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1

Anomalous Diffusion of Phospholipids and Cholesterols in a Lipid Bilayer and its Origins

Jeon, Jae-Hyung, Monne, Hector Martinez-Seara, Javanainen, Matti, Metzler, Ralf

Journal:

Physical Review Letters

Year:

2012

Language:

english

File:

PDF, 3.09 MB

english, 2012

2

doGlycans – Tools for Preparing Carbohydrate Structures for Atomistic Simulations of Glycoproteins, Glycolipids, and Carbohydrate Polymers with GROMACS

Danne, Reinis, Poojari, Chetan, Martinez-Seara, Hector, Rissanen, Sami, Lolicato, Fabio, Rog, Tomasz, Vattulainen, Ilpo

Journal:

Journal of Chemical Information and Modeling

Year:

2017

Language:

english

File:

PDF, 1.41 MB

english, 2017

3

Travelling waves in two-dimensional smectic-C domains

J. Claret, J. Crusats, R. Albalat, J. Ignés-Mullol, H. Martınez-Seara, R. Reigada, F. Sagués

Journal:

The European Physical Journal E

Year:

2006

Language:

english

File:

PDF, 320 KB

english, 2006

4

Role of Cardiolipins in the Inner Mitochondrial Membrane: Insight Gained through Atom-Scale Simulations

Róg, Tomasz, Martinez-Seara, Hector, Munck, Nana, Orešič, Matej, Karttunen, Mikko, Vattulainen, Ilpo

Journal:

Journal of Physical Chemistry B

Year:

2009

Language:

english

File:

PDF, 1.30 MB

english, 2009

5

Interplay of Unsaturated Phospholipids and Cholesterol in Membranes: Effect of the Double-Bond Position

Martinez-Seara, Hector, Róg, Tomasz, Pasenkiewicz-Gierula, Marta, Vattulainen, Ilpo, Karttunen, Mikko, Reigada, Ramon

Journal:

Biophysical Journal

Year:

2008

Language:

english

File:

PDF, 232 KB

english, 2008

6

Structure of Glycocalyx

Martinez-Seara Monne, Hector, Danne, Reinis, Róg, Tomasz, Ilpo, Vattulainen, Gurtovenko, Andrey

Journal:

Biophysical Journal

Year:

2013

Language:

english

File:

PDF, 39 KB

english, 2013

7

Effect of Double Bond Position on Lipid Bilayer Properties: Insight through Atomistic Simulations

Martinez-Seara, Hector, Róg, Tomasz, Pasenkiewicz-Gierula, Marta, Vattulainen, Ilpo, Karttunen, Mikko, Reigada, Ramon

Journal:

Journal of Physical Chemistry B

Year:

2007

Language:

english

File:

PDF, 256 KB

english, 2007

8

Effect of PEGylation on Drug Entry into Lipid Bilayer

Rissanen, Sami, Kumorek, Marta, Martinez-Seara, Hector, Li, Yen-Chin, Jamróz, Dorota, Bunker, Alex, Nowakowska, Maria, Vattulainen, Ilpo, Kepczynski, Mariusz, Róg, Tomasz

Journal:

Journal of Physical Chemistry B

Year:

2014

Language:

english

File:

PDF, 3.88 MB

english, 2014

9

Atomistic Simulations of Functional Au 144 (SR) 60 Gold Nanoparticles in Aqueous Environment

Heikkilä, Elena, Gurtovenko, Andrey A., Martinez-Seara, Hector, Häkkinen, Hannu, Vattulainen, Ilpo, Akola, Jaakko

Journal:

The Journal of Physical Chemistry C

Year:

2012

Language:

english

File:

PDF, 3.82 MB

english, 2012

10

Atomistic Simulations of Functional Gold Nanoparticles Au144(Sr)60 Interacting with Membranes

Heikkilä, Elena, Gurtovenko, Andrey, Martinez-Seara, Hector, Häkkinen, Hannu, Vattulainen, Ilpo, Akola, Jaakko

Journal:

Biophysical Journal

Year:

2013

Language:

english

File:

PDF, 132 KB

english, 2013

11

Cell Membrane Composition Affects GPCR Aggregation

Guixà-González, Ramon, Javanainen, Matti, Martinez-Seara, Hector, Gómez-Soler, Maricel, Domingo, Joan Carles, Vattulainen, Ilpo, Ciruela, Francisco, Selent, Jana

Journal:

Biophysical Journal

Year:

2014

Language:

english

File:

PDF, 82 KB

english, 2014

12

Specific Spatial and Orientational Order in Phospholipid Membranes Induced by Cholesterol

Martinez-Seara, Hector, Rog, Tomasz, Karttunen, Mikko, Reigada, Ramon, Vattulainen, Ilpo

Journal:

Biophysical Journal

Year:

2010

Language:

english

File:

PDF, 36 KB

english, 2010

13

Characterisation of Coexisting Liquid Phases in Mixtures of Dipalmitoylphosphatidylcholine and Cholesterol

Javanainen, Matti, Martinez-Seara, Hector, Vattulainen, Ilpo

Journal:

Biophysical Journal

Year:

2014

Language:

english

File:

PDF, 56 KB

english, 2014

14

MEMBPLUGIN: studying membrane complexity in VMD

Guixa-Gonzalez, R., Rodriguez-Espigares, I., Ramirez-Anguita, J. M., Carrio-Gaspar, P., Martinez-Seara, H., Giorgino, T., Selent, J.

Journal:

Year:

2014

Language:

english

File:

PDF, 2.59 MB

english, 2014

15

Atomistic simulations of anionic Au144(SR)60 nanoparticles interacting with asymmetric model lipid membranes

Heikkilä, Elena, Martinez-Seara, Hector, Gurtovenko, Andrey A., Vattulainen, Ilpo, Akola, Jaakko

Journal:

Biochimica et Biophysica Acta (BBA) - Biomembranes

Year:

2014

Language:

english

File:

PDF, 2.16 MB

english, 2014

16

Cationic Au Nanoparticle Binding with Plasma Membrane-like Lipid Bilayers: Potential Mechanism for Spontaneous Permeation to Cells Revealed by Atomistic Simulations

Heikkilä, Elena, Martinez-Seara, Hector, Gurtovenko, Andrey A., Javanainen, Matti, Häkkinen, Hannu, Vattulainen, Ilpo, Akola, Jaakko

Journal:

The Journal of Physical Chemistry C

Year:

2014

Language:

english

File:

PDF, 754 KB

english, 2014

17

Why is the sn -2 Chain of Monounsaturated Glycerophospholipids Usually Unsaturated whereas the sn -1 Chain Is Saturated? Studies of 1-Stearoyl-2-oleoyl- sn -glycero-3-phosphatidylcholine (SOPC) and 1-Oleoyl-2-stearoyl- sn -glycero-3-phosphatidylcholine (OSPC) Membranes with and without Cholesterol

Martinez-Seara, Hector, Róg, Tomasz, Karttunen, Mikko, Vattulainen, Ilpo, Reigada, Ramon

Journal:

Journal of Physical Chemistry B

Year:

2009

Language:

english

File:

PDF, 735 KB

english, 2009

18

Influence of cis double-bond parametrization on lipid membrane properties: How seemingly insignificant details in force-field change even qualitative trends

Martinez-Seara, Hector, Róg, Tomasz, Karttunen, Mikko, Reigada, Ramon, Vattulainen, Ilpo

Journal:

The Journal of Chemical Physics

Year:

2008

Language:

english

File:

PDF, 725 KB

english, 2008

19

Efficient preparation and analysis of membrane and membrane protein systems

Javanainen, Matti, Martinez-Seara, Hector

Journal:

Biochimica et Biophysica Acta (BBA) - Biomembranes

Year:

2016

Language:

english

File:

PDF, 4.60 MB

english, 2016

20

Protein Crowding in Lipid Bilayers Gives Rise to Non-Gaussian Anomalous Lateral Diffusion of Phospholipids and Proteins

Jeon, Jae-Hyung, Javanainen, Matti, Martinez-Seara, Hector, Metzler, Ralf, Vattulainen, Ilpo

Journal:

Physical Review X

Year:

2016

Language:

english

File:

PDF, 5.68 MB

english, 2016

21

What Can We Learn about Cholesterol’s Transmembrane Distribution Based on Cholesterol-Induced Changes in Membrane Dipole Potential

Falkovich, Stanislav G., Martinez-Seara, Hector, Nesterenko, Alexey M., Vattulainen, Ilpo, Gurtovenko, Andrey A.

Journal:

The Journal of Physical Chemistry Letters

Year:

2016

Language:

english

File:

PDF, 475 KB

english, 2016

22

Membrane omega-3 fatty acids modulate the oligomerisation kinetics of adenosine A2A and dopamine D2 receptors

Guixà-González, Ramon, Javanainen, Matti, Gómez-Soler, Maricel, Cordobilla, Begoña, Domingo, Joan Carles, Sanz, Ferran, Pastor, Manuel, Ciruela, Francisco, Martinez-Seara, Hector, Selent, Jana

Journal:

Scientific Reports

Year:

2016

Language:

english

File:

PDF, 1.97 MB

english, 2016

23

Membrane cholesterol access into a G-protein-coupled receptor

Guixà-González, Ramon, Albasanz, José L., Rodriguez-Espigares, Ismael, Pastor, Manuel, Sanz, Ferran, Martí-Solano, Maria, Manna, Moutusi, Martinez-Seara, Hector, Hildebrand, Peter W., Martín, Mairena,

Journal:

Nature Communications

Year:

2017

Language:

english

File:

PDF, 1.44 MB

english, 2017

24

Long-chain GM1 gangliosides alter transmembrane domain registration through interdigitation

Manna, Moutusi, Javanainen, Matti, Monne, Hector Martinez-Seara, Gabius, Hans-Joachim, Rog, Tomasz, Vattulainen, Ilpo

Journal:

Biochimica et Biophysica Acta (BBA) - Biomembranes

Year:

2017

Language:

english

File:

PDF, 2.94 MB

english, 2017

25

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

26

Two cations, two mechanisms: interactions of sodium and calcium with zwitterionic lipid membranes

Javanainen, Matti, Melcrová, Adéla, Magarkar, Aniket, Jurkiewicz, Piotr, Hof, Martin, Jungwirth, Pavel, Martinez-Seara, Hector

Journal:

Chemical Communications

Year:

2017

Language:

english

File:

PDF, 1.96 MB

english, 2017

27

Nanoscale Membrane Domain Formation Driven by Cholesterol

Javanainen, Matti, Martinez-Seara, Hector, Vattulainen, Ilpo

Journal:

Scientific Reports

Year:

2017

Language:

english

File:

PDF, 1.92 MB

english, 2017

28

Diffusion of Integral Membrane Proteins in Protein-Rich Membranes

Javanainen, Matti, Martinez-Seara, Hector, Metzler, Ralf, Vattulainen, Ilpo

Journal:

The Journal of Physical Chemistry Letters

Year:

2017

Language:

english

File:

PDF, 2.35 MB

english, 2017

29

Binding of Divalent Cations to Insulin: Capillary Electrophoresis and Molecular Simulations

Duboué-Dijon, Elise, Delcroix, Pauline, Martinez-Seara, Hector, Hladílková, Jana, Coufal, Pavel, Křížek, Tomáš, Jungwirth, Pavel

Journal:

Journal of Physical Chemistry B

Year:

2018

Language:

english

File:

PDF, 1.96 MB

english, 2018

30

Diffusion of Proteins and Lipids in Protein-Rich Membranes

Javanainen, Matti, Martinez-Seara, Hector, Metzler, Ralf, Vattulainen, Ilpo

Journal:

Biophysical Journal

Year:

2018

Language:

english

File:

PDF, 40 KB

english, 2018

31

Accurate Binding of Sodium and Calcium to a POPC Bilayer by Effective Inclusion of Electronic Polarization

Melcr, Josef, Martinez-Seara, Hector, Nencini, Ricky, Kolafa, Jiri, Jungwirth, Pavel, Ollila, O.H. Samuli

Journal:

Journal of Physical Chemistry B

Year:

2018

Language:

english

File:

PDF, 3.79 MB

english, 2018

32

A Ceramide-Regulated Element in the Late Endosomal Protein LAPTM4B Controls Amino Acid Transporter Interaction

Zhou, Kecheng, Dichlberger, Andrea, Martinez-Seara, Hector, Nyholm, Thomas K. M., Li, Shiqian, Kim, Young Ah, Vattulainen, Ilpo, Ikonen, Elina, Blom, Tomas

Journal:

ACS Central Science

Year:

2018

Language:

english

File:

PDF, 5.80 MB

english, 2018

33

Atomistic fingerprint of hyaluronan–CD44 binding

Vuorio, Joni, Vattulainen, Ilpo, Martinez-Seara, Hector, MacKerell, Alexander

Journal:

PLoS Computational Biology

Year:

2017

Language:

english

File:

PDF, 2.11 MB

english, 2017

34

The Key Role of Temperature and Lipid Composition in Modulating the Intake of Gold Nanoparticles into the Plasma Membrane

Lolicato, Fabio, Joly, Loic, Martinez-Seara Monne, Hector, Fragneto, Giovanna, Akola, Jaakko, Maccarini, Marco, Vattulainen, Ilpo

Journal:

Biophysical Journal

Year:

2019

Language:

english

File:

PDF, 46 KB

english, 2019

35

Distinct Interactions of Sodium and Calcium Cations and Neutral Phospholipid Membranes and How to Simulate Them

Martinez-Seara, Hector, Javanainen, Matti, Melcrová, Adéla, Jurkiewicz, Piotr, Jungwirth, Pavel, Magarkar, Aniket, Hof, Martin, Melcr, Josef, Nencini, Ricky, Ollila, Samuli O.

Journal:

Biophysical Journal

Year:

2019

Language:

english

File:

PDF, 70 KB

english, 2019

36

Rapid Diffusion of Cholesterol Along Polyunsaturated Membranes via Deep Dives

Javanainen, Matti, Martinez-Seara, Hector

Journal:

Physical Chemistry Chemical Physics

Year:

2019

Language:

english

File:

PDF, 2.95 MB

english, 2019

37

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

38

Rapid Diffusion of Cholesterol Along Polyunsaturated Membranes via Deep Dives

Javanainen, Matti, Martinez-Seara, Hector

Journal:

Physical Chemistry Chemical Physics

Year:

2019

File:

PDF, 2.95 MB

2019

39

Simulation of Raman and Raman optical activity of saccharides in solution

Palivec, Vladimír, Kopecký, Vladimír, Jungwirth, Pavel, Bouř, Petr, Kaminský, Jakub, Martinez-Seara, Hector

Journal:

Physical Chemistry Chemical Physics

Year:

2020

Language:

english

File:

PDF, 5.35 MB

english, 2020

40

Benefits of the Electronic Continuum Correction in Bio-Force Fields

Nencini, Ricky, Palivec, Vladimir, Tempra, Carmelo, Delcroix, Pauline, Ollila, Samuli O., Javanainen, Matti, Jungwirth, Pavel, Martinez-Seara, Hector

Journal:

Biophysical Journal

Year:

2020

File:

PDF, 43 KB

2020

41

Rotational Diffusion of Membrane Proteins in Crowded Membranes

Javanainen, Matti, Ollila, O.H. Samuli, Martinez-Seara, Hector

Journal:

Journal of Physical Chemistry B

Year:

2020

Language:

english

File:

PDF, 4.00 MB

english, 2020

42

Obtaining 3D Atomistic Structure of Saccharides from Raman/ROA/NMR Spectroscopic Techniques

Palivec, Vladimir, Bour, Petr, Jungwirth, Pavel, Kaminsky, Jakub, Martinez-Seara, Hector

Journal:

Biophysical Journal

Year:

2020

File:

PDF, 40 KB

2020

43

A practical guide to biologically relevant molecular simulations with charge scaling for electronic polarization

DubouÃ©-Dijon, E., Javanainen, M., Delcroix, P., Jungwirth, P., Martinez-Seara, H.

Journal:

The Journal of Chemical Physics

Year:

2020

File:

PDF, 2.83 MB

2020