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1

Capturing Functional Motions of Membrane Channels and Transporters with Molecular Dynamics Simulation

Shaikh, Saher Afshan, Wen, Po-Chao, Enkavi, Giray, Huang, Zhijian, Tajkhorshid, Emad

Journal:

Journal of Computational and Theoretical Nanoscience

Year:

2010

Language:

english

File:

PDF, 29.89 MB

english, 2010

2

ChemInform Abstract: Capturing Functional Motions of Membrane Channels and Transporters with Molecular Dynamics Simulation

Saher Afshan Shaikh, Po-Chao Wen, Giray Enkavi, Zhijian Huang, Emad Tajkhorshid

Journal:

Year:

2012

File:

PDF, 19 KB

2012

3

Visualizing Functional Motions of Membrane Transporters with Molecular Dynamics Simulations

Shaikh, Saher A., Li, Jing, Enkavi, Giray, Wen, Po-Chao, Huang, Zhijian, Tajkhorshid, Emad

Journal:

Year:

2013

Language:

english

File:

PDF, 17.03 MB

english, 2013

4

Spontaneous Substrate Binding and Formation of the Bound State in Glycerol-3-Phosphate Transporter (GlpT)

Enkavi, Giray, Tajkhorsid, Emad

Journal:

Biophysical Journal

Year:

2009

Language:

english

File:

PDF, 76 KB

english, 2009

5

Structural Basis of Substrate Selectivity in the Glycerol-3-Phosphate: Phosphate Antiporter GlpT

Law, Christopher J., Enkavi, Giray, Wang, Da-Neng, Tajkhorshid, Emad

Journal:

Biophysical Journal

Year:

2009

Language:

english

File:

PDF, 712 KB

english, 2009

6

Energetics and Molecular Mechanisms of Permeation and Selectivity of Transport in the Urea Transporter

Enkavi, Giray, Levin, Elena J., Zhou, Ming, Tajkhorshid, Emad

Journal:

Biophysical Journal

Year:

2011

Language:

english

File:

PDF, 83 KB

english, 2011

7

Transport Cycle of Mitochondrial Carriers from Internal Symmetries

Enkavi, Giray, Tajkhorshid, Emad

Journal:

Biophysical Journal

Year:

2012

Language:

english

File:

PDF, 35 KB

english, 2012

8

British library Harleian manuscript 433, 1. Register of grants for the reigns of Edward V and Richard III

Levin, Elena J., Cao, Yu, Enkavi, Giray, Quick, Matthias, Pan, Yaping, Tajkhorshid, Emad, Zhou, Ming

Journal:

Journal of Medieval History

Year:

1980

Language:

english

File:

PDF, 67 KB

english, 1980

9

Mechanism and Regulation of Urea Permeation in a Mammalian Urea Channel

Levin, Elena J., Cao, Yu, Enkavi, Giray, Quick, Matthias, Pan, Yaping, Tajkhorshid, Emad, Zhou, Ming

Journal:

Biophysical Journal

Year:

2012

Language:

english

File:

PDF, 77 KB

english, 2012

10

An Insight into the XylE Transport Cycle by Characterizing Proton Binding Site and its Coupling to the Substrate Transport

Shekhar, Mrinal, Enkavi, Giray, Tajkhorshid, Emad

Journal:

Biophysical Journal

Year:

2014

Language:

english

File:

PDF, 42 KB

english, 2014

11

Characterizing the Pathway, Free Energy, and the Effect of Substrate Binding on Structural Transition of MFS Transporter GlpT between Inward- and Outward-Facing States

Moradi, Mahmoud, Enkavi, Giray, Tajkhorshid, Emad

Journal:

Biophysical Journal

Year:

2013

Language:

english

File:

PDF, 42 KB

english, 2013

12

Novel Structural and Dynamical Features of Water Permeation through an Aquaporin Crystallized at Sub-Angstrom Resolution

Enkavi, Giray, Tajkhorshid, Emad

Journal:

Biophysical Journal

Year:

2013

Language:

english

File:

PDF, 48 KB

english, 2013

13

Conformational Transition Pathway of GlpT Transporter, Characterized by Nonequilibrium Molecular Dynamics Simulations

Moradi, Mahmoud, Enkavi, Giray, Tajkhorshid, Emad

Journal:

Biophysical Journal

Year:

2012

Language:

english

File:

PDF, 85 KB

english, 2012

14

Molecular Determinants of the Stoichiometry of Transport in GlpT

Enkavi, Giray, Tajkhorshid, Emad

Journal:

Biophysical Journal

Year:

2010

Language:

english

File:

PDF, 36 KB

english, 2010

15

Simulation of Spontaneous Substrate Binding Revealing the Binding Pathway and Mechanism and Initial Conformational Response of GlpT

Enkavi, Giray, Tajkhorshid, Emad

Journal:

Year:

2010

Language:

english

File:

PDF, 5.36 MB

english, 2010

16

Proton-coupled electron transfer and the role of water molecules in proton pumping by cytochrome c oxidase

Sharma, Vivek, Enkavi, Giray, Vattulainen, Ilpo, Róg, Tomasz, Wikström, Mårten

Journal:

Proceedings of the National Academy of Sciences

Year:

2015

Language:

english

File:

PDF, 1.17 MB

english, 2015

17

Atomic-level characterization of transport cycle thermodynamics in the glycerol-3-phosphate:phosphate antiporter

Moradi, Mahmoud, Enkavi, Giray, Tajkhorshid, Emad

Journal:

Nature Communications

Year:

2015

Language:

english

File:

PDF, 1.94 MB

english, 2015

18

Towards Thermodynamic Characterization of Transport Cycle in Secondary Transporters using Enhanced Sampling Techniques

Moradi, Mahmoud, Enkavi, Giray, Tajkhorshid, Emad

Journal:

Biophysical Journal

Year:

2015

Language:

english

File:

PDF, 42 KB

english, 2015

19

The Effect of Membrane Polyunsaturated Fatty Acids on Receptor Partitioning to Ordered Domains

Javanainen, Matti, Enkavi, Giray, Guixa-Gonzalez, Ramon, Kulig, Waldemar, Martinez-Seara, Hector, Vattulainen, Ilpo

Journal:

Biophysical Journal

Year:

2017

Language:

english

File:

PDF, 64 KB

english, 2017

20

Molecular mechanism for inhibition of twinfilin by phosphoinositides

Hakala, Markku, Kalimeri, Maria, Enkavi, Giray, Vattulainen, Ilpo, Lappalainen, Pekka

Journal:

Journal of Biological Chemistry

Year:

2018

Language:

english

File:

PDF, 4.51 MB

english, 2018

21

Structural basis of actin monomer re-charging by cyclase-associated protein

Kotila, Tommi, Kogan, Konstantin, Enkavi, Giray, Guo, Siyang, Vattulainen, Ilpo, Goode, Bruce L., Lappalainen, Pekka

Journal:

Nature Communications

Year:

2018

Language:

english

File:

PDF, 6.58 MB

english, 2018

22

Concerted regulation of npc2 binding to endosomal/lysosomal membranes by bis(monoacylglycero)phosphate and sphingomyelin

Enkavi, Giray, Mikkolainen, Heikki, Güngör, Burçin, Ikonen, Elina, Vattulainen, Ilpo, MacKerell, Alexander

Journal:

PLoS Computational Biology

Year:

2017

Language:

english

File:

PDF, 6.89 MB

english, 2017

23

Reduced level of docosahexaenoic acid shifts GPCR neuroreceptors to less ordered membrane regions

Javanainen, Matti, Enkavi, Giray, Guixà-Gonzaléz, Ramon, Kulig, Waldemar, Martinez-Seara, Hector, Levental, Ilya, Vattulainen, Ilpo, de Groot, Bert L.

Journal:

PLoS Computational Biology

Year:

2019

Language:

english

File:

PDF, 7.35 MB

english, 2019

24

Mechanism of synergistic actin filament pointed end depolymerization by cyclase-associated protein and cofilin

Kotila, Tommi, Wioland, Hugo, Enkavi, Giray, Kogan, Konstantin, Vattulainen, Ilpo, Jégou, Antoine, Romet-Lemonne, Guillaume, Lappalainen, Pekka

Journal:

Nature Communications

Year:

2019

Language:

english

File:

PDF, 3.63 MB

english, 2019

25

Mechanism of synergistic actin filament pointed end depolymerization by cyclase-associated protein and cofilin

Kotila, Tommi, Wioland, Hugo, Enkavi, Giray, Kogan, Konstantin, Vattulainen, Ilpo, Jégou, Antoine, Romet-Lemonne, Guillaume, Lappalainen, Pekka

Journal:

Nature Communications

Year:

2019

File:

PDF, 3.63 MB

2019

26

Pulmonary Surfactant Lipid Reorganization Induced by the Adsorption of the Oligomeric Surfactant Protein B Complex

Liekkinen, Juho, Enkavi, Giray, Javanainen, Matti, Olmeda, Barbara, PÃ©rez-Gil, JesÃºs, Vattulainen, Ilpo

Journal:

Journal of Molecular Biology

Year:

2020

File:

PDF, 23.95 MB

2020

27

Highâcontent imaging and structureâbased predictions reveal functional differences between NiemannâPick C1 variants

Vanharanta, Lauri, PerÃ¤nen, Johan, Pfisterer, Simon G., Enkavi, Giray, Vattulainen, Ilpo, Ikonen, Elina

Journal:

Year:

2020

File:

PDF, 4.33 MB

2020

28

Membrane-Dependent Binding and Entry Mechanism of Dopamine into Its Receptor

Lolicato, Fabio, Juhola, Hanna, Zak, Agata, Postila, Pekka A., Saukko, Annina, Rissanen, Sami, Enkavi, Giray, Vattulainen, Ilpo, Kepczynski, Mariusz, RÃ³g, Tomasz

Journal:

ACS Chemical Neuroscience

Year:

2020

File:

PDF, 3.97 MB

2020