Biology subjects

Karttunen, M.

Publications and source records attributed to Karttunen, M..

15 recordsLinked to original sources

bioRxiv2026

Impact of viral membrane oxidation on SARS-CoV-2 spike protein transmembrane anchoring stability

Reactive oxygen species generated during inflammation can oxidize viral envelope lipids, with outcomes ranging from modulated infectivity to viral inactivation. For SARS-CoV-2, the molecular mechanisms by which membrane lipid oxidation influences spike protein anchoring remain poorly understood. We use all-atom molecular dynamics (MD) simulations to quantify how graded oxidation of 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine (POPC) affects the anchoring of the SARS-CoV-2 spike transmembrane (TM) region in an endoplasmic-reticulum-Golgi intermediate compartment (ERGIC)-like multicomponent membrane. Viral envelopes containing 0, 25, 50, 75, and 100% oxidized POPC (PoxnoPC) corresponding to 0 - 55% oxidation of all PO-type phospholipids were simulated with the spike TM helix and cytoplasmic tail embedded in a POPC/POPE/POPI/POPS/cholesterol mixture. Steered MD and umbrella sampling were used to calculate the potential of mean force (PMF) for extracting the TM+CT region along the membrane normal. Partial oxidation (25 - 75% POPC) produced reductions in the detachment barrier that were not statistically distinguishable from the native system within the sampling uncertainty, whereas full POPC oxidation lowered the anchoring free energy by about 23% (from 606 {+/-} 39 to 464 {+/-} 38 kJ mol-1), indicating that oxidation of roughly half of the glycerophospholipids can measurably weaken spike-membrane coupling. Despite this reduction, the remaining barrier (about 180kBT ) is still large, suggesting that oxidation alone may be insufficient for spontaneous spike detachment and likely acts synergistically with mechanical forces during fusion or immune engagement. Analysis of acyl-chain order parameters, area per lipid, membrane thickness, number-density profiles, and lateral lipid clustering reveals that POPC peroxidation decreases lipid order, thins and softens the bilayer, and disrupts cholesterol-stabilized clusters that refer to large cooperative lipid assemblies (>10 lipids) identified via RDF-based clustering. These oxidation-induced changes reduce hydrophobic matching around the TM helix and facilitate its extraction from the viral envelope. Our results provide a mechanistic link between lipid peroxidation, membrane nanostructure, and spike anchoring, supporting lipid oxidation for example during cold atmospheric plasma or ozone treatment as a physically grounded contributing antiviral mechanism against SARS-CoV-2.

biochemistry↗

bioRxiv2025

STIP1/HOP Promotes the Formation of Cytotoxic α-Synuclein Oligomers

The accumulation of alpha-synuclein (a-Syn) as toxic oligomers, and subsequently in Lewy bodies, is a pathological hallmark of Parkinsons disease (PD) and other synucleinopathies. Molecular chaperones and co-chaperones are expected to act in concert to maintain physiological activities of proteins, including a-Syn, but in neurodegeneration this process can become mal-adaptive. Transcript levels of Stress inducible phosphoprotein 1 (STIP1), a co-chaperone of Hsp90/Hsp70, are elevated in brain samples from PD patients. In synucleinopathy mouse models, STIP1 has unexpected bidirectional effects on a-Syn, with overexpression of STIP1 aggravating a-Syn toxicity, whereas knockdown of STIP1 improves toxicity and behavioural phenotypes. However, it is unclear how STIP1 enhances the toxicity of a-Syn. Here we unravel the mechanisms by which the direct interaction between STIP1/HOP and a-Syn regulates the neurotoxicity of a-Syn. Specifically, two binding motifs in the C-terminus of a-Syn directly interact with the TPR2A domain of STIP1/HOP in a dynamic manner, competing for a shared interface on TPR2A. Binding of STIP1/HOP to a-Syn attenuates the formation of a-Syn fibrils while promoting the accumulation of high molecular weight amorphous a-Syn species. Samples of a-Syn aggregated in the presence of STIP1/HOP contain significantly more A11-positive oligomeric species and cause a greater reduction in cell viability than a-Syn aggregated in the absence of STIP1/HOP in neuronal cells. Our results provide a mechanism by which the direct interaction between STIP1/HOP and the C-terminus of a-Syn promotes the formation of cytotoxic, non-amyloidogenic, high molecular weight a-Syn species. Our model offers an explanation for the unexpected pathological link between STIP1 and a-Syn toxicity, thus opening new therapeutic avenues for the treatment of synucleinopathies.

biochemistry↗

bioRxiv2022

Identification of Catechins Binding Pockets in Monomeric Aβ42 Through Ensemble Docking and MD Simulations

The assembly of the Amyloid-{beta} peptide (A{beta}) into toxic oligomers and fibrils is associated with Alzheimers disease and dementia. Therefore, disrupting amyloid assembly by direct targeting of the A{beta} monomeric form with small molecules or antibodies is a promising therapeutic strategy. However, given the dynamic nature of A{beta}, standard computational tools cannot be easily applied for high-throughput structure-based virtual screening in drug discovery projects. In the current study, we propose a computational pipeline - in the framework of the ensemble docking strategy - to identify catechins binding pockets in monomeric A{beta}42. It is shown that both hydrophobic aromatic interactions and hydrogen bonding are crucial for the binding of catechins to A{beta}42. Also, it has been found that all the studied ligands, especially the EGCG, can act as potent inhibitors against amyloid aggregation by blocking the central hydrophobic region of the A{beta}. Our findings are evaluated and confirmed with multi-microsecond MD simulations. Finally, it is suggested that our proposed pipeline, with low computational cost in comparison with MD simulations, is a suitable approach for the virtual screening of ligand libraries against A{beta}.

biophysics↗

bioRxiv2021

The structure of the enigmatic ripple phase in saturated bilayers resolved: Machine learning reveals four lipid populations

A new mixed radial-angular, three-particle correlation function method in combination with unsupervised machine learning (ML) was applied to examine the emergence of the ripple phase in dipalmitoyphosphatidylcholine (DPPC) lipid bilayers using data from atomistic molecular dynamics (MD) simulations of system sizes ranging from 128 to 4,096 lipids. Based on the acyl tail conformations, the analysis revealed the presence of four distinct conformational populations of lipids in the ripple phases of the DPPC lipid bilayers. The expected gel- (ordered; Lo) and fluid-like (disordered; Ld) lipids are found along with their splayed tail equivalents (Lo,s and Ld,s). These lipids differ based on their gauche distribution and tail packing. The disordered (Ld) and disordered splayed (Ld,s) lipids spatially cluster in the ripple in the groove side, that is, in an asymmetric manner across the bilayer leaflets. The ripple phase does not contain large numbers of Ld lipids, instead they only exist on the interface of the groove side of the undulation. The bulk of the groove side is a complex coexistence of Lo, Lo,s and Ld,s lipids. The convex side of the undulation contains predominantly Lo lipids. Thus, the structure of the ripple phase is neither a simple coexistence of ordered and disordered lipids nor a coexistence of ordered interdigitating gel-like (Lo) and ordered splayed (Lo,s) lipids, but instead a coexistence of an ordered phase and a complex mixed phase. Principal component analysis (PCA) further confirmed the existence of the four lipid groups.

biophysics↗

bioRxiv2021

A multiscale computational study of the conformation of the full-length intrinsically disordered protein MeCP2

The malfunction of the Methyl CpG binding protein 2 (MeCP2) is associated to the Rett syndrome, one of the most common causes of cognitive impairment in females. MeCP2 is an intrinsically disordered protein (IDP), making its experimental characterization a challenge. There is currently no structure available for the full-length MeCP2 in any of the databases, and only the structure of its MBD domain has been solved. We used this structure to build a full-length model of MeCP2 by completing the rest of the protein via ab initio modelling. Using a combination of all-atom and coarse-grained simulations, we characterized its structure and dynamics as well as the conformational space sampled by the ID and TRD domains in the absence of the rest of the protein. The present work is the first computational study of the full-length protein. Two main conformations were sampled in the coarse-grained simulations: a globular structure similar to the one observed in the all-atom force field and a two-globule conformation. Our all-atom model is in good agreement with the available experimental data, predicting amino acid W104 to be buried, amino acids R111 and R133 to be solvent accessible, and having 4.1% of -helix content, compared to the 4% found experimentally. Finally, we compared the model predicted by AlphaFold to our Modeller model. The model was not stable in water and underwent further folding. Together, these simulations provide a detailed (if perhaps incomplete) conformational ensemble of the full-length MeCP2, which is compatible with experimental data and can be the basis of further studies, e.g., on mutants of the protein or its interactions with its biological partners.

biochemistry↗

bioRxiv2021

Highly similar sequence and structure yet different biophysical behaviour: A computational study of two triosephosphate isomerases

Homodimeric triosephosphate isomerases (TIM) from Trypanosoma cruzi (TcTIM) and Trypanosoma brucei (TbTIM) have a markedly similar amino acid sequences and three-dimensional structures. However, several of their biophysical parameters, such as their susceptibility to sulfhydryl agents and their reactivation speed after being denatured, have significant differences. The causes of these differences were explored with microsecond-scale molecular dynamics (MD) simulations of three different TIM proteins: TcTIM, TbTIM and a chimeric protein, Mut1. We examined their electrostatic interactions and explored the impact of simulation length on them. The same salt bridge between catalytic residues Lys 14 and Glu 98 was observed in all three proteins but key differences were found in other interactions that the catalytic amino acids form. In particular, a cation-{pi} interaction between catalytic amino acids Lys 14 and His 96, and both a salt bridge and a hydrogen bond between catalytic Glu168 and residue Arg100, were only observed in TcTIM. Furthermore, although TcTIM forms less hydrogen bonds than TbTIM and Mut1, its hydrogen bond network spans almost the entire protein, connecting the residues in both monomers. This work provides new insight on the mechanisms that give rise to the different behaviour of these proteins. The results also show the importance of long simulations.

biochemistry↗

bioRxiv2021

AlphaFold2: A role for disordered protein prediction?

The development of AlphaFold2 was a paradigm-shift in the structural biology community; herein we assess the ability of AlphaFold2 to predict disordered regions against traditional sequence-based disorder predictors. We find that a naaive use of Dictionary of Secondary Structure of Proteins (DSSP) to separate ordered from disordered regions leads to a dramatic overestimation in disorder content, and that the predicted Local Distance Difference Test (pLDDT) provides a much more rigorous metric. In addition, we show that even when used for disorder prediction, conventional predictors can outperform the pLDDT in disorder identification, and note an interesting relationship between the pLDDT and secondary structure, that may explain our observations, and hints at a broader application of the pLDDT to IDP dynamics.

bioinformatics↗

bioRxiv2021

Free energy and stacking of eumelaninnanoaggregates

Eumelanin, a member of the melanin family, is a black-brown insoluble pigment. It possesses a broad range of properties such as antioxidation, free radical scavenging, photo-protection, and charge carrier transportation. Surprisingly, the exact molecular structure of eumelanin remains undefined. It is, however, generally considered to consist of two main building blocks, 5,6-dihydroxyindole (DHI) and 5,6-dihydroxyindole carboxylic acid (DHICA). We focus on DHI and report, for the first time, a computational investigation of structural properties of DHI eumelanin aggregates in aqueous solutions. First, multi-microsecond molecular dynamics (MD) simulations at different concentrations were performed to investigate aggregation and ordering of tetrameric DHI-eumelanin protomolecules. This was followed by umbrella sampling (US) and density functional theory (DFT) calculations to study the physical mechanisms of stacking. Aggregation occurs through formation of nanoscale stacks and was observed in all systems. Further analyses showed that aggregation and coarsening of the domains is due to decrease in hydrogen bonds between the eumelanins and water; while domains exist, there is no long-range order. The results show non-covalent stacks with and interlayer distance between eumelanin protomolecules being less than 3.5 [A]. This is in good agreement with transmission electron microscopy data. Both free energy calculations and DFT revealed strong stacking interactions. The electrostatic potential map provides an explanation and a rationale for the slightly sheared relative orientations and, consequently, for the curved shapes of the nanoscale domains.

biophysics↗

bioRxiv2020

Cholesterol Sequestration by Xenon Leads to Lipid Raft Destabilization

Combined coarse-grained (CG) and atomistic molecular dynamics (MD) simulations were performed to study the interactions of xenon with model lipid rafts consisting of 1,2-dipalmitoyl-sn-glycero-3-phosphocholine (DPPC), 1,2-dilauroyl-sn-glycero-3-phosphocholine (DLPC) and cholesterol (Chol). At a concentration of 2 Xe/lipid we observed an unexpected result: Spontaneous nucleation of Xe nanoclusters which then rapidly plunged into the bilayer. In this process Chol, essential for raft stabilization, was pulled out from the raft into the hydrophobic zone. When concentration was further increased (3 Xe/lipid), the clusters disrupted both the membrane and raft. We computed the radial distribution functions, pair-wise potentials, second virial coefficients and Schlit-ter entropy to scrutinize the nature of the interactions. Our findings suggest that the well-known anaesthetic effect of Xe could be mediated by sequestration of Chol, which, in turn, compromises the stability of rafts where specialized proteins needed to produce the nervous signal are anchored.

biophysics↗

bioRxiv2020

Insights into the Polyhexamethylene Biguanide (PHMB) Mechanism of Action on Bacterial Membrane and DNA: A Molecular Dynamics Study

Polyhexamethylene biguanide (PHMB) is a cationic polymer with antimicrobial and antiviral properties. It has been commonly accepted that the antimicrobial activity is due the ability of PHMB to perforate the bacterial phospholipid membrane leading ultimately to its death. In this study we show by the means of atomistic molecular dynamics (MD) simulations that while the PHMB molecules attach to the surface of the phospholipid bilayer and partially penetrate it, they do not cause any pore formation at least within the microsecond simulation times. The polymers initially adsorb onto the membrane surface via the favourable electrostatic interactions between the phospholipid headgroups and the biguanide groups, and then partially penetrate the membrane slightly disrupting its structure. This, however, does not lead to the formation of any pores. The microsecond-scale simulations reveal that it is unlikely for PHMB to spontaneously pass through the phospholipid membrane. Our findings suggest that PHMB translocation across the bilayer may take place through binding to the phospholipids. Once inside the cell, the polymer can effectively bind to DNA through extensive interactions with DNA phosphate backbone, which can potentially block the DNA replication process or activate DNA repair pathways. TOC Graphic O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=161 SRC="FIGDIR/small/007732v1_ufig1.gif" ALT="Figure 1"> View larger version (93K): org.highwire.dtl.DTLVardef@17c8c69org.highwire.dtl.DTLVardef@1e65ceeorg.highwire.dtl.DTLVardef@df0f42org.highwire.dtl.DTLVardef@62ba9a_HPS_FORMAT_FIGEXP M_FIG C_FIG

biophysics↗

bioRxiv2020

Formation of aggregates, icosahedral structures and percolation clusters of fullerenes in lipids bilayers: The key role of lipid saturation

Carbon nanoparticles (CNPs) are attractive materials for a great number of applications but there are serious concerns regarding their influence on health and environment. Here, our focus is on the behavior of fullerenes in lipid bilayers with varying lipid saturations, chain lengths and fullerene concentrations using coarse-grained molecular dynamics (CG-MD) simulations. Our findings show that the lipid saturation level is a key factor in determining how fullerenes behave and where the fullerenes are located inside a lipid bilayer. In saturated and monounsaturated bilayers fullerenes aggregated and formed clusters with some of them showing icosahedral structures. In polyunsaturated lipid bilayers, no such structures were observed: In polyunsaturated lipid bilayers at high fullerene concentrations, connected percolation-like networks of fullerenes spanning the whole lateral area emerged at the bilayer center. In other systems only separate isolated aggregates were observed. The effects of fullerenes on lipid bilayers depend strongly on fullerene aggregation. When fullerenes aggregate, their interactions with the lipid tails change.

biophysics↗

bioRxiv2018

The role of matrix-oriented salt-bridge on the proton transport in a multimeric uncoupling protein 2

Uncoupling proteins (UCPs) are members of the mitochondrial carrier family (MCF) that transport protons across the inner mitochondrial membrane, thereby uncoupling electron transport from ATP synthesis. The stoichiometry of UCPs, and the possibility of co-existence of this protein as mono-meric and associated forms in lipid membranes remain an intriguing open question. In the current study, the tertiary structure of UCP2 was analyzed both experimentally and through molecular dynamics (MD) simulations. After recombinant expression of UCP2 in the inner membrane of E. coli, the protein was directly extracted from the bacterial membranes with a non-denaturing detergent and purified both as a pure monomer and as a mixture of monomers, dimers and tetramers. Both protein preparations were re-constituted in egg yolk lipid vesicles. Gel electrophoresis, circular dichroism spectroscopy and fluorescence methods were used to characterize the structure and the proton transport function of protein. UCP2 showed unique stable tetrameric forms in lipid bilayers. MD simulations using membrane lipids and principal component analysis support the experimental results and provided new molecular insights into the nature of noncovalent interactions in oligomeric UCP2. MD simulations indicate that UCP2 tetramers are asymmetric dimers of dimers, in which the interactions between the monomers forming the dimer are stronger than the interactions between the dimers within the tetramer. It is also shown that UCP2 has a specific tendency to form functional tetramers in lipid bilayers, capable of proton transport. The asymmetric nature of the UCP2 tetramer could act as a scaffold for regulating the activity of the monomeric units through cooperative intercommunication between these subunits. Under similar experimental conditions, the structurally comparable ADP/ATP carrier protein did not form tetramers in vesicles, implying that spontaneous tetramerization cannot be generalized to all MCF members.\n\nSTATEMENT OF SIGNIFICANCESelf-assembly of membrane proteins plays a significant role in their biological function. In this article, both experimental and computational evidence are provided for spontaneous tetramerization of one of the mitochondrial uncoupling proteins (UCP2) in model lipid membranes. It is also shown that the tetrameric form of UCP2 is capable of proton transport, which leads to regulation of ATP synthesis in mitochondrion. Molecular dynamics simulations confirm the presence of asymmetric UCP2 tetramers as a potential scaffold for regulating the activity of the monomeric units through mutual intercommunication. The outcome of this study provides a solid ground for potential co-existence of monomeric and multimeric functional forms of UCPs that contributes to a deeper molecular insight into their structure and function.

biophysics↗

bioRxiv2018

Phospholipid-Cellulose Interactions: Insight from Atomistic Computer Simulations for Understanding the Impact of Cellulose-Based Materials on Plasma Membranes

Cellulose is an important biocompatible and nontoxic polymer widely used in numerous biomedical applications. The impact of cellulose-based materials on cells and, more specifically, on plasma membranes that surround cells, however, remains poorly understood. To this end, here we performed atomic-scale molecular dynamics (MD) simulations of phosphatidylcholine (PC) and phosphatidylethanolamine (PE) bilayers interacting with the surface of a cellulose crystal. Both biased umbrella sampling and unbiased simulations clearly show the existence of strong attractive interactions between phospholipids and cellulose: the free energy of the cellulose-bilayer binding was found to be -1.89 and -1.96 kJ/mol per cellulose dimer for PC and PE bilayers, respectively. Although the values are similar, there is a pronounced difference between PC and PE bilayers. The driving force in both cases is the formation of hydrogen bonds. There are two distinct types of hydrogen bonds: 1) between the lipid head groups and the hydroxyl (hydroxymethyl) groups of cellulose, and 2) lipid-water and cellulose-water bonds. The former is the dominant component for PE systems whereas the latter dominates in PC systems. This suggests that achieving controlled binding via new cellulose modifications must pay close attention to the lipid head groups involved. The observed attractive phospholipid-cellulose interactions have a significant impact on bilayer properties: a cellulose crystal induces noticeable structural perturbations on the bilayer leaflet next to the crystal. Given that such perturbations can be undesirable when it comes to the interactions of cellulose-based materials with cell membranes, our computational studies suggest that the impact of cellulose could be reduced through chemical modification of the cellulose surface which prevents cellulose-phospholipid hydrogen bonding.

biophysics↗

bioRxiv2018

Does alpha-tocopherol flip-flop help to protect membranes against oxidation?

Alpha-tocopherols (-toc) are crucial in protecting biological membranes against oxidation by free radicals. We investigate the behavior of -toc molecules in lipid bilayers containing oxidized lipids by molecular dynamics (MD) simulations. To verify the approach, the location and orientation of -toc are first shown to be in agreement with previous experimental results. The simulations further show that -toc molecules stay inside the lipid bilayer with their hydroxyl groups in contact with the bilayer surface. Interestingly, interbilayer -toc flip-flop was observed in both oxidized and non-oxidized bilayers with significantly higher frequency in aldehyde lipid bilayer. Free energy calculations were performed and estimates of the flip-flop rates across the bilayers were determined. As the main finding, our results show that the presence of oxidized lipids leads to a significant decrease of free energy barriers and that the flip-flop rates depend on the type of oxidized lipid present. Our results suggest that -toc molecules could potentially act as high efficacy scavengers of free radicals to protect membranes from oxidative attack and help stabilize them under oxidative stress.

biophysics↗

bioRxiv2018

The extracellular gate shapes the energy profile of an ABC exporter

ABC exporters harness the energy of ATP to pump substrates across membranes. Extracellular gate opening and closure are key steps of the transport cycle, but the underlying mechanism is poorly understood. Here, we generated a synthetic single domain antibody (sybody) that recognizes the heterodimeric ABC exporter TM287/288 exclusively in the presence of ATP, which was essential to solve a 3.2 [A] crystal structure of the outward-facing transporter. The sybody binds to an extracellular wing and strongly inhibits ATPase activity by shifting the transporters conformational equilibrium towards the outward-facing state, as shown by double electron-electron resonance (DEER). Mutations that facilitate extracellular gate opening resulted in a comparable equilibrium shift and strongly reduced ATPase activity and drug transport. Using the sybody as conformational probe, we demonstrate that efficient extracellular gate closure is required to dissociate the NBD dimer after ATP hydrolysis to reset the transporter back to its inward-facing state.

biochemistry↗