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1

Using Graphs of Dynamic Hydrogen-Bond Networks To Dissect Conformational Coupling in a Protein Motor

Karathanou, Konstantina, Bondar, Ana-Nicoleta

Journal:

Journal of Chemical Information and Modeling

Year:

2019

Language:

english

File:

PDF, 9.50 MB

english, 2019

2

Bridge: A graph-based algorithm to analyze dynamic H-bond networks in membrane proteins

Siemers, Malte, Lazaratos, Michalis, KARATHANOU, KONSTANTINA, Guerra, Federico, Brown, Leonid S., Bondar, Ana-Nicoleta

Journal:

Journal of Chemical Theory and Computation

Year:

2019

Language:

english

File:

PDF, 3.58 MB

english, 2019

3

Proton-Coupled Dynamics in Lactose Permease

Magnus Andersson, Ana-Nicoleta Bondar, J. Alfredo Freites, Douglas J. Tobias, H. Ronald Kaback, Stephen H. White

Journal:

Year:

2012

Language:

english

File:

PDF, 6.87 MB

english, 2012

4

Excitation energies of a water-bridged twisted retinal structure in the bacteriorhodopsin proton pump: a theoretical investigation

Wolter, Tino, Welke, Kai, Phatak, Prasad, Bondar, Ana-Nicoleta, Elstner, Marcus

Journal:

Physical Chemistry Chemical Physics

Year:

2013

Language:

english

File:

PDF, 1.90 MB

english, 2013

5

Proton-Coupled Water and Hydrogen-Bond Dynamics in Channelrhodopsin

Mielack, Christopher, del Val, Coral, Luiza Bondar, Maria, Bondar, Ana Nicoleta

Journal:

Biophysical Journal

Year:

2014

Language:

english

File:

PDF, 61 KB

english, 2014

6

Ser/Thr Motifs in Transmembrane Proteins: Conservation Patterns and Effects on Local Protein Structure and Dynamics

Val, Coral, White, Stephen H., Bondar, Ana-Nicoleta

Journal:

Journal of Membrane Biology

Year:

2012

Language:

english

File:

PDF, 882 KB

english, 2012

7

Masthead

Heyden, Matthias, Jardon-Valadez, Hector Eduardo, Bondar, Ana-Nicoleta, Tobias, Douglas J.

Journal:

Journal of Vascular and Interventional Radiology

Year:

2009

Language:

english

File:

PDF, 61 KB

english, 2009

8

Opening the Lateral Gate of the Rhomboid Protease Couples to Lipid Binding

Bondar, Ana Nicoleta, Lemieux, M. Joanne

Journal:

Biophysical Journal

Year:

2015

Language:

english

File:

PDF, 44 KB

english, 2015

9

Interplay of Chloride and Proton Transfers in the Novel Class of Light-Driven Anion Transporters

Brown, Leonid S., Harris, Andrew, Saita, Mattia, Resler, Tom, Hughes-Visentin, Alexandra, Maia, Raiza, Pranga-Sellnau, Franziska, Bondar, Ana-Nicoleta, Heberle, Joachim

Journal:

Biochimica et Biophysica Acta (BBA) - Bioenergetics

Year:

2018

File:

PDF, 46 KB

2018

10

Extended protein/water H-bond networks in photosynthetic water oxidation

Ana-Nicoleta Bondar, Holger Dau

Journal:

Biochimica et Biophysica Acta (BBA) - Bioenergetics

Year:

2012

Language:

english

File:

PDF, 2.36 MB

english, 2012

11

Mechanism of a Molecular Valve in the Halorhodopsin Chloride Pump

Andreea D. Gruia, Ana-Nicoleta Bondar, Jeremy C. Smith, Stefan Fischer

Journal:

Year:

2005

Language:

english

File:

PDF, 435 KB

english, 2005

12

ERRATUM.

Heyden, Matthias, Jardon-Valadez, Hector Eduardo, Bondar, Ana-Nicoleta, Tobias, Douglas J.

Journal:

Year:

1835

Language:

english

File:

PDF, 95 KB

english, 1835

13

Biophysical mechanism of rhomboid proteolysis: Setting a foundation for therapeutics

Bondar, Ana-Nicoleta

Journal:

Seminars in Cell & Developmental Biology

Year:

2016

Language:

english

File:

PDF, 615 KB

english, 2016

14

Dynamic hydrogen-bond networks in bacterial protein secretion

Karathanou, Konstantina, Bondar, Ana-Nicoleta

Journal:

FEMS Microbiology Letters

Year:

2018

Language:

english

File:

PDF, 3.49 MB

english, 2018

15

Molecular movie of nucleotide binding to a motor protein

Bondar, Ana-Nicoleta, Mishima, Hirokazu, Okamoto, Yuko

Journal:

Biochimica et Biophysica Acta (BBA) - General Subjects

Year:

2020

File:

PDF, 2.97 MB

2020

16

A graph-based approach identifies dynamic H-bond communication networks in spike protein S of SARS-CoV-2

Karathanou, Konstantina, Lazaratos, Michalis, Bertalan, Ãva, Siemers, Malte, Buzar, Krzysztof, Schertler, Gebhard F.X., del Val, Coral, Bondar, Ana-Nicoleta

Journal:

Journal of Structural Biology

Year:

2020

File:

PDF, 17.00 MB

2020

17

Mechanism by which Untwisting of Retinal Leads to Productive Bacteriorhodopsin Photocycle States

Wolter, Tino, Elstner, Marcus, Fischer, Stefan, Smith, Jeremy C., Bondar, Ana-Nicoleta

Journal:

Journal of Physical Chemistry B

Year:

2015

Language:

english

File:

PDF, 5.58 MB

english, 2015

18

Role of Lipids in the Reaction Coordinate of GlpG Rhomboid Protease

Bondar, Ana-Nicoleta

Journal:

Biophysical Journal

Year:

2017

Language:

english

File:

PDF, 42 KB

english, 2017

19

Dynamic Water Hydrogen-Bond Networks at the Interface of a Lipid Membrane Containing Palmitoyl-Oleoyl Phosphatidylglycerol

Karathanou, Konstantina, Bondar, Ana-Nicoleta

Journal:

Journal of Membrane Biology

Year:

2018

Language:

english

File:

PDF, 4.36 MB

english, 2018

20

Ground-state properties of the retinal molecule: from quantum mechanical to classical mechanical computations of retinal proteins

Ana-Nicoleta Bondar, Michaela Knapp-Mohammady, Sándor Suhai, Stefan Fischer, Jeremy C. Smith

Journal:

Theoretical Chemistry Accounts: Theory, Computation, and Modeling (Theoretica Chimica Acta)

Year:

2011

Language:

english

File:

PDF, 826 KB

english, 2011

21

Hydrogen bond dynamics in membrane protein function

Ana-Nicoleta Bondar, Stephen H. White

Journal:

Biochimica et Biophysica Acta (BBA) - Biomembranes

Year:

2012

Language:

english

File:

PDF, 1.24 MB

english, 2012

22

Dynamics of the Internal Water Molecules in Squid Rhodopsin

Jardón-Valadez, Eduardo, Bondar, Ana-Nicoleta, Tobias, Douglas J.

Journal:

Biophysical Journal

Year:

2009

Language:

english

File:

PDF, 797 KB

english, 2009

23

Dynamic Hydrogen-Bonding Networks in Photosystem II

Guerra, Federico, Bondar, Ana-Nicoleta

Journal:

Biophysical Journal

Year:

2017

Language:

english

File:

PDF, 44 KB

english, 2017

24

Dynamics of Long-Distance Hydrogen-Bond Networks in Photosystem II

Guerra, Federico, Siemers, Malte, Mielack, Christopher, Bondar, Ana-Nicoleta

Journal:

Journal of Physical Chemistry B

Year:

2018

Language:

english

File:

PDF, 2.72 MB

english, 2018

25

Membrane cholesterol as regulator of human rhomboid protease RHBDL4.

Paschkowsky, Sandra, Recinto, Sherilyn Junelle, Young, Jason C., Bondar, Ana Nicoleta, Munter, Lisa Marie

Journal:

Journal of Biological Chemistry

Year:

2018

Language:

english

File:

PDF, 2.96 MB

english, 2018

26

Festschrift in the Honor of Stephen H. White’s 70th Birthday

Ana-Nicoleta Bondar, Thomas B. Woolf, Douglas J. Tobias

Journal:

Journal of Membrane Biology

Year:

2011

Language:

english

File:

PDF, 124 KB

english, 2011

27

The Retinal Conformation and its Environment in Rhodopsin in Light of a New 2.2 Å Crystal Structure

Tetsuji Okada, Minoru Sugihara, Ana-Nicoleta Bondar, Marcus Elstner, Peter Entel, Volker Buss

Journal:

Journal of Molecular Biology

Year:

2004

Language:

english

File:

PDF, 559 KB

english, 2004

28

Electrostatic interactions and hydrogen bond dynamics in chloride pumping by halorhodopsin

Jardón-Valadez, Eduardo, Bondar, Ana-Nicoleta, Tobias, Douglas J.

Journal:

Biochimica et Biophysica Acta (BBA) - Bioenergetics

Year:

2014

Language:

english

File:

PDF, 3.27 MB

english, 2014

29

Long-Distance Proton Transfer with a Break in the Bacteriorhodopsin Active Site

Phatak, Prasad, Frähmcke, Jan S., Wanko, Marius, Hoffmann, Michael, Strodel, Paul, Smith, Jeremy C., Suhai, Sándor, Bondar, Ana-Nicoleta, Elstner, Marcus

Journal:

Journal of the American Chemical Society

Year:

2009

Language:

english

File:

PDF, 4.87 MB

english, 2009

30

Coupling between inter-helical hydrogen bonding and water dynamics in a proton transporter

del Val, Coral, Bondar, Luiza, Bondar, Ana-Nicoleta

Journal:

Journal of Structural Biology

Year:

2014

Language:

english

File:

PDF, 5.28 MB

english, 2014

31

Tuning of Retinal Twisting in Bacteriorhodopsin Controls the Directionality of the Early Photocycle Steps

Bondar, Ana-Nicoleta, Fischer, Stefan, Suhai, Sándor, Smith, Jeremy C.

Journal:

Journal of Physical Chemistry B

Year:

2005

Language:

english

File:

PDF, 84 KB

english, 2005

32

Mechanism of conformational coupling in SecA: Key role of hydrogen-bonding networks and water interactions

Milenkovic, Stefan, Bondar, Ana-Nicoleta

Journal:

Biochimica et Biophysica Acta (BBA) - Biomembranes

Year:

2016

Language:

english

File:

PDF, 1.28 MB

english, 2016

33

Exploring cavity dynamics in biomolecular systems

Lindow, Norbert, Baum, Daniel, Bondar, Ana-Nicoleta, Hege, Hans-Christian

Journal:

BMC Bioinformatics

Year:

2013

Language:

english

File:

PDF, 2.31 MB

english, 2013

34

BLANCO-80: Thematic Collection of Structural and Thermodynamic Studies on Membranes

Ladokhin, Alexey S., Bondar, Ana-Nicoleta

Journal:

Journal of Membrane Biology

Year:

2020

File:

PDF, 389 KB

2020

35

Rhomboid Protease Dynamics and Lipid Interactions

Ana-Nicoleta Bondar, Coral del Val, Stephen H. White

Journal:

Year:

2009

Language:

english

File:

PDF, 4.22 MB

english, 2009

36

Water Molecules in Short- and Long-Distance Proton Transfer Steps of Bacteriorhodopsin Proton Pumping

Ana-Nicoleta Bondar, Jeremy C. Smith

Journal:

Israel Journal of Chemistry

Year:

2009

Language:

english

File:

PDF, 651 KB

english, 2009

37

A Relay Mechanism in Rhomboid Intramembrane Protease

Bondar, Ana Nicoleta, White, Stephen H.

Journal:

Biophysical Journal

Year:

2009

Language:

english

File:

PDF, 37 KB

english, 2009

38

Opening the Protein Translocon

Bondar, Ana Nicoleta, Tobias, Douglas J., White, Stephen H.

Journal:

Biophysical Journal

Year:

2011

Language:

english

File:

PDF, 63 KB

english, 2011

39

A new group of eubacterial light-driven retinal-binding proton pumps with an unusual cytoplasmic proton donor

Harris, Andrew, Ljumovic, Milena, Bondar, Ana-Nicoleta, Shibata, Yohei, Ito, Shota, Inoue, Keiichi, Kandori, Hideki, Brown, Leonid S.

Journal:

Biochimica et Biophysica Acta (BBA) - Bioenergetics

Year:

2015

Language:

english

File:

PDF, 1.67 MB

english, 2015

40

Mechanism of a proton pump analyzed with computer simulations

Ana-Nicoleta Bondar, Jeremy C. Smith, Marcus Elstner

Journal:

Theoretical Chemistry Accounts: Theory, Computation, and Modeling (Theoretica Chimica Acta)

Year:

2010

Language:

english

File:

PDF, 460 KB

english, 2010

41

Structural and energetic determinants of primary proton transfer in bacteriorhodopsin

Bondar, Ana-Nicoleta, Smith, Jeremy C., Fischer, Stefan

Journal:

Photochemical & Photobiological Sciences

Year:

2006

Language:

english

File:

PDF, 203 KB

english, 2006

42

Dynamic Carboxylate/Water Networks on the Surface of the PsbO Subunit of Photosystem II

Lorch, Sebastian, Capponi, Sara, Pieront, Florian, Bondar, Ana-Nicoleta

Journal:

Journal of Physical Chemistry B

Year:

2015

Language:

english

File:

PDF, 2.83 MB

english, 2015

43

Catalysis of Ground State cis$$\rightarrow$$→ trans Isomerization of Bacteriorhodopsin’s Retinal Chromophore by a Hydrogen-Bond Network

Elghobashi-Meinhardt, Nadia, Phatak, Prasad, Bondar, Ana-Nicoleta, Elstner, Marcus, Smith, Jeremy C.

Journal:

Journal of Membrane Biology

Year:

2018

Language:

english

File:

PDF, 1.66 MB

english, 2018

44

Dynamics Of Water Molecules In Bacteriorhodopsin Mutants

Dulea, Mihnea, Bondar, Ana-Nicoleta

Journal:

Biophysical Journal

Year:

2009

Language:

english

File:

PDF, 92 KB

english, 2009

45

Lipid-Coupled Docking of Transmembrane Substrate by the GlpG Rhomboid Protease from Escherichia Coli

Bondar, Ana-Nicoleta, White, Stephen H.

Journal:

Biophysical Journal

Year:

2012

Language:

english

File:

PDF, 36 KB

english, 2012

46

Dynamics of the Internal Water Molecules in Squid Rhodopsin

Jardón-Valadez, Eduardo, Bondar, Ana-Nicoleta, Tobias, Douglas J.

Journal:

Biophysical Journal

Year:

2009

Language:

english

File:

PDF, 39 KB

english, 2009

47

Crystallographic and computational analysis of the barrel part of the PsbO protein of photosystem II – carboxylate-water clusters as putative proton transfer relays and structural switches

Bommer, Martin, Bondar, Ana-Nicoleta, Zouni, Athina, Dobbek, Holger, Dau, Holger

Journal:

Year:

2016

Language:

english

File:

PDF, 1.95 MB

english, 2016

48

Lipid Membrane Composition has A Dramatic Effect on the Dynamics of the GlpG Rhomboid Protease from Escherichia Coli

Bondar, Ana Nicoleta, White, Stephen H.

Journal:

Biophysical Journal

Year:

2010

Language:

english

File:

PDF, 37 KB

english, 2010

49

Key Role of Active-Site Water Molecules in Bacteriorhodopsin Proton-Transfer Reactions

Bondar, Ana-Nicoleta, Baudry, Jerome, Suhai, Sándor, Fischer, Stefan, Smith, Jeremy C.

Journal:

Journal of Physical Chemistry B

Year:

2008

Language:

english

File:

PDF, 1.78 MB

english, 2008

50

Phosphatidylglyerol Lipid Binding at the Active Site of an Intramembrane Protease

Bondar, Ana-Nicoleta

Journal:

Journal of Membrane Biology

Year:

2020

File:

PDF, 2.56 MB

2020

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