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  • 1. Engin, Ozge
    et al.
    Villa, Alessandra
    Sayar, Mehmet
    Hess, Berk
    Driving forces for adsorption of amphiphilic peptides to the air-water interface.2010Inngår i: Journal of Physical Chemistry B, ISSN 1520-6106, E-ISSN 1520-5207, Vol. 114, nr 34, s. 11093-11101Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    We have studied the partitioning of amphiphilic peptides at the air-water interface. The free energy of adsorption from bulk to interface was calculated by determining the potential of mean force via atomistic molecular dynamics simulations. To this end a method is introduced to restrain or constrain the center of mass of a group of molecules in a periodic system. The model amphiphilic peptides are composed of alternating valine and asparagine residues. The decomposition of the free energy difference between the bulk and interface is studied for different peptide block lengths. Our analysis revealed that for short amphiphilic peptides the surface driving force dominantly stems from the dehydration of hydrophobic side chains. The only opposing force is associated with the loss of orientational freedom of the peptide at the interface. For the peptides studied, the free energy difference scales linearly with the size of the molecule, since the peptides mainly adopt extended conformations both in bulk and at the interface. The free energy difference depends strongly on the water model, which can be rationalized through the hydration thermodynamics of hydrophobic solutes. Finally, we measured the reduction of the surface tension associated with complete coverage of the interface with peptides.

  • 2.
    Krahn, Natalie
    et al.
    Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06520, USA.
    Zhang, Jingji
    Department of Structural Biology, Stanford University School of Medicine, Stanford, CA 94305, USA.
    Melnikov, Sergey V.
    Biosciences Institute, Newcastle University, Newcastle upon Tyne, NE2 4HH, UK.
    Tharp, Jeffery M.
    Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06520, USA.
    Villa, Alessandra
    KTH, Skolan för elektroteknik och datavetenskap (EECS), Centra, Parallelldatorcentrum, PDC.
    Patel, Armaan
    Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06520, USA.
    Howard, Rebecca J.
    Department of Biochemistry and Biophysics, Science for Life Laboratory, Stockholm University, Solna, SE-171 65, Sweden.
    Gabir, Haben
    Department of Chemistry, University of Manitoba, Winnipeg, MB R3T 2N2, Canada.
    Patel, Trushar R.
    Department of Chemistry and Biochemistry, Alberta RNA Research and Training Institute, University of Lethbridge, Lethbridge, AB T1K 2E1, Canada; Li Ka Shing Institute of Virology, University of Alberta, Edmonton, AB T6G 2E1, Canada; Department of Microbiology, Immunology & Infectious Diseases, Cumming School of Medicine, University of Calgary, Calgary, AB T2N 4N1, Canada.
    Stetefeld, Jörg
    Department of Chemistry, University of Manitoba, Winnipeg, MB R3T 2N2, Canada; Department of Microbiology, University of Manitoba, Winnipeg, MB R3T 2N2, Canada.
    Puglisi, Joseph
    Department of Structural Biology, Stanford University School of Medicine, Stanford, CA 94305, USA.
    Söll, Dieter
    Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06520, USA; Department of Chemistry, Yale University, New Haven, CT 06520, USA.
    tRNA shape is an identity element for an archaeal pyrrolysyl-tRNA synthetase from the human gut2024Inngår i: Nucleic Acids Research, ISSN 0305-1048, E-ISSN 1362-4962, Vol. 52, nr 2, s. 513-524Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    Protein translation is orchestrated through tRNA aminoacylation and ribosomal elongation. Among the highly conserved structure of tRNAs, they have distinguishing features which promote interaction with their cognate aminoacyl tRNA synthetase (aaRS). These key features are referred to as identity elements. In our study, we investigated the tRNA:aaRS pair that installs the 22nd amino acid, pyrrolysine (tRNAPyl:PylRS). Pyrrolysyl-tRNA synthetases (PylRSs) are naturally encoded in some archaeal and bacterial genomes to acylate tRNAPyl with pyrrolysine. Their large amino acid binding pocket and poor recognition of the tRNA anticodon have been instrumental in incorporating >200 noncanonical amino acids. PylRS enzymes can be divided into three classes based on their genomic structure. Two classes contain both an N-terminal and C-terminal domain, however the third class (ΔpylSn) lacks the N-terminal domain. In this study we explored the tRNA identity elements for a ΔpylSn tRNAPyl from Candidatus Methanomethylophilus alvus which drives the orthogonality seen with its cognate PylRS (MaPylRS). From aminoacylation and translation assays we identified five key elements in ΔpylSn tRNAPyl necessary for MaPylRS activity. The absence of a base (position 8) and a G-U wobble pair (G28:U42) were found to affect the high-resolution structure of the tRNA, while molecular dynamic simulations led us to acknowledge the rigidity imparted from the G-C base pairs (G3:C70 and G5:C68).

  • 3.
    Majdolhosseini, Maryam
    et al.
    KTH, Skolan för kemi, bioteknologi och hälsa (CBH), Medicinteknik och hälsosystem, Neuronik.
    Zhou, Zhou
    KTH, Skolan för kemi, bioteknologi och hälsa (CBH), Medicinteknik och hälsosystem, Neuronik.
    Kleiven, Svein
    KTH, Skolan för kemi, bioteknologi och hälsa (CBH), Medicinteknik och hälsosystem, Neuronik.
    Villa, Alessandra
    KTH, Skolan för elektroteknik och datavetenskap (EECS), Centra, Parallelldatorcentrum, PDC.
    Which part of axonal membrane is the most vulnerable: A molecular dynamics/Finite Element study2023Inngår i: European Biophysics Journal, ISSN 0175-7571, E-ISSN 1432-1017, Vol. 52, nr SUPPL 1, s. S39-S39Artikkel i tidsskrift (Annet vitenskapelig)
  • 4.
    Montanino, Annaclauida
    et al.
    KTH, Skolan för kemi, bioteknologi och hälsa (CBH), Medicinteknik och hälsosystem, Neuronik.
    Saeedimasine, Marzieh
    Villa, Alessandra
    Kleiven, Svein
    KTH, Skolan för kemi, bioteknologi och hälsa (CBH), Medicinteknik och hälsosystem, Neuronik.
    Axons Embedded in a Tissue May Withstand Larger Deformations Than Isolated Axons Before Mechanoporation Occurs2019Inngår i: Journal of Biomechanical Engineering, ISSN 0148-0731, E-ISSN 1528-8951, Vol. 141, nr 12Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    Diffuse axonal injury (DAI) is the pathological consequence of traumatic brain injury (TBI) that most of all requires a multiscale approach in order to be, first, understood and then possibly prevented. While in fact the mechanical insult usually happens at the head (or macro) level, the consequences affect structures at the cellular (or microlevel). The quest for axonal injury tolerances has so far been addressed both with experimental and computational approaches. On one hand, the experimental approach presents challenges connected to both temporal and spatial resolution in the identification of a clear axonal injury trigger after the application of a mechanical load. On the other hand, computational approaches usually consider axons as homogeneous entities and therefore are unable to make inferences about their viability, which is thought to depend on subcellular damages. Here, we propose a computational multiscale approach to investigate the onset of axonal injury in two typical experimental scenarios. We simulated single-cell and tissue stretch injury using a composite finite element axonal model in isolation and embedded in a matrix, respectively. Inferences on axonal damage are based on the comparison between axolemma strains and previously established mechanoporation thresholds. Our results show that, axons embedded in a tissue could withstand higher deformations than isolated axons before mechanoporation occurred and this is exacerbated by the increase in strain rate from 1/s to 10/s.

  • 5.
    Montanino, Annaclauida
    et al.
    KTH, Skolan för kemi, bioteknologi och hälsa (CBH), Medicinteknik och hälsosystem, Neuronik.
    Saeedimasine, Marzieh
    Villa, Alessandra
    Kleiven, Svein
    KTH, Skolan för kemi, bioteknologi och hälsa (CBH), Medicinteknik och hälsosystem, Neuronik.
    Localized axolemma deformations suggest mechanoporation as axonal injury triggerInngår i: Frontiers in Neurology, E-ISSN 1664-2295Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    Traumatic brain injuries are a leading cause of morbidity and mortality worldwide. With almost 50% of traumatic brain injuries being related to axonal damage, understanding the nature of cellular level impairment is crucial. Experimental observations have so far led to the formulation of conflicting theories regarding the cellular primary injury mechanism. Disruption of the axolemma, or alternatively cytoskeletal damage has been suggested mainly as injury trigger. However, mechanoporation thresholds of generic membranes seem not to overlap with the axonal injury deformation range and microtubules appear too stiff and too weakly connected to undergo mechanical breaking. Here, we aim to shed a light on the mechanism of primary axonal injury, bridging finite element and molecular dynamics simulations. Despite the necessary level of approximation, our models can accurately describe the mechanical behavior of the unmyelinated axon and its membrane. More importantly, they give access to quantities that would be inaccessible with an experimental approach. We show that in a typical injury scenario, the axonal cortex sustains deformations large enough to entail pore formation in the adjoining lipid bilayer. The observed axonal deformation of 10-12% agree well with the thresholds proposed in the literature for axonal injury and, above all, allow us to provide quantitative evidences that do not exclude pore formation in the membrane as a result of trauma. Our findings bring to an increased knowledge of axonal injury mechanism that will have positive implications for the prevention and treatment of brain injuries.

  • 6.
    Saeedimasine, Marzieh
    et al.
    Department of Biosciences and Nutrition, Karolinska Institutet, Huddinge, Sweden.
    Montanino, Annaclaudia
    KTH, Skolan för kemi, bioteknologi och hälsa (CBH), Medicinteknik och hälsosystem, Neuronik.
    Kleiven, Svein
    KTH, Skolan för kemi, bioteknologi och hälsa (CBH), Medicinteknik och hälsosystem, Neuronik.
    Villa, Alessandra
    KTH, Skolan för elektroteknik och datavetenskap (EECS), Centra, Parallelldatorcentrum, PDC.
    Elucidating axonal injuries through molecular modelling of myelin sheaths and nodes of Ranvier2021Inngår i: Frontiers in Molecular Biosciences, E-ISSN 2296-889X, Vol. 8Artikkel i tidsskrift (Fagfellevurdert)
  • 7.
    Saeedimasine, Marzieh
    et al.
    Department of Biosciences and Nutrition, Karolinska Institutet, Huddinge, Sweden.
    Montanino, Annaclaudia
    KTH, Skolan för kemi, bioteknologi och hälsa (CBH), Medicinteknik och hälsosystem, Neuronik.
    Kleiven, Svein
    KTH, Skolan för kemi, bioteknologi och hälsa (CBH), Medicinteknik och hälsosystem, Neuronik.
    Villa, Alessandra
    Department of Biosciences and Nutrition, Karolinska Institutet, Huddinge, Sweden.
    Role of lipid composition on the structural and mechanical features of axonal membranes: a molecular simulation study2019Inngår i: Scientific Reports, E-ISSN 2045-2322, Vol. 18, s. 27-39Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    The integrity of cellular membranes is critical for the functionality of axons. Failure of the axonal membranes (plasma membrane and/or myelin sheath) can be the origin of neurological diseases. The two membranes differ in the content of sphingomyelin and galactosylceramide lipids. We investigate the relation between lipid content and bilayer structural-mechanical properties, to better understand the dependency of membrane properties on lipid composition. A sphingomyelin/phospholipid/cholesterol bilayer is used to mimic a plasma membrane and a galactosylceramide/phospholipid/cholesterol bilayer to mimic a myelin sheath. Molecular dynamics simulations are performed at atomistic and coarse-grained levels to characterize the bilayers at equilibrium and under deformation. For comparison, simulations of phospholipid and phospholipid/cholesterol bilayers are also performed. The results clearly show that the bilayer biomechanical and structural features depend on the lipid composition, independent of the molecular models. Both galactosylceramide or sphingomyelin lipids increase the order of aliphatic tails and resistance to water penetration. Having 30% galactosylceramide increases the bilayers stiffness. Galactosylceramide lipids pack together via sugar-sugar interactions and hydrogen-bond phosphocholine with a correlated increase of bilayer thickness. Our findings provide a molecular insight on role of lipid content in natural membranes.

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