Charged small molecule binding to membranes in MD simulations evaluated against NMR experiments
R. Nencini and O.H. Samuli Ollila
Journal of Physical Chemistry B, accepted (2022)
Emerging Era of Biomolecular Membrane Simulations: Automated Physically-Justified Force Field Development and Quality-Evaluated Databanks
H. Antila, B. Kav, M. S. Miettinen, H. Martinez-Seara, P. Jungwirth, and O. H. Samuli Ollila
Journal of Physical Chemistry B, 126 4169 (2022)
Accurate Simulations of Lipid Monolayers Require a Water Model With Correct Surface Tension
C. Tempra, O. H. Samuli Ollila, and M. Javanainen
Journal of Chemical Theory and Computation, 18 1862 (2022)
Rotational decoupling between the hydrophilic and hydrophobic regions in lipidmembranes
H. Antila, A. Wurl, O. H. Samuli Ollila, M. S. Miettinen and T. M. Ferreira
Biophysical Journal, 121 68 (2022)
Inverse Conformational Selection in Lipid–Protein Binding
A. Bacle, P. Buslaev, R. Garcia-Fandino, F. Favela-Rosales, T. M. Ferreira, P. F. J. Fuchs, I. Gushchin, M. Javanainen, A. M. Kiirikki, J. J. Madsen, J. Melcr, P. M. Rodríguez, M. S. Miettinen, O. H. Samuli Ollila, C. G. Papadopoulos, A. Peón, T. J. Piggot, A. Pineiro, and S. I. Virtanen
Journal of American Chemical Society 143, 13701–13709 (2021)
Using open data to rapidly benchmark biomolecular simulations: Phospholipid conformational dynamics
H. S. Antila, T. M. Ferreira, O. H. Samuli Ollila, M. S. Miettinen
Journal of chemical information and modeling 61, 938-949 (2021)
The Convergence of the Hedgehog/Intein Fold in Different Protein Splicing Mechanisms
H. M. Beyer, S. I. Virtanen, A. S. Aranko, K. M. Mikula, G. T. Lountos, A. Wlodawer, O. H. Samuli Ollila and H. Iwaï
International Journal of Molecular Sciences, 21, 8367 (2020)
Heterogeneous dynamics in partially disordered proteins
S. I. Virtanen, A. M. Kiirikki, K. M. Mikula, H. Iwaı ̈and O. H. Samuli Ollila
Physical Chemistry Chemical Physics, 22, 21185-21196 (2020)
Rotational Diffusion of Membrane Proteins in Crowded Membrane
M. Javanainen, O. H. Samuli Ollila and H. Martinez-Seara
The Journal of Physical Chemistry B, 124, 2994-3001 (2020)
NMR structure and dynamics of TonB investigated by scar-less segmental isotopic labeling using a salt-inducible split intein
A. Ciragan, S. M. Backlund, K. M. Mikula, H. M. Beyer, O. H. Samuli Ollila and H. Iwaı̈
Frontiers in Chemistry, 8, 136 (2020)
Improved Cation Binding to Lipid Bilayer with Negatively Charged POPS by Effective Inclusion of Electronic Polarization
J. Melcr, T. M. Ferreira, P. Jungwirth and O.H. Samuli Ollila
J. Chem. Theory Comp., 16, 738-748 (2020)
Headgroup Structure and Cation Binding in Phosphatidylserine Lipid Bilayers
H. S. Antila, P. Buslaev, F. Favela-Rosales, T. M. Ferreira, I. Gushchin, M. Javanainen, B. Kav,
J. J. Madsen, J. Melcr, M. S. Miettinen, J. Määttä, R. Nencini, O.H. Samuli Ollila and T. J. Piggot
J. Phys. Chem. B, 123, 9066-9079 (2019)
Sharing Data from Molecular Simulations
M. J. Abraham, R. P. Apostolov, J. Barnoud, P. Bauer, C. Blau, A. Bonvin, M. Chavent,
J. D. Chodera, K. Č. Čondić-Jurkić, L. Delemotte, H. Grubmüller, R. J. Howard, E. J. Jordan,
E. Lindal, O.H. Samuli Ollila, J. Selent, D. Smith, P. J. Stansfeld, J. Tiemann, M. Trellet, C. J. Woods, A. Zhmurov
J Chem. Inf. Model, 59, 4093-4099 (2019)
NMR structure of the C-terminal domain of TonB protein from Pseudomonas aeruginosa.
J. S. Oeemig, O. H. S. Ollila and H. Iwaï
PeerJ, 6:e5412, DOI:10.7717/peerj.5412 (2018)
Rotational Dynamics of Proteins from Spin Relaxation Times and Molecular Dynamics Simulations
O.H. S. Ollila, H. A. Heikkinen and H. Iwaï
J. Phys. Chem. B, 122, 6559-6569 (2018)
Accurate Binding of Sodium and Calcium to a POPC Bilayer by Effective Inclusion of Electronic Polarization
J. Melcr, H. Martinez-Seara, R. Nencini, J. Kolafa, P. Jungwirth and O. H. S. Ollila
J. Phys. Chem. B, 122, 4546-4557 (2018)
Calcium Sensing by Recoverin: Effect of Protein Conformation on Ion Affinity
S. Timr, J. Kadlec, P. Srb, O. H. S. Ollila and P. Jungwirth
J. Phys. Chem. Lett., 9, 1613-1619 (2018)
Atomistic Model for Near-Quantitative Simulations of Langmuir Monolayers
M. Javanainen, A. Lamberg, L. Cwiklik, I. Vattulainen, and O.H. S. Ollila
Langmuir, 34, 2565-2572 (2018)
Molecular electrometer and binding of cations to phospholipid bilayers
A. Catte, M. Girych,M. Javanainen, C. Loison, J. Melcr, M. S. Miettinen, L. Monticelli,
J. Määttä, V. S. Oganesyan, O. H. S. Ollila, J. Tynkkynen and S. Vilov
Physical Chemistry Chemical Physics, 18, 32560 (2016)
Acyl chain disorder and azelaoyl orientation in lipid membranes containing oxidized lipids
T. M. Ferreira, R Sood, R. Bärenwald, G. Carlström, D. Topgaard,
K. Saalwächter, P. K. J. Kinnunen and O. H. S. Ollila
Langmuir, 32, 6524 (2016)
Atomistic resolution structure and dynamics of lipid bilayers in simulations and experiments
O. H. S. Ollila and G. Pabst
Biochimica et Biophysica Acta (BBA) - Biomembranes, 1858, 2512 (2016)
Toward atomistic resolution structure of phosphatidylcholine headgroup
and glycerol backbone at different ambient conditions
A. Botan, F. Favela-Rosales, P. Fuchs, M. Javanainen, Matej Kanduc, W. Kulig,
A. Lamberg, C. Loison, A. Lyubartsev, M. S. Miettinen, L. Monticelli, J. Määttä,
O. H. S. Ollila, M. Retegan, T. Rog, H. Santuz and J. Tynkkynen
The Journal of Physical Chemistry B, 119, 15075 (2015)
Model-free estimation of the effective correlation time for C-H bond reorientation in
amphiphilic bilayers: 1H-13C solid-state NMR and MD simulations
T. M. Ferreira, O. H. S. Ollila, R. Pigliapochi, A. P. Dabkowska, and D. Topgaard
The Journal of Chemical Physics, 142, 044905 (2015)
Comment on "Structural Properties of POPC Monolayers under Lateral Compression:
Computer Simulations Analysis"
A. Lamberg and O. H. S. Ollila
Langmuir, 31, 886-887 (2015)
Can pyrene probes be used to measure lateral pressure proles of lipid
membranes? Perspective through atomistic simulations
M. Dekany Franova, I. Vattulainen and O. H. S. Ollila
Biochimica et Biophysica Acta (BBA) - Biomembranes, 1838, 1406-1411 (2014)
Molecular conformation and bilayer pores in a nonionic surfactant lamellar phase studied
with 1H-13C solid-state NMR and molecular dynamics simulations
T. M. Ferreira, D. Topgaard and O. H. S. Ollila
Langmuir, 30, 461-469 (2014)
1H-13C CP and INEPT in a glass-forming lamellar liquid crystal with
dynamics from nano- to milliseconds
A. Nowacka, N. Bongartz, O. H. S. Ollila, T. Nylander, and D. Topgaard
Journal of Magnetic Resonance, 230, 165-175 (2013)
Interfacial properties of high density liporotein-like
lipid droplets with different lipid and apoA-I compositions
A. Koivuniemi, M. Sysi-Aho, M. Oresic and O. H. S. Ollila
Biophysical Journal, 104, 2193-2201 (2013)
1H-13C NMR studies and MD simulations of lipid bilayer order
in 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine membranes containing cholesterol
T. M. Ferreira, F. Coreta-Gomes, O. H. S. Ollila, M. J. Moreno, W. L. C. Vaz, and D. Topgaard
Physical Chemistry Chemical Physics, 15, 1976-1989 (2013)
Interfacial Tension and Surface Pressure of High Density Lipoprotein,
Low Density Lipoprotein, and Related Lipid Droplets
O. H. S. Ollila, A. Lamberg, M. Lehtivaara, A. Koivuniemi, and I. Vattulainen
Biophysical Journal, 103, 1236-1244 (2012)
Protein shape change has a major effect on the gating energy of a mechanosensitive channel
O. H. S. Ollila, M. Louhivuori, S. J. Marrink, and I. Vattulainen
Biophysical Journal, 100, 1651-1659 (2011)
Lateral pressure proles in Lipid Membranes: Dependence on molecular composition
in Molecular Simulations and Biomembranes: From Biophysics to Function
edited by M. Sansom and P. Biggin, Royal Society of Chemistry (2010)
O. H. S. Ollila and I. Vattulainen
Membrane simulations mimicking acidic pH reveal increased thickness and negative
curvature in a bilayer consisting of lysophosphatidylcholines and free fatty acids
K. Lähdesmäki, O. H. S. Ollila, A. Koivuniemi, P. T. Kovanen, M. T. Hyvönen
Biochimica et Biophysica Acta (BBA) - Biomembranes, 1798, 938-946 (2010)
3D Pressure Field in Lipid Membranes and Membrane-Protein Complexes,
O. H. S. Ollila, H. J. Risselada, M. Louhivuori, E. Lindahl, I. Vattulainen and S. J. Marrink
Physical Review Letters 102,078101 (2009)
Infuence of Ethanol on Lipid Membranes: From Lateral Pressure Proles to
Dynamics and Partitioning.
E. Terama, O. H. S. Ollila, E. Salonen, A. Rowat, C. Trandum, P. Westh, M. Patra,
M. Karttunen, and I. Vattulainen.
Journal of Physical Chemistry B 112, 4131-4139 (2008).
Polyunsaturation in lipid membranes - dynamic properties and
lateral pressure proles.
O. H. S. Ollila, M.T. Hyvönen, and I. Vattulainen,
Journal of Physical Chemistry B 111, 3139-3150 (2007)
Role of sterol type on lateral pressure proles of lipid
membranes affecting membrane protein functionality: Comparison
between cholesterol, desmosterol, 7-dehydrocholesterol and
ketosterol.
O. H. S. Ollila, T. Rog, M. Karttunen, and I. Vattulainen,
Journal of Structural Biology 159, 311-323 (2007)
Assessing the Nature of Lipid Raft Membranes
P. Niemelä, O. H. S. Ollila, M.T. Hyvönen, M. Karttunen, and I. Vattulainen,
PLoS Computational Biology 3, 304-312 (2007)
Free Volume Properties of Sphingomyelin, DMPC, DPPC, and PLPC Bilayers.
M. Kupiainen, E. Falck, S. Ollila, P. Niemelä, A. Gurtovenko,
M.T. Hyvönen, M. Patra, M. Karttunen, and I. Vattulainen,
Journal of Computational and Theoretical Nanoscience 2, 401-413 (2005)
Beyond open access: the changing culture of producing and disseminating scientic knowledge
H. Laine, L. Lahti, A. Lehto, O. H. S. Ollila and M. Miettinen
AcademicMindTrek '15 Proceedings of the 19th International Academic Mindtrek Conference,
Pages 202-205, Tampere, Finland, September 22-24, 2015
Response of the hydrophilic part of lipid membranes to changing conditions -
a critical comparison of simulations to experiments.
O. H. Samuli Ollila,
arXiv:1309.2131v1 (2013)
This publication initiated the NMRlipids project.
Lateral pressure in lipid membranes and its role
in function of membrane proteins
O. H. Samuli Ollila,
Ph.D. Thesis, Tampere University of Technology (2010)
Lateral Pressure Prole Calculations of Lipid Membranes
from Atomic Scale Molecular Dynamics Simulations
O. H. Samuli Ollila,
Master Thesis, Helsinki University of Technology (2006)