scholarly journals A molecular view on the escape of lipoplexed DNA from the endosome

eLife ◽  
2020 ◽  
Vol 9 ◽  
Author(s):  
Bart MH Bruininks ◽  
Paulo CT Souza ◽  
Helgi Ingolfsson ◽  
Siewert J Marrink
Keyword(s):  
Viral Vectors ◽  
Membrane Surface ◽  
Genetic Material ◽  
Cationic Liposome ◽  
Coarse Grained ◽  
Fusion Pore ◽  
Endosomal Membrane ◽  
Dynamics Simulations ◽  
The Cost

The use of non-viral vectors for in vivo gene therapy could drastically increase safety, whilst reducing the cost of preparing the vectors. A promising approach to non-viral vectors makes use of DNA/cationic liposome complexes (lipoplexes) to deliver the genetic material. Here we use coarse-grained molecular dynamics simulations to investigate the molecular mechanism underlying efficient DNA transfer from lipoplexes. Our computational fusion experiments of lipoplexes with endosomal membrane models show two distinct modes of transfection: parallel and perpendicular. In the parallel fusion pathway, DNA aligns with the membrane surface, showing very quick release of genetic material shortly after the initial fusion pore is formed. The perpendicular pathway also leads to transfection, but release is slower. We further show that the composition and size of the lipoplex, as well as the lipid composition of the endosomal membrane, have a significant impact on fusion efficiency in our models.

scholarly journals Reaction–diffusion basis of retroviral infectivity

2016 ◽  
Vol 374 (2080) ◽  
pp. 20160148 ◽  
Author(s):  
S. Kashif Sadiq
Keyword(s):  
Chemical Reactions ◽  
Membrane Surface ◽  
Reaction Diffusion ◽  
Coarse Graining ◽  
Coarse Grained ◽  
Multiscale Approach ◽  
The Matrix ◽  
Membrane Bound ◽  
Spatio Temporal ◽  
Dynamics Simulations

Retrovirus particle (virion) infectivity requires diffusion and clustering of multiple transmembrane envelope proteins (Env 3 ) on the virion exterior, yet is triggered by protease-dependent degradation of a partially occluding, membrane-bound Gag polyprotein lattice on the virion interior. The physical mechanism underlying such coupling is unclear and only indirectly accessible via experiment. Modelling stands to provide insight but the required spatio-temporal range far exceeds current accessibility by all-atom or even coarse-grained molecular dynamics simulations. Nor do such approaches account for chemical reactions, while conversely, reaction kinetics approaches handle neither diffusion nor clustering. Here, a recently developed multiscale approach is considered that applies an ultra-coarse-graining scheme to treat entire proteins at near-single particle resolution, but which also couples chemical reactions with diffusion and interactions. A model is developed of Env 3 molecules embedded in a truncated Gag lattice composed of membrane-bound matrix proteins linked to capsid subunits, with freely diffusing protease molecules. Simulations suggest that in the presence of Gag but in the absence of lateral lattice-forming interactions, Env 3 diffuses comparably to Gag-absent Env 3 . Initial immobility of Env 3 is conferred through lateral caging by matrix trimers vertically coupled to the underlying hexameric capsid layer. Gag cleavage by protease vertically decouples the matrix and capsid layers, induces both matrix and Env 3 diffusion, and permits Env 3 clustering. Spreading across the entire membrane surface reduces crowding, in turn, enhancing the effect and promoting infectivity. This article is part of the themed issue ‘Multiscale modelling at the physics–chemistry–biology interface’.

scholarly journals Quantification of in-plane flexoelectricity in lipid bilayers

2021 ◽  
Author(s):  
Nidhin Thomas ◽  
Ashutosh Agrawal
Keyword(s):  
Molecular Dynamics ◽  
Electric Field ◽  
Lipid Bilayers ◽  
Material Parameter ◽  
Membrane Surface ◽  
Dielectric Materials ◽  
Coarse Grained ◽  
Molecular Architecture ◽  
Dynamics Simulations ◽  
Continuum Theories

Lipid bilayers behave as 2D dielectric materials that undergo polarization and deformation in the presence of an electric field. This effect has been previously modeled by continuum theories which assume a polarization field oriented normal to the membrane surface. However, the molecular architecture of the lipids reveals that the heqadgroup dipoles are primarily oriented tangential to the membrane surface. Here, we perform atomistic and coarse-grained molecular dynamics simulations to quantify the in-plane polarization undergone by a flat bilayer and a spherical vesicle in the presence of an applied electric field. We use these predictions to compute an effective in-plane flexoelectric coefficient for four different lipid types. Our findings provide the first molecular proof of the in-plane polarization undergone by lipid bilayers and furnish the material parameter required to quantify membrane-electric field interactions.

scholarly journals Gene Therapy Approaches

2021 ◽  
Vol 1 (1) ◽  
pp. 52-56
Author(s):  
Hogir Saadi
Keyword(s):  
Gene Therapy ◽  
Viral Vectors ◽  
Nuclear Translocation ◽  
Viral Vector ◽  
Ex Vivo ◽  
Genetic Material ◽  
Target Tissue ◽  
Human Beings ◽  
Vector Systems

Gene therapy can be described broadly as the transfer of genetic material to control a disease or at least to enhance a patient's clinical status. The transformation of viruses into genetic shuttles is one of the core principles of gene therapy, which will introduce the gene of interest into the target tissue and cells. To do this, safe strategies have been invented, using many viral and non-viral vector delivery. Two major methods have emerged: modification in vivo and modification ex vivo. For gene therapeutic approaches which are focused on lifelong expression of the therapeutic gene, retrovirus, adenovirus, adeno-associated viruses are acceptable. Non-viral vectors are much less successful than viral vectors, but because of their low immune responses and their broad therapeutic DNA ability, they have advantages. The addition of viral functions such as receptor-mediated uptake and nuclear translocation of DNA may eventually lead to the development of an artificial virus in order to improve the role of non-viral vectors. For human use in genetic conditions, cancers and acquired illnesses, gene transfer techniques have been allowed. The ideal delivery vehicle has not been identified, although the accessible vector systems are capable of transporting genes in vivo into cells. Therefore, only with great caution can the present viral vectors be used in human beings and further progress in the production of vectors is required. Current progresses in our understanding of gene therapy approaches and their delivery technology, as well as the victors used to deliver therapeutic genes, are the primary goals of this review. For that reason, a literature search on PubMed and Google Scholar was carried out using different keywords.

scholarly journals Size-dependent leak of soluble and membrane proteins through the yeast nuclear pore complex

2015 ◽  
Vol 26 (7) ◽  
pp. 1386-1394 ◽  
Author(s):  
Petra Popken ◽  
Ali Ghavami ◽  
Patrick R. Onck ◽  
Bert Poolman ◽  
Liesbeth M. Veenhoff
Keyword(s):  
Molecular Dynamics ◽  
Membrane Proteins ◽  
Coarse Grained ◽  
Nuclear Pore ◽  
Permeability Barrier ◽  
Nuclear Pore Complexes ◽  
Structural And Functional Properties ◽  
Dynamics Simulations ◽  
Pore Complexes

Nuclear pore complexes (NPCs) allow selective import and export while forming a barrier for untargeted proteins. Using fluorescence microscopy, we measured in vivo the permeability of the Saccharomyces cerevisiae NPC for multidomain proteins of different sizes and found that soluble proteins of 150 kDa and membrane proteins with an extralumenal domain of 90 kDa were still partly localized in the nucleus on a time scale of hours. The NPCs thus form only a weak barrier for the majority of yeast proteins, given their monomeric size. Using FGΔ-mutant strains, we showed that specific combinations of Nups, especially with Nup100, but not the total mass of FG-nups per pore, were important for forming the barrier. Models of the disordered phase of wild-type and mutant NPCs were generated using a one bead per amino acid molecular dynamics model. The permeability measurements correlated with the density predictions from coarse-grained molecular dynamics simulations in the center of the NPC. The combined in vivo and computational approach provides a framework for elucidating the structural and functional properties of the permeability barrier of nuclear pore complexes.

scholarly journals Chiral twisting in cytoskeletal polymers regulates filament size and orientation

2018 ◽  
Author(s):  
Handuo Shi ◽  
David Quint ◽  
Ajay Gopinathan ◽  
Kerwyn Casey Huang
Keyword(s):  
Molecular Dynamics ◽  
Molecular Dynamics Simulations ◽  
Caulobacter Crescentus ◽  
Membrane Binding ◽  
Membrane Curvature ◽  
Cytoskeletal Proteins ◽  
Coarse Grained ◽  
Biophysical Model ◽  
Dynamics Simulations

AbstractWhile cytoskeletal proteins in the actin family are structurally similar, as filaments they act as critical components of diverse cellular processes across all kingdoms of life. In many rod-shaped bacteria, the actin homolog MreB directs cell-wall insertion and maintains cell shape, but it remains unclear how structural changes to MreB affect its physiological function. To bridge this gap, we performed molecular dynamics simulations forCaulobacter crescentusMreB and then utilized a coarse-grained biophysical model to successfully predict MreB filament propertiesin vivo.We discovered that MreB double protofilaments exhibit left-handed twisting that is dependent on the bound nucleotide and membrane binding; the degree of twisting determines the limit length and orientation of MreB filamentsin vivo.Membrane binding of MreB also induces a stable membrane curvature that is physiologically relevant. Together, our data empower the prediction of cytoskeletal filament size from molecular dynamics simulations, providing a paradigm for connecting protein filament structure and mechanics to cellular functions.

scholarly journals Structure and Formation Mechanism of Antimicrobial Peptides Temporin B- and L-Induced Tubular Membrane Protrusion

2021 ◽  
Vol 22 (20) ◽  
pp. 11015
Author(s):  
Shan Zhang ◽  
Ming Ma ◽  
Zhuang Shao ◽  
Jincheng Zhang ◽  
Lei Fu ◽  
...  
Keyword(s):  
Antimicrobial Peptides ◽  
Morphological Changes ◽  
Membrane Surface ◽  
Coarse Grained ◽  
Tubular Structures ◽  
Membrane Pore ◽  
Anionic Phospholipids ◽  
Bactericidal Activities ◽  
Highly Hydrophobic ◽  
Dynamics Simulations

Temporins are a family of antimicrobial peptides (AMPs) isolated from frog skin, which are very short, weakly charged, and highly hydrophobic. They execute bactericidal activities in different ways from many other AMPs. This work investigated morphological changes of planar bilayer membranes composed of mixed zwitterionic and anionic phospholipids induced by temporin B and L (TB and TL) using all-atom and coarse-grained molecular dynamics simulations. We found that TB and TL fold to α-helices at the membrane surface and penetrate shallowly into the bilayer. These short AMPs have low propensity to induce membrane pore formation but possess high ability to extract lipids out. At relatively high peptide concentrations, the strong hydrophobicity of TB and TL promotes them to aggregate into clusters on the membrane surface. These aggregates attract a large amount of lipids out of the membrane to release compression induced by other dispersed peptides binding to the membrane. The extruded lipids mix evenly with the peptides in the cluster and form tubule-like protrusions. Certain water molecules follow the movement of lipids, which not only fill the cavities of the protrusion but also assist in maintaining the tubular structures. In contrast, the peptide-free leaflet remains intact. The present results unravel distinctive antimicrobial mechanisms of temporins disturbing membranes.

scholarly journals Molecular mechanism of fusion pore formation driven by the neuronal SNARE complex

2018 ◽  
Vol 115 (50) ◽  
pp. 12751-12756 ◽  
Author(s):  
Satyan Sharma ◽  
Manfred Lindau
Keyword(s):  
Pore Formation ◽  
Structural Model ◽  
Snare Complex ◽  
Coarse Grained ◽  
Fusion Pore ◽  
Protein Mutants ◽  
Experimental Values ◽  
Dynamics Simulations ◽  
External Forces ◽  
Fusion Pores

Release of neurotransmitters from synaptic vesicles begins with a narrow fusion pore, the structure of which remains unresolved. To obtain a structural model of the fusion pore, we performed coarse-grained molecular dynamics simulations of fusion between a nanodisc and a planar bilayer bridged by four partially unzipped SNARE complexes. The simulations revealed that zipping of SNARE complexes pulls the polar C-terminal residues of the synaptobrevin 2 and syntaxin 1A transmembrane domains to form a hydrophilic core between the two distal leaflets, inducing fusion pore formation. The estimated conductances of these fusion pores are in good agreement with experimental values. Two SNARE protein mutants inhibiting fusion experimentally produced no fusion pore formation. In simulations in which the nanodisc was replaced by a 40-nm vesicle, an extended hemifusion diaphragm formed but a fusion pore did not, indicating that restricted SNARE mobility is required for rapid fusion pore formation. Accordingly, rapid fusion pore formation also occurred in the 40-nm vesicle system when SNARE mobility was restricted by external forces. Removal of the restriction is required for fusion pore expansion.

scholarly journals Vector-mediated cancer gene therapy: A review

2020 ◽  
Vol 13 (2) ◽  
pp. 152-165
Author(s):  
Manisha. B. Shinde ◽  
Dr. Archana D. Kajale ◽  
Dr. Madhuri A. Channawar ◽  
Dr. Shilpa R. Gawande
Keyword(s):  
Gene Therapy ◽  
Viral Vectors ◽  
Nuclear Translocation ◽  
Ex Vivo ◽  
Gene Knockout ◽  
Genetic Material ◽  
Target Cells ◽  
Human Beings ◽  
Vector Systems

Gene therapy is the transfer of genetic material to cure a disease or at least to improve the clinical status of a patient. One of the basic concepts of gene therapy is to transform viruses into genetic shuttles, which will deliver the gene of interest into the target cells. Safe methods have been devised to do this, using several viral and non-viral vectors. Two main approaches emerged: in vivo modification and ex vivo modification. Retrovirus, adenovirus, adenoassociated virus are suitable for gene therapeutic approaches which are based on permanent expression of the therapeutic gene. Non-viral vectors are far less efficient than viral vectors, but they have advantages due to their low immunogenicity and their large capacity for therapeutic DNA. The most commonly used DNA virus vectors are based on adenoviruses and adeno-associated viruses. An example of gene-knockout mediated gene therapy is the knockout of the human CCR5 gene in T-cells in order to control HIV infection. To improve the function of non-viral vectors, the addition of viral functions such as receptor mediated uptake and nuclear translocation of DNA may finally lead to the development of an artificial virus. Gene transfer protocols have been approved for human use in inherited diseases, cancers and acquired disorders. Although the available vector systems are able to deliver genes in vivo into cells, the ideal delivery vehicle has not been found. Thus, the present viral vectors should be used only with great caution in human beings and further progress in vector development is necessary.

scholarly journals Interaction of Aβ42 with Membranes Triggers the Self-Assembly into Oligomers

2020 ◽  
Vol 21 (3) ◽  
pp. 1129 ◽  
Author(s):  
Siddhartha Banerjee ◽  
Mohtadin Hashemi ◽  
Karen Zagorski ◽  
Yuri L. Lyubchenko
Keyword(s):  
Self Assembly ◽  
Membrane Surface ◽  
Amyloid Β ◽  
The Self ◽  
Bulk Solution ◽  
Aggregation Process ◽  
Physiological Concentration ◽  
Dynamics Simulations

The self-assembly of amyloid β (Aβ) proteins into oligomers is the major pathogenic event leading to Alzheimer’s disease (AD). Typical in vitro experiments require high protein concentrations, whereas the physiological concentration of Aβ is in the picomolar to low nanomolar range. This complicates the translation of results obtained in vitro to understanding the aggregation process in vivo. Here, we demonstrate that Aβ42 self-assembles into aggregates on membrane bilayers at low nanomolar concentrations - a pathway in which the membrane plays the role of a catalyst. Additionally, physiological ionic conditions (150 mM NaCl) significantly enhance on-membrane aggregation, leading to the rapid formation of oligomers. The self-assembly process is reversible, so assembled aggregates can dissociate from the membrane surface into the bulk solution to further participate in the aggregation process. Molecular dynamics simulations demonstrate that the transient membrane-Aβ interaction dramatically changes the protein conformation, facilitating the assembly of dimers. The results indicate peptide–membrane interaction is the critical step towards oligomer formation at physiologically low protein concentrations.

scholarly journals Pulmonary gene delivery—Realities and possibilities

2020 ◽  
pp. 153537022096598
Author(s):  
Uday K Baliga ◽  
David A Dean
Keyword(s):  
Gene Therapy ◽  
Gene Delivery ◽  
Extracellular Vesicles ◽  
Viral Vectors ◽  
Neutral Lipids ◽  
Genetic Material ◽  
Building Blocks ◽  
Electrical Pulses ◽  
Primary Focus

Delivery of genetic material to tissues in vivo is an important technique used in research settings and is the foundation upon which clinical gene therapy is built. The lung is a prime target for gene delivery due to a host of genetic, acquired, and infectious diseases that manifest themselves there, resulting in many pathologies. However, the in vivo delivery of genetic material to the lung remains a practical problem clinically and is considered the major obstacle needed to be overcome for gene therapy. Currently there are four main strategies for in vivo gene delivery to the lung: viral vectors, liposomes, nanoparticles, and electroporation. Viral delivery uses several different genetically modified viruses that enter the cell and express desired genes that have been inserted to the viral genome. Liposomes use combinations of charged and neutral lipids that can encapsulate genetic cargo and enter cells through endogenous mechanisms, thereby delivering their cargoes. Nanoparticles are defined by their size (typically less than 100 nm) and are made up of many different classes of building blocks, including biological and synthetic polymers, cell penetrant and other peptides, and dendrimers, that also enter cells through endogenous mechanisms. Electroporation uses mild to moderate electrical pulses to create pores in the cell membrane through which delivered genetic material can enter a cell. An emerging fifth category, exosomes and extracellular vesicles, may have advantages of both viral and non-viral approaches. These extracellular vesicles bud from cellular membranes containing receptors and ligands that may aid cell targeting and which can be loaded with genetic material for efficient transfer. Each of these vectors can be used for different gene delivery applications based on mechanisms of action, side-effects, and other factors, and their use in the lung and possible clinical considerations is the primary focus of this review.

Sign in / Sign up

Export Citation Format

Share Document