Search filters

List of works by Tomasz Rog

A Perspective: Active Role of Lipids in Neurotransmitter Dynamics

scientific article published on 08 October 2019

A computational study suggests that replacing PEG with PMOZ may increase exposure of hydrophobic targeting moiety

scientific article published on 8 March 2017

Analysis of Twisting of Cellulose Nanofibrils in Atomistic Molecular Dynamics Simulations

article

Analysis of cause of failure of new targeting peptide in PEGylated liposome: molecular modeling as rational design tool for nanomedicine

article

Antidepressant drugs act by directly binding to TRKB neurotrophin receptors

scientific article published on 18 February 2021

Association of lipidome remodeling in the adipocyte membrane with acquired obesity in humans

scientific article

Atomic-scale structure and electrostatics of anionic palmitoyloleoylphosphatidylglycerol lipid bilayers with Na+ counterions

scientific article

Atomistic Molecular Dynamics Simulations of Mitochondrial DNA Polymerase γ: Novel Mechanisms of Function and Pathogenesis

scientific article published on 16 February 2017

Atomistic determinants of co-enzyme Q reduction at the Qi-site of the cytochrome bc1 complex

scientific article published on 26 September 2016

Atomistic simulations indicate cardiolipin to have an integral role in the structure of the cytochrome bc1 complex

scientific article published on 23 March 2013

Behavior of 2,6-bis(decyloxy)naphthalene inside lipid bilayer

scientific article

Bobbing of Oxysterols: Molecular Mechanism for Translocation of Tail-Oxidized Sterols through Biological Membranes.

scientific article published on 13 February 2018

Building Synthetic Sterols Computationally - Unlocking the Secrets of Evolution?

scientific article

Calcium Assists Dopamine Release by Preventing Aggregation on the Inner Leaflet of Presynaptic Vesicles

scientific article published on 6 February 2017

Calcium Directly Regulates Phosphatidylinositol 4,5-Bisphosphate Headgroup Conformation and Recognition

scientific article published on 08 February 2017

Cholesterol Protects the Oxidized Lipid Bilayer from Water Injury: An All-Atom Molecular Dynamics Study

scientific article published on 17 March 2018

Cholesterol Reduces Partitioning of Antifungal Drug Itraconazole into Lipid Bilayers

scientific article published on 05 March 2020

Cholesterol effects on a mixed-chain phosphatidylcholine bilayer: a molecular dynamics simulation study

scientific article published on 7 November 2005

Cholesterol effects on the phosphatidylcholine bilayer polar region: a molecular simulation study

scientific article published on March 2000

Cholesterol effects on the phospholipid condensation and packing in the bilayer: a molecular simulation study

scientific article published in July 2001

Cholesterol induces specific spatial and orientational order in cholesterol/phospholipid membranes

scientific article (publication date: 17 June 2010)

Cholesterol level affects surface charge of lipid membranes in saline solution

scientific article

Cholesterol modulates glycolipid conformation and receptor activity

Cholesterol oxidation products and their biological importance

scientific article published on 5 March 2016

Cholesterol under oxidative stress—How lipid membranes sense oxidation as cholesterol is being replaced by oxysterols

scientific article published on 17 March 2015

Cholesterol, sphingolipids, and glycolipids: what do we know about their role in raft-like membranes?

scientific article

Cholesterol-sphingomyelin interactions: a molecular dynamics simulation study

scientific article

Cholesteryl Hemisuccinate Is Not a Good Replacement for Cholesterol in Lipid Nanodiscs

scientific article published on 12 November 2019

Cis and trans unsaturated phosphatidylcholine bilayers: A molecular dynamics simulation study

article

Co-exposure with fullerene may strengthen health effects of organic industrial chemicals

scientific article

Comparison of cholesterol and its direct precursors along the biosynthetic pathway: effects of cholesterol, desmosterol and 7-dehydrocholesterol on saturated and unsaturated lipid bilayers

scientific article

Complex Behavior of Phosphatidylcholine-Phosphatidic Acid Bilayers and Monolayers: Effect of Acyl Chain Unsaturation

scientific article published on 16 April 2019

Data including GROMACS input files for atomistic molecular dynamics simulations of mixed, asymmetric bilayers including molecular topologies, equilibrated structures, and force field for lipids compatible with OPLS-AA parameters

scientific article

Dehydroergosterol as an Analogue for Cholesterol: Why It Mimics Cholesterol So Well—or Does It?

Design of cholesterol arabinogalactan anchored liposomes for asialoglycoprotein receptor mediated targeting to hepatocellular carcinoma: In silico modeling, in vitro and in vivo evaluation

scientific article published on 23 May 2016

Deuteration of water enables self-organization of phospholipid-based reverse micelles

scientific article

Distribution and dynamics of quinones in the lipid bilayer mimicking the inner membrane of mitochondria

scientific article published on 21 June 2016

Drug-Lipid Membrane Interaction Mechanisms Revealed Through Molecular Simulations

Dynamics of water at membrane surfaces: Effect of headgroup structure

scientific article published in September 2006

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

article by Hector Martinez-Seara et al published September 2007 in Journal of Physical Chemistry

Effect of Galactosylceramide on the Dynamics of Cholesterol-Rich Lipid Membranes

article

Effect of PEGylation on Drug Entry into Lipid Bilayer

Effect of Phosphatidic Acid on Biomembrane: Experimental and Molecular Dynamics Simulations Study

scientific article published on 23 July 2015

Effect of piroxicam on lipid membranes: Drug encapsulation and gastric toxicity aspects

scientific article

Effect of sphingomyelin headgroup size on molecular properties and interactions with cholesterol

scientific article

Effects of Membrane PEGylation on Entry and Location of Antifungal Drug Itraconazole and Their Pharmacological Implications

scientific article published on 24 February 2017

Effects of phospholipid unsaturation on the bilayer nonpolar region: a molecular simulation study

scientific article published in November 2003

Effects of phospholipid unsaturation on the membrane/water interface: a molecular simulation study

scientific article published on July 2001

Effects of the Lipid Bilayer Phase State on the Water Membrane Interface

Enzymatic oxidation of cholesterol: properties and functional effects of cholestenone in cell membranes

scientific article

Experimental determination and computational interpretation of biophysical properties of lipid bilayers enriched by cholesteryl hemisuccinate

scientific article published on 25 October 2014

Functionalized lipids and surfactants for specific applications

scientific article published on 2 March 2016

Glycolipid membranes through atomistic simulations: effect of glucose and galactose head groups on lipid bilayer properties.

scientific article published on 3 August 2007

Glycosylation and Lipids Working in Concert Direct CD2 Ectodomain Orientation and Presentation

scientific article

How To Minimize Artifacts in Atomistic Simulations of Membrane Proteins, Whose Crystal Structure Is Heavily Engineered: β₂-Adrenergic Receptor in the Spotlight.

scientific article

How anacetrapib inhibits the activity of the cholesteryl ester transfer protein? Perspective through atomistic simulations

scientific article (publication date: November 2014)

How endoglucanase enzymes act on cellulose nanofibrils: role of amorphous regions revealed by atomistic simulations

How to tackle the issues in free energy simulations of long amphiphiles interacting with lipid membranes: convergence and local membrane deformations.

scientific article

How well does cholesteryl hemisuccinate mimic cholesterol in saturated phospholipid bilayers?

Identifying involvement of Lys251/Asp252 pair in electron transfer and associated proton transfer at the quinone reduction site of Rhodobacter capsulatus cytochrome bc1.

scientific article published on 12 July 2016

Indocyanine Green-Loaded Liposomes for Light-Triggered Drug Release

scientific article published on 20 April 2016

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

scientific article

Influence of the disulfide bond configuration on the dynamics of the spin label attached to cytochrome c.

scientific article

Interaction of hematoporphyrin with lipid membranes

scientific article published on 16 April 2012

Interdigitation of long-chain sphingomyelin induces coupling of membrane leaflets in a cholesterol dependent manner

scientific article published on 2 December 2015

Interplay of unsaturated phospholipids and cholesterol in membranes: effect of the double-bond position

scientific article

Key role of water in proton transfer at the Qo-site of the cytochrome bc1 complex predicted by atomistic molecular dynamics simulations.

scientific article published on 18 February 2013

Lateral Diffusion in Lipid Membranes through Collective Flows

article

Lateral sorting in model membranes by cholesterol-mediated hydrophobic matching.

scientific article

Lipid membranes: Theory and simulations bridged to experiments

scientific article published on 14 June 2016

Lipid simulations: a perspective on lipids in action

scientific article published on April 2011

Long-chain GM1 gangliosides alter transmembrane domain registration through interdigitation

scientific article published on 28 January 2017

Mechanism for translocation of fluoroquinolones across lipid membranes

Membrane bound COMT isoform is an interfacial enzyme: general mechanism and new drug design paradigm

scientific article published on 15 February 2018

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

scientific article published on 15 June 2020

Mitochondrial Membranes with Mono- and Divalent Salt: Changes Induced by Salt Ions on Structure and Dynamics

article

Molecular Dynamics Simulation of Inverse-Phosphocholine Lipids

article

Molecular Dynamics Simulation of PEGylated Bilayer Interacting with Salt Ions: A Model of the Liposome Surface in the Bloodstream

article

Molecular Dynamics Simulation of PEGylated Membranes with Cholesterol: Building Toward the DOXIL Formulation

article

Molecular Dynamics Simulations of Lipid Bilayers: Simple Recipe of How to Do It ⬇️

scientific article published on January 1, 2013

Molecular Dynamics Simulations of the Bacterial ABC Transporter SAV1866 in the Closed Form

article

Molecular dynamics simulations of the enzyme catechol-O-methyltransferase: methodological issues.

scientific article

Molecular dynamics simulations reveal fundamental role of water as factor determining affinity of binding of beta-blocker nebivolol to beta(2)-adrenergic receptor

scientific article published in July 2010

Molecular dynamics study of prolyl oligopeptidase with inhibitor in binding cavity.

scientific article

Molecular dynamics, crystallography and mutagenesis studies on the substrate gating mechanism of prolyl oligopeptidase

scientific article

Molecular lipidomics of exosomes released by PC-3 prostate cancer cells

scientific article published on July 2013

Multiscale Simulations of Biological Membranes: The Challenge To Understand Biological Phenomena in a Living Substance

scientific article published on 12 March 2019

N- and O-methylation of sphingomyelin markedly affects its membrane properties and interactions with cholesterol

N-Glycosylation as determinant of epidermal growth factor receptor conformation in membranes

scientific article

Non-polar interactions between cholesterol and phospholipids: a molecular dynamics simulation study

scientific article published in February 2004

Nonpolar interactions between trans-membrane helical EGF peptide and phosphatidylcholines, sphingomyelins and cholesterol. Molecular dynamics simulation studies

scientific article published in April 2008

Ordering effects of cholesterol and its analogues

scientific article published on 10 September 2008

PEGylated Liposomes as Carriers of Hydrophobic Porphyrins

article published in 2015

PIP2 and Talin Join Forces to Activate Integrin

article

Parameterization of the prosthetic redox centers of the bacterial cytochrome bc 1 complex for atomistic molecular dynamics simulations

article

Phosphatidylethanolamine-phosphatidylglycerol bilayer as a model of the inner bacterial membrane

scientific article published on 19 November 2004

Properties of the Membrane Binding Component of Catechol-O-methyltransferase Revealed by Atomistic Molecular Dynamics Simulations

article

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

scientific article

Redox-induced activation of the proton pump in the respiratory complex I.

scientific article

Refined OPLS all-atom force field for saturated phosphatidylcholine bilayers at full hydration

scientific article published on 18 April 2014

Replacing the cholesterol hydroxyl group with the ketone group facilitates sterol flip-flop and promotes membrane fluidity

scientific article published on 25 January 2008

Rigorous computational study reveals what docking overlooks: Double trouble from membrane association in protein kinase C modulators

scientific article published on 11 September 2020

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

scientific article published on 01 March 2009

Role of glycolipids in lipid rafts: a view through atomistic molecular dynamics simulations with galactosylceramide

scientific article published in June 2010

Role of phosphatidylglycerols in the stability of bacterial membranes

scientific article published on 08 March 2008

Role of sterol type on lateral pressure profiles of lipid membranes affecting membrane protein functionality: Comparison between cholesterol, desmosterol, 7-dehydrocholesterol and ketosterol

scientific article published on 01 February 2007

Role of subunit III and its lipids in the molecular mechanism of cytochrome c oxidase

scientific article published on 17 April 2015

Selective effect of cell membrane on synaptic neurotransmission

scientific article

Significance of cholesterol methyl groups

scientific article

Significance of sterol structural specificity. Desmosterol cannot replace cholesterol in lipid rafts

scientific article

Stearic Acid Spin Labels in Lipid Bilayers: Insight through Atomistic Simulations

Strong preferences of dopamine and l-dopa towards lipid head group: importance of lipid composition and implication for neurotransmitter metabolism

article

Study of Interaction Between PEG Carrier and Three Relevant Drug Molecules: Piroxicam, Paclitaxel, and Hematoporphyrin

Study of PEGylated Lipid Layers as a Model for PEGylated Liposome Surfaces: Molecular Dynamics Simulation and Langmuir Monolayer Studies

article

Syndecan-4 tunes cell mechanics by activating the kindlin-integrin-RhoA pathway

scientific article published on 06 January 2020

Tail-Oxidized Cholesterol Enhances Membrane Permeability for Small Solutes

scientific article published on 17 August 2020

Tat(48-60) peptide amino acid sequence is not unique in its cell penetrating properties and cell-surface glycosaminoglycans inhibit its cellular uptake

scientific article

The Integrin Receptor in Biologically Relevant Bilayers: Insights from Molecular Dynamics Simulations. ⬇️

scientific article published on 27 July 2016

The biophysical properties of ethanolamine plasmalogens revealed by atomistic molecular dynamics simulations

scientific article published on 30 October 2015

The challenges of understanding glycolipid functions: An open outlook based on molecular simulations

scientific article published on 07 January 2014

The dynamics of water at the phospholipid bilayer surface: a molecular dynamics simulation study

article

Tilt: Major Factor in Sterols' Ordering Capability in Membranes

Topologies, structures and parameter files for lipid simulations in GROMACS with the OPLS-aa force field: DPPC, POPC, DOPC, PEPC, and cholesterol

scientific article

Toward Atomistic Resolution Structure of Phosphatidylcholine Headgroup and Glycerol Backbone at Different Ambient Conditions

scientific article

Transient Ordered Domains in Single-Component Phospholipid Bilayers

scientific article published in Physical Review Letters

Use of Umbrella Sampling to Calculate the Entrance/Exit Pathway for Z-Pro-Prolinal Inhibitor in Prolyl Oligopeptidase

scientific article

Water isotope effect on the phosphatidylcholine bilayer properties: a molecular dynamics simulation study

scientific article published in February 2009

What happens if cholesterol is made smoother: importance of methyl substituents in cholesterol ring structure on phosphatidylcholine-sterol interaction

scientific article published on 9 February 2007

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 (O

scientific article published in June 2009

doGlycans-Tools for Preparing Carbohydrate Structures for Atomistic Simulations of Glycoproteins, Glycolipids, and Carbohydrate Polymers for GROMACS.

scientific article published on 14 September 2017

nMoldyn: a program package for a neutron scattering oriented analysis of molecular dynamics simulations.

scientific article

Paulina is supported by:

About Paulina

Help