yaping, Hu, Liya, Hudson, M. Ashley, Hofstetter, Katrina S., Xu, Zhichun, Rong, Mingqiang, Wang, Zhao, Prasad, B. V. Venkataram, Lockless, Steve W., Chiu, Wah, and Zhou, Ming. Tue . "TrkA undergoes a tetramer-to-dimer conversion to open TrkH which enables changes in membrane potential". United States. https://doi.org/10.1038/s41467-019-14240-9. https://www.osti.gov/servlets/purl/1598012.
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@article{osti_1598012,
title = {TrkA undergoes a tetramer-to-dimer conversion to open TrkH which enables changes in membrane potential},
author = {Zhang, Hanzhi and Pan, Yaping and Hu, Liya and Hudson, M. Ashley and Hofstetter, Katrina S. and Xu, Zhichun and Rong, Mingqiang and Wang, Zhao and Prasad, B. V. Venkataram and Lockless, Steve W. and Chiu, Wah and Zhou, Ming},
abstractNote = {TrkH is a bacterial ion channel implicated in K+ uptake and pH regulation. TrkH assembles with its regulatory protein, TrkA, which closes the channel when bound to ADP and opens it when bound to ATP. However, it is unknown how nucleotides control the gating of TrkH through TrkA. Here we report the structures of the TrkH-TrkA complex in the presence of ADP or ATP. TrkA forms a tetrameric ring when bound to ADP and constrains TrkH to a closed conformation. The TrkA ring splits into two TrkA dimers in the presence of ATP and releases the constraints on TrkH, resulting in an open channel conformation. Functional studies show that both the tetramer-to-dimer conversion of TrkA and the loss of constraints on TrkH are required for channel gating. In addition, deletion of TrkA in Escherichia coli depolarizes the cell, suggesting that the TrkH-TrkA complex couples changes in intracellular nucleotides to membrane potential.},
doi = {10.1038/s41467-019-14240-9},
journal = {Nature Communications},
number = 1,
volume = 11,
place = {United States},
year = {Tue Jan 28 00:00:00 EST 2020},
month = {Tue Jan 28 00:00:00 EST 2020}
}
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Publisher's Version of Record
https://doi.org/10.1038/s41467-019-14240-9
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Works referenced in this record:

Structure and transport mechanism of a high-affinity potassium uptake transporter from higher plants
journal, August 1994

  • Schachtman, Daniel P.; Schroeder, Julian I.
  • Nature, Vol. 370, Issue 6491
  • DOI: 10.1038/370655a0

Two systems mediate rubidium uptake in Neurospora crassa: one exhibits the dual-uptake isotherm
journal, May 1986

  • Rodríguez-Navarro, Alonso; Ramos, José
  • Biochimica et Biophysica Acta (BBA) - Biomembranes, Vol. 857, Issue 2
  • DOI: 10.1016/0005-2736(86)90351-2

Ion channels enable electrical communication in bacterial communities
journal, October 2015

  • Prindle, Arthur; Liu, Jintao; Asally, Munehiro
  • Nature, Vol. 527, Issue 7576
  • DOI: 10.1038/nature15709

The bacterial flagellar motor and its structural diversity
journal, May 2015

Osmotic stress response in C. glutamicum: impact of channel- and transporter-mediated potassium accumulation
journal, May 2011

  • Ochrombel, Ines; Becker, Markus; Krämer, Reinhard
  • Archives of Microbiology, Vol. 193, Issue 11
  • DOI: 10.1007/s00203-011-0717-6

Overview of the CCP 4 suite and current developments
journal, March 2011

  • Winn, Martyn D.; Ballard, Charles C.; Cowtan, Kevin D.
  • Acta Crystallographica Section D Biological Crystallography, Vol. 67, Issue 4
  • DOI: 10.1107/S0907444910045749

PHENIX: a comprehensive Python-based system for macromolecular structure solution.
text, January 2010

  • Adams, Paul D.; Afonine, Pavel V.; Bunkóczi, Gábor
  • Apollo - University of Cambridge Repository
  • DOI: 10.17863/cam.45787

Computed Origami Tomography
preprint, January 2020

Electron counting and beam-induced motion correction enable near-atomic-resolution single-particle cryo-EM
journal, May 2013

  • Li, Xueming; Mooney, Paul; Zheng, Shawn
  • Nature Methods, Vol. 10, Issue 6
  • DOI: 10.1038/nmeth.2472

Accurate model annotation of a near-atomic resolution cryo-EM map
journal, March 2017

  • Hryc, Corey F.; Chen, Dong-Hua; Afonine, Pavel V.
  • Proceedings of the National Academy of Sciences, Vol. 114, Issue 12
  • DOI: 10.1073/pnas.1621152114

Patch Clamp and Phenotypic Analyses of a Prokaryotic Cyclic Nucleotide-gated K + Channel Using Escherichia coli as a Host
journal, June 2007

  • Kuo, Mario Meng-Chiang; Saimi, Yoshiro; Kung, Ching
  • Journal of Biological Chemistry, Vol. 282, Issue 33
  • DOI: 10.1074/jbc.m703618200

The K+ uptake regulator TrkA controls membrane potential, pH homeostasis and multidrug susceptibility in Mycobacterium smegmatis
journal, May 2011

  • Castaneda-Garcia, A.; Do, T. T.; Blazquez, J.
  • Journal of Antimicrobial Chemotherapy, Vol. 66, Issue 7
  • DOI: 10.1093/jac/dkr165

Evolutionary Relationship between K+ Channels and Symporters
journal, August 1999

Real-space refinement in PHENIX for cryo-EM and crystallography
journal, May 2018

  • Afonine, Pavel V.; Poon, Billy K.; Read, Randy J.
  • Acta Crystallographica Section D Structural Biology, Vol. 74, Issue 6
  • DOI: 10.1107/S2059798318006551

LigPlot+: Multiple Ligand–Protein Interaction Diagrams for Drug Discovery
journal, October 2011

  • Laskowski, Roman A.; Swindells, Mark B.
  • Journal of Chemical Information and Modeling, Vol. 51, Issue 10
  • DOI: 10.1021/ci200227u

UCSF Chimera?A visualization system for exploratory research and analysis
journal, January 2004

  • Pettersen, Eric F.; Goddard, Thomas D.; Huang, Conrad C.
  • Journal of Computational Chemistry, Vol. 25, Issue 13
  • DOI: 10.1002/jcc.20084

Partial Resolution of the Enzymes Catalyzing Oxidative Phosphorylation
journal, May 1966

Impact of improved potassium accumulation on pH homeostasis, membrane potential adjustment and survival of Corynebacterium glutamicum
journal, April 2011

  • Ochrombel, Ines; Ott, Lisa; Krämer, Reinhard
  • Biochimica et Biophysica Acta (BBA) - Bioenergetics, Vol. 1807, Issue 4
  • DOI: 10.1016/j.bbabio.2011.01.008

The Structure of the KtrAB Potassium Transporter
journal, January 2013

  • Vieira-Pires, Ricardo; Szollosi, Andras; Morais-Cabral, João
  • Biophysical Journal, Vol. 104, Issue 2
  • DOI: 10.1016/j.bpj.2012.11.162

Improved low-resolution crystallographic refinement with Phenix and Rosetta
journal, September 2013

  • DiMaio, Frank; Echols, Nathaniel; Headd, Jeffrey J.
  • Nature Methods, Vol. 10, Issue 11
  • DOI: 10.1038/nmeth.2648

Cloning of the trkAH gene cluster and characterization of the Trk K+-uptake system of Vibrio alginolyticus
journal, August 1998

Strength of Selection Pressure Is an Important Parameter Contributing to the Complexity of Antibiotic Resistance Evolution
journal, June 2014

  • Oz, Tugce; Guvenek, Aysegul; Yildiz, Sadik
  • Molecular Biology and Evolution, Vol. 31, Issue 9
  • DOI: 10.1093/molbev/msu191

Structural basis for the transition from translation initiation to elongation by an 80S-eIF5B complex
journal, October 2020

Production of giant cells of Escherichia coli.
journal, January 1978

Cloned Potassium Channels from Eukaryotes and Prokaryotes
journal, March 1997

Structure that Opens the Gate and Opens the Door
journal, March 2001

EMAN2: An extensible image processing suite for electron microscopy
journal, January 2007

  • Tang, Guang; Peng, Liwei; Baldwin, Philip R.
  • Journal of Structural Biology, Vol. 157, Issue 1
  • DOI: 10.1016/j.jsb.2006.05.009

Potassium Transport Loci in Escherichia coli K-12
journal, January 1971

Gating of the TrkH ion channel by its associated RCK protein TrkA
journal, April 2013

A rapid microtiter plate assay for measuring the effect of compounds on Staphylococcus aureus membrane potential
journal, November 2010

  • Gentry, Daniel R.; Wilding, Imogen; Johnson, John M.
  • Journal of Microbiological Methods, Vol. 83, Issue 2
  • DOI: 10.1016/j.mimet.2010.08.012

Electrically induced bacterial membrane-potential dynamics correspond to cellular proliferation capacity
journal, April 2019

  • Stratford, James P.; Edwards, Conor L. A.; Ghanshyam, Manjari J.
  • Proceedings of the National Academy of Sciences, Vol. 116, Issue 19
  • DOI: 10.1073/pnas.1901788116

TRK1 encodes a plasma membrane protein required for high-affinity potassium transport in Saccharomyces cerevisiae.
journal, July 1988

  • Gaber, R. F.; Styles, C. A.; Fink, G. R.
  • Molecular and Cellular Biology, Vol. 8, Issue 7
  • DOI: 10.1128/MCB.8.7.2848

PHENIX: a comprehensive Python-based system for macromolecular structure solution
journal, January 2010

  • Adams, Paul D.; Afonine, Pavel V.; Bunkóczi, Gábor
  • Acta Crystallographica Section D Biological Crystallography, Vol. 66, Issue 2, p. 213-221
  • DOI: 10.1107/S0907444909052925

Crystal structure of a potassium ion transporter, TrkH
journal, February 2011

Bacterial evolution of antibiotic hypersensitivity
journal, January 2013

  • Lázár, Viktória; Pal Singh, Gajinder; Spohn, Réka
  • Molecular Systems Biology, Vol. 9, Issue 1
  • DOI: 10.1038/msb.2013.57

K+-transport Protein TrkA of Escherichia coli Is a Peripheral Membrane Protein That Requires other trk Gene Products for Attachment to the Cytoplasmic Membrane
journal, October 1989

Structure of the RCK Domain from the E. coli K+ Channel and Demonstration of Its Presence in the Human BK Channel
journal, March 2001

The RCK Domain of the KtrAB K+ Transporter: Multiple Conformations of an Octameric Ring
journal, September 2006

ConSurf 2016: an improved methodology to estimate and visualize evolutionary conservation in macromolecules
journal, May 2016

  • Ashkenazy, Haim; Abadi, Shiran; Martz, Eric
  • Nucleic Acids Research, Vol. 44, Issue W1
  • DOI: 10.1093/nar/gkw408

RosettaScripts: A Scripting Language Interface to the Rosetta Macromolecular Modeling Suite
journal, June 2011

[20] Processing of X-ray diffraction data collected in oscillation mode
book, January 1997

Structure and transport mechanism of a high-affinity potassium uptake transporter from higher plants
journal, August 1994

  • Schachtman, Daniel P.; Schroeder, Julian I.
  • Nature, Vol. 370, Issue 6491
  • DOI: 10.1038/370655a0

Two systems mediate rubidium uptake in Neurospora crassa: one exhibits the dual-uptake isotherm
journal, May 1986

  • Rodríguez-Navarro, Alonso; Ramos, José
  • Biochimica et Biophysica Acta (BBA) - Biomembranes, Vol. 857, Issue 2
  • DOI: 10.1016/0005-2736(86)90351-2

Ion channels enable electrical communication in bacterial communities
journal, October 2015

  • Prindle, Arthur; Liu, Jintao; Asally, Munehiro
  • Nature, Vol. 527, Issue 7576
  • DOI: 10.1038/nature15709

Cloning of the trkAH gene cluster and characterization of the Trk K+-uptake system of Vibrio alginolyticus
journal, August 1998

Accurate model annotation of a near-atomic resolution cryo-EM map
journal, March 2017

  • Hryc, Corey F.; Chen, Dong-Hua; Afonine, Pavel V.
  • Proceedings of the National Academy of Sciences, Vol. 114, Issue 12
  • DOI: 10.1073/pnas.1621152114

PHENIX: a comprehensive Python-based system for macromolecular structure solution.
text, January 2010

  • Adams, Paul D.; Afonine, Pavel V.; Bunkóczi, Gábor
  • Apollo - University of Cambridge Repository
  • DOI: 10.17863/cam.45787

Impact of improved potassium accumulation on pH homeostasis, membrane potential adjustment and survival of Corynebacterium glutamicum
journal, April 2011

  • Ochrombel, Ines; Ott, Lisa; Krämer, Reinhard
  • Biochimica et Biophysica Acta (BBA) - Bioenergetics, Vol. 1807, Issue 4
  • DOI: 10.1016/j.bbabio.2011.01.008

Energy coupling to net K+ transport in Escherichia coli K-12.
journal, February 1977

Osmotic stress response in C. glutamicum: impact of channel- and transporter-mediated potassium accumulation
journal, May 2011

  • Ochrombel, Ines; Becker, Markus; Krämer, Reinhard
  • Archives of Microbiology, Vol. 193, Issue 11
  • DOI: 10.1007/s00203-011-0717-6

The RCK Domain of the KtrAB K+ Transporter: Multiple Conformations of an Octameric Ring
journal, September 2006

RosettaScripts: A Scripting Language Interface to the Rosetta Macromolecular Modeling Suite
journal, June 2011

Quantitative measurements of membrane potential in Escherichia coli
journal, July 1980

  • Felle, H.; Porter, J. S.; Slayman, C. L.
  • Biochemistry, Vol. 19, Issue 15
  • DOI: 10.1021/bi00556a026

Na + -dependent K + Uptake Ktr System from the Cyanobacterium Synechocystis sp. PCC 6803 and Its Role in the Early Phases of Cell Adaptation to Hyperosmotic Shock
journal, September 2004

  • Matsuda, Nobuyuki; Kobayashi, Hiroshi; Katoh, Hirokazu
  • Journal of Biological Chemistry, Vol. 279, Issue 52
  • DOI: 10.1074/jbc.M407268200

Coot model-building tools for molecular graphics
journal, November 2004

  • Emsley, Paul; Cowtan, Kevin
  • Acta Crystallographica Section D Biological Crystallography, Vol. 60, Issue 12, p. 2126-2132
  • DOI: 10.1107/s0907444904019158

Improved low-resolution crystallographic refinement with Phenix and Rosetta
journal, September 2013

  • DiMaio, Frank; Echols, Nathaniel; Headd, Jeffrey J.
  • Nature Methods, Vol. 10, Issue 11
  • DOI: 10.1038/nmeth.2648

Effects of potassium ions on the electrical and pH gradients across the membrane of Streptococcus lactis cells.
journal, January 1977

Impact of transport processes in the osmotic response of Corynebacterium glutamicum
journal, September 2003

Structure of the Human BK Channel Ca2+-Activation Apparatus at 3.0 A Resolution
journal, May 2010

CTFFIND4: Fast and accurate defocus estimation from electron micrographs
journal, November 2015

RosettaScripts: A Scripting Language Interface to the Rosetta Macromolecular Modeling Suite
text, January 2011

  • Paul, Murphy,; David, Baker,; Nobuyasu, Koga,
  • The University of North Carolina at Chapel Hill University Libraries
  • DOI: 10.17615/qh1b-9733

Potassium and sodium transport in non-animal cells: the Trk/Ktr/HKT transporter family
journal, March 2010

  • Corratgé-Faillie, C.; Jabnoune, M.; Zimmermann, S.
  • Cellular and Molecular Life Sciences, Vol. 67, Issue 15
  • DOI: 10.1007/s00018-010-0317-7

The structure of the KtrAB potassium transporter
journal, April 2013

  • Vieira-Pires, Ricardo S.; Szollosi, Andras; Morais-Cabral, João H.
  • Nature, Vol. 496, Issue 7445
  • DOI: 10.1038/nature12055

Interconversion of components of the bacterial proton motive force by electrogenic potassium transport.
journal, January 1981

SerialEM: A Program for Automated Tilt Series Acquisition on Tecnai Microscopes Using Prediction of Specimen Position
journal, July 2003

Helical jackknives control the gates of the double-pore K+ uptake system KtrAB
journal, May 2017

  • Diskowski, Marina; Mehdipour, Ahmad Reza; Wunnicke, Dorith
  • eLife, Vol. 6
  • DOI: 10.7554/eLife.24303

Potassium ion is required for the generation of pH-dependent membrane potential and .DELTA.pH by the marine bacterium Vibrio alginolyticus
journal, July 1981

  • Tokuda, Hajime; Nakamura, Tatsunosuke; Unemoto, Tsutomu
  • Biochemistry, Vol. 20, Issue 14
  • DOI: 10.1021/bi00517a038

The bacterial flagellar motor and its structural diversity
journal, May 2015

Strength of Selection Pressure Is an Important Parameter Contributing to the Complexity of Antibiotic Resistance Evolution
journal, June 2014

  • Oz, Tugce; Guvenek, Aysegul; Yildiz, Sadik
  • Molecular Biology and Evolution, Vol. 31, Issue 9
  • DOI: 10.1093/molbev/msu191

Cloned Potassium Channels from Eukaryotes and Prokaryotes
journal, March 1997

ConSurf 2016: an improved methodology to estimate and visualize evolutionary conservation in macromolecules
journal, May 2016

  • Ashkenazy, Haim; Abadi, Shiran; Martz, Eric
  • Nucleic Acids Research, Vol. 44, Issue W1
  • DOI: 10.1093/nar/gkw408

RELION: Implementation of a Bayesian approach to cryo-EM structure determination
journal, December 2012

Crystal structure of the potassium-importing KdpFABC membrane complex
journal, June 2017

  • Huang, Ching-Shin; Pedersen, Bjørn Panyella; Stokes, David L.
  • Nature, Vol. 546, Issue 7660
  • DOI: 10.1038/nature22970

The intrinsic structure of poly(A) RNA determines the specificity of Pan2 and Caf1 deadenylases
journal, May 2019

  • Tang, Terence T. L.; Stowell, James A. W.; Hill, Chris H.
  • Nature Structural & Molecular Biology, Vol. 26, Issue 6
  • DOI: 10.1038/s41594-019-0227-9

Potassium and sodium transport in non-animal cells: the Trk/Ktr/HKT transporter family
journal, March 2010

  • Corratgé-Faillie, C.; Jabnoune, M.; Zimmermann, S.
  • Cellular and Molecular Life Sciences, Vol. 67, Issue 15
  • DOI: 10.1007/s00018-010-0317-7

Overview of the CCP4 suite and current developments.
text, January 2011

  • Winn, Martyn D.; Ballard, Charles C.; Cowtan, Kevin D.
  • Apollo - University of Cambridge Repository
  • DOI: 10.17863/cam.52322

The Structure of the KtrAB Potassium Transporter
journal, January 2013

  • Vieira-Pires, Ricardo; Szollosi, Andras; Morais-Cabral, João
  • Biophysical Journal, Vol. 104, Issue 2
  • DOI: 10.1016/j.bpj.2012.11.162

Crystal structure and mechanism of a calcium-gated potassium channel
journal, May 2002

  • Jiang, Youxing; Lee, Alice; Chen, Jiayun
  • Nature, Vol. 417, Issue 6888
  • DOI: 10.1038/417515a

A rapid microtiter plate assay for measuring the effect of compounds on Staphylococcus aureus membrane potential
journal, November 2010

  • Gentry, Daniel R.; Wilding, Imogen; Johnson, John M.
  • Journal of Microbiological Methods, Vol. 83, Issue 2
  • DOI: 10.1016/j.mimet.2010.08.012

Evolution of high-level resistance during low-level antibiotic exposure
journal, April 2018

Electrically induced bacterial membrane-potential dynamics correspond to cellular proliferation capacity
journal, April 2019

  • Stratford, James P.; Edwards, Conor L. A.; Ghanshyam, Manjari J.
  • Proceedings of the National Academy of Sciences, Vol. 116, Issue 19
  • DOI: 10.1073/pnas.1901788116

Dissecting the Molecular Mechanism of Nucleotide-Dependent Activation of the KtrAB K+ Transporter
journal, January 2016

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    • Yousefzadeh, S. Aryana; Jarah, Mostafa; Riazi, Gholam Hossein
    • Journal of Molecular Neuroscience, Vol. 70, Issue 4
    • DOI: 10.1007/s12031-019-01457-y

    Insights into the antibiotic resistance and inhibition mechanism of aminoglycoside phosphotransferase from Bacillus cereus : In silico and in vitro perspective
    journal, August 2018

    • Parulekar, Rishikesh Satish; Sonawane, Kailas Dashrath
    • Journal of Cellular Biochemistry, Vol. 119, Issue 11
    • DOI: 10.1002/jcb.27261

    Understanding the Molecular Dynamics of Type-2 Diabetes Drug Target DPP-4 and its Interaction with Sitagliptin and Inhibitor Diprotin-A
    journal, May 2014

    • Chakraborty, Chiranjib; Hsu, Minna J.; Agoramoorthy, Govindasamy
    • Cell Biochemistry and Biophysics, Vol. 70, Issue 2
    • DOI: 10.1007/s12013-014-9998-0

    X-ray structure of alisporivir in complex with cyclophilin A at 1.5 Å resolution
    journal, September 2018

    • Dujardin, Marie; Bouckaert, Julie; Rucktooa, Prakash
    • Acta Crystallographica Section F Structural Biology Communications, Vol. 74, Issue 9
    • DOI: 10.1107/s2053230x18010415

    Zinc binding proteome of a phytopathogen Xanthomonas translucens pv. undulosa
    journal, September 2019

    • Sharma, Ankita; Sharma, Dixit; Verma, Shailender Kumar
    • Royal Society Open Science, Vol. 6, Issue 9
    • DOI: 10.1098/rsos.190369

    Novel coumarin derivatives as potent acetylcholinesterase inhibitors: insight into efficacy, mode and site of inhibition
    journal, May 2018

    • Baruah, Prayasee; Basumatary, Grace; Yesylevskyy, Semen O.
    • Journal of Biomolecular Structure and Dynamics, Vol. 37, Issue 7
    • DOI: 10.1080/07391102.2018.1465853

    Molecular Docking Studies of Catechin and Its Derivatives as Anti-bacterial Inhibitor for Glucosamine-6-Phosphate Synthase
    journal, January 2016

    Molecular mechanism of quinone signaling mediated through S-quinonization of a YodB family repressor QsrR
    journal, March 2013

    • Ji, Q.; Zhang, L.; Jones, M. B.
    • Proceedings of the National Academy of Sciences, Vol. 110, Issue 13
    • DOI: 10.1073/pnas.1219446110

    Structure-Based Virtual Screening and In Vitro Evaluation of New Trypanosoma cruzi Cruzain Inhibitors
    journal, April 2019

    • Herrera-Mayorga, Verónica; Lara-Ramírez, Edgar; Chacón-Vargas, Karla
    • International Journal of Molecular Sciences, Vol. 20, Issue 7
    • DOI: 10.3390/ijms20071742

    A mononuclear diketone-based oxido-vanadium( iv ) complex: structure, DNA and BSA binding, molecular docking and anticancer activities against MCF-7, HPG-2, and HT-29 cell lines
    journal, January 2015

    • Mohamadi, Maryam; Yousef Ebrahimipour, S.; Torkzadeh-Mahani, Masoud
    • RSC Advances, Vol. 5, Issue 122
    • DOI: 10.1039/c5ra13715b

    Xylo- and arabinoxylooligosaccharides from wheat bran by endoxylanases, utilisation by probiotic bacteria, and structural studies of the enzymes
    journal, February 2018

    • Mathew, Sindhu; Aronsson, Anna; Karlsson, Eva Nordberg
    • Applied Microbiology and Biotechnology, Vol. 102, Issue 7
    • DOI: 10.1007/s00253-018-8823-x

    In silico investigation by conceptual DFT and molecular docking of antitrypanosomal compounds for understanding cruzain inhibition
    journal, May 2016

    • Salah, Toufik; Belaidi, Salah; Melkemi, Nadjib
    • Journal of Theoretical and Computational Chemistry, Vol. 15, Issue 03
    • DOI: 10.1142/s0219633616500218

    Structure of Mycobacterium tuberculosis phosphatidylinositol phosphate synthase reveals mechanism of substrate binding and metal catalysis
    journal, May 2019

    • Grāve, Kristīne; Bennett, Matthew D.; Högbom, Martin
    • Communications Biology, Vol. 2, Issue 1
    • DOI: 10.1038/s42003-019-0427-1

    The protein kinase CK2 catalytic domain from Plasmodium falciparum: crystal structure, tyrosine kinase activity and inhibition
    journal, May 2018

    Host Cofactors and Pharmacologic Ligands Share an Essential Interface in HIV-1 Capsid That Is Lost upon Disassembly
    journal, October 2014

    Molecular characterization of a Trichinella spiralis enolase and its interaction with the host’s plasminogen
    journal, December 2019

    Crystal structure of chorismate mutase from Burkholderia thailandensis
    journal, April 2018

    • Asojo, Oluwatoyin A.; Dranow, David M.; Serbzhinskiy, Dmitry
    • Acta Crystallographica Section F Structural Biology Communications, Vol. 74, Issue 5
    • DOI: 10.1107/s2053230x1800506x

    Structural basis for ligand recognition of the human thromboxane A2 receptor
    journal, December 2018

    iview: an interactive WebGL visualizer for protein-ligand complex
    journal, February 2014

    • Li, Hongjian; Leung, Kwong-Sak; Nakane, Takanori
    • BMC Bioinformatics, Vol. 15, Issue 1
    • DOI: 10.1186/1471-2105-15-56

    FBXW7 regulates DISC1 stability via the ubiquitin-proteosome system
    journal, July 2017

    • Yalla, K.; Elliott, C.; Day, J. P.
    • Molecular Psychiatry, Vol. 23, Issue 5
    • DOI: 10.1038/mp.2017.138

    Decreased serum PON1 arylesterase activity in familial hypercholesterolemia patients with a mutated LDLR gene
    journal, September 2018

    In silico mapping of allosteric ligand binding sites in type-1 cannabinoid receptor: CB 1 Binding Pockets
    journal, January 2018

    • Sabatucci, Annalaura; Tortolani, Daniel; Dainese, Enrico
    • Biotechnology and Applied Biochemistry, Vol. 65, Issue 1
    • DOI: 10.1002/bab.1589

    Inhibition of Oncogenic Kinases: An In Vitro Validated Computational Approach Identified Potential Multi-Target Anticancer Compounds
    journal, March 2019

    • Ikram, Nazia; Mirza, Muhammad Usman; Vanmeert, Michiel
    • Biomolecules, Vol. 9, Issue 4
    • DOI: 10.3390/biom9040124

    Structure of the glucagon receptor in complex with a glucagon analogue
    journal, January 2018

    • Zhang, Haonan; Qiao, Anna; Yang, Linlin
    • Nature, Vol. 553, Issue 7686
    • DOI: 10.1038/nature25153

    Structural basis of ligand binding modes at the neuropeptide Y Y1 receptor
    journal, April 2018

    Structure of Gremlin-1 and analysis of its interaction with BMP-2
    journal, May 2016

    • Kišonaitė, Miglė; Wang, Xuelu; Hyvönen, Marko
    • Biochemical Journal, Vol. 473, Issue 11
    • DOI: 10.1042/BCJ20160254

    Specific keratinase derived designer peptides potently inhibit Aβ aggregation resulting in reduced neuronal toxicity and apoptosis
    journal, June 2019

    • Rajput, Rinky; G. L., Balasubramani; Srivastava, Ankit
    • Biochemical Journal, Vol. 476, Issue 12
    • DOI: 10.1042/bcj20190183

    Investigation of specific binding of designed oligodeoxynucleotide decoys to transcription factors in HT29 cell line undergoing epithelial–mesenchymal transition (EMT)
    journal, May 2019

    • Bigdelou, Zahra; Johari, Behrooz; Kadivar, Mehdi
    • Journal of Cellular Physiology, Vol. 234, Issue 12
    • DOI: 10.1002/jcp.28841

    The solvent component of macromolecular crystals
    journal, April 2015

    • Weichenberger, Christian X.; Afonine, Pavel V.; Kantardjieff, Katherine
    • Acta Crystallographica Section D Biological Crystallography, Vol. 71, Issue 5
    • DOI: 10.1107/s1399004715006045

    Thienopyrimidine sulphonamide hybrids: design, synthesis, antiprotozoal activity and molecular docking studies
    journal, January 2016

    • Leeza Zaidi, Saadia; Agarwal, Subhash M.; Chavalitshewinkoon-Petmitr, Porntip
    • RSC Advances, Vol. 6, Issue 93
    • DOI: 10.1039/c6ra15181g

    D224V and S128Y mutation in FSHR ED influence thumb movement differentially: An intricate insight gained by short‐term molecular dynamics simulation
    journal, November 2018

    • Gharemirshamlu, Fatemeh Rahimi; Afsar, Maliha; Mokhdomi, Taseem A.
    • Journal of Cellular Biochemistry, Vol. 120, Issue 5
    • DOI: 10.1002/jcb.28044

    Deciphering the binding behavior of flavonoids to the cyclin dependent kinase 6/cyclin D complex
    journal, May 2018

    Convergent allostery in ribonucleotide reductase
    journal, June 2019

    Lysozyme's lectin-like characteristics facilitates its immune defense function
    text, January 2017

    • Zhang, Ruiyan; Wu, Lisha; Eckert, Thomas
    • Deutsches Elektronen-Synchrotron, DESY, Hamburg
    • DOI: 10.3204/pubdb-2017-13512

    Identification of potential natural inhibitors of SARS-CoV2 main protease by molecular docking and simulation studies
    text, January 2020

    Microencapsulation of Anthocyanins from Grape Skins by Whey Protein Isolates and Different Polymers
    journal, June 2017

    • Stănciuc, Nicoleta; Turturică, Mihaela; Oancea, Ana Maria
    • Food and Bioprocess Technology, Vol. 10, Issue 9
    • DOI: 10.1007/s11947-017-1938-8

    Defining ICR-Mo, an intrinsic colistin resistance determinant from Moraxella osloensis
    journal, May 2018

    First structure of archaeal branched-chain amino acid aminotransferase from Thermoproteus uzoniensis specific for l-amino acids and R-amines
    journal, February 2016

    • Boyko, Konstantin M.; Stekhanova, Tatiana N.; Nikolaeva, Alena Yu.
    • Extremophiles, Vol. 20, Issue 2
    • DOI: 10.1007/s00792-016-0816-z

    Comparative Studies of the Dynamics Effects of BAY60-2770 and BAY58-2667 Binding with Human and Bacterial H-NOX Domains
    journal, August 2018

    Novel calcitriol analogue with an oxolane group: In vitro, in vivo, and in silico studies
    journal, April 2019

    • Obiol, Diego J.; Martínez, Andrea; Ferronato, María J.
    • Archiv der Pharmazie, Vol. 352, Issue 5
    • DOI: 10.1002/ardp.201800315

    Insight into microtubule destabilization mechanism of 3,4,5-trimethoxyphenyl indanone derivatives using molecular dynamics simulation and conformational modes analysis
    journal, March 2018

    • Tripathi, Shubhandra; Srivastava, Gaurava; Singh, Aastha
    • Journal of Computer-Aided Molecular Design, Vol. 32, Issue 4
    • DOI: 10.1007/s10822-018-0109-y

    Human substance P receptor binding mode of the antagonist drug aprepitant by NMR and crystallography.
    text, January 2019

    Crystal structures of multidrug efflux pump MexB bound with high-molecular-mass compounds
    journal, March 2019

    X-ray structure of Fasciola hepatica Sigma class glutathione transferase 1 reveals a disulfide bond to support stability in gastro-intestinal environment
    journal, January 2019

    UDP-Glucose 4-Epimerase and β-1,4-Galactosyltransferase from the Oyster Magallana gigas as Valuable Biocatalysts for the Production of Galactosylated Products
    journal, May 2018

    • Song, Hui-Bo; He, Meng; Cai, Zhi-Peng
    • International Journal of Molecular Sciences, Vol. 19, Issue 6
    • DOI: 10.3390/ijms19061600

    Synthesis of adenosine analogues with indole moiety as human adenosine A 3 receptor ligands
    journal, February 2018

    • Xia, Yan; Zheng, Xiliang; Wang, Erkang
    • Royal Society Open Science, Vol. 5, Issue 2
    • DOI: 10.1098/rsos.171596

    Insights into cytochrome bc1 complex binding mode of antimalarial 2-hydroxy-1,4-naphthoquinones through molecular modelling
    journal, April 2017

    • Sodero, Ana Carolina Rennó; Abrahim-Vieira, Bárbara; Torres, Pedro Henrique Monteiro
    • Memórias do Instituto Oswaldo Cruz, Vol. 112, Issue 4
    • DOI: 10.1590/0074-02760160417

    High throughput in silico identification and characterization of Plasmodium falciparum PRL phosphatase inhibitors
    journal, November 2017

    • Pandey, Rajan; Kumar, Rakesh; Gupta, Priya
    • Journal of Biomolecular Structure and Dynamics, Vol. 36, Issue 13
    • DOI: 10.1080/07391102.2017.1392365

    Analysis of non-peptidic compounds as potential malarial inhibitors against Plasmodial cysteine proteases via integrated virtual screening workflow
    journal, January 2016

    • Musyoka, Thommas M.; Kanzi, Aquillah M.; Lobb, Kevin A.
    • Journal of Biomolecular Structure and Dynamics, Vol. 34, Issue 10
    • DOI: 10.1080/07391102.2015.1108231

    Comparative structural analysis of the caspase family with other clan CD cysteine peptidases
    journal, February 2015

    • McLuskey, Karen; Mottram, Jeremy C.
    • Biochemical Journal, Vol. 466, Issue 2
    • DOI: 10.1042/BJ20141324

    The intrinsic structure of poly(A) RNA determines the specificity of Pan2 and Caf1 deadenylases
    journal, May 2019

    • Tang, Terence T. L.; Stowell, James A. W.; Hill, Chris H.
    • Nature Structural & Molecular Biology, Vol. 26, Issue 6
    • DOI: 10.1038/s41594-019-0227-9
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