scholarly journals Exploring the binding dynamics of BAR proteins

2011 ◽  
Vol 16 (3) ◽  
Author(s):  
Doron Kabaso ◽  
Ekaterina Gongadze ◽  
Jernej Jorgačevski ◽  
Marko Kreft ◽  
Ursula Rienen ◽  
...  
Keyword(s):  
Free Energy ◽  
Binding Energy ◽  
Membrane Lipids ◽  
Structural Data ◽  
Membrane Curvature ◽  
Fusion Pore ◽  
Intrinsic Curvature ◽  
Bar Domain ◽  
Binding Interface ◽  
Negative Binding Energy

AbstractWe used a continuum model based on the Helfrich free energy to investigate the binding dynamics of a lipid bilayer to a BAR domain surface of a crescent-like shape of positive (e.g. I-BAR shape) or negative (e.g. F-BAR shape) intrinsic curvature. According to structural data, it has been suggested that negatively charged membrane lipids are bound to positively charged amino acids at the binding interface of BAR proteins, contributing a negative binding energy to the system free energy. In addition, the cone-like shape of negatively charged lipids on the inner side of a cell membrane might contribute a positive intrinsic curvature, facilitating the initial bending towards the crescent-like shape of the BAR domain. In the present study, we hypothesize that in the limit of a rigid BAR domain shape, the negative binding energy and the coupling between the intrinsic curvature of negatively charged lipids and the membrane curvature drive the bending of the membrane. To estimate the binding energy, the electric potential at the charged surface of a BAR domain was calculated using the Langevin-Bikerman equation. Results of numerical simulations reveal that the binding energy is important for the initial instability (i.e. bending of a membrane), while the coupling between the intrinsic shapes of lipids and membrane curvature could be crucial for the curvature-dependent aggregation of negatively charged lipids near the surface of the BAR domain. In the discussion, we suggest novel experiments using patch clamp techniques to analyze the binding dynamics of BAR proteins, as well as the possible role of BAR proteins in the fusion pore stability of exovesicles.

scholarly journals Mechanism of negative membrane curvature generation by I-BAR domains

2020 ◽  
Author(s):  
Binod Nepal ◽  
Aliasghar Sepehri ◽  
Themis Lazaridis
Keyword(s):  
Binding Energy ◽  
Surface Density ◽  
Membrane Curvature ◽  
Implicit Solvent ◽  
Oligomeric Structure ◽  
Intrinsic Curvature ◽  
Bar Domain ◽  
Binding Interface ◽  
Bar Domains ◽  
Membrane Bending

AbstractThe membrane sculpting ability of BAR domains has been attributed to the intrinsic curvature of their banana-shaped dimeric structure. However, there is often a mismatch between this intrinsic curvature and the diameter of the membrane tubules generated. I-BAR domains have been especially mysterious: they are almost flat but generate high negative membrane curvature. Here, we use atomistic implicit-solvent computer modeling to show that the membrane bending of the IRSP53 I-BAR domain is dictated by its higher oligomeric structure, whose curvature is completely unrelated to the intrinsic curvature of the dimer. Two other I-BARs gave similar results, whereas a flat F-BAR sheet developed a concave membrane binding interface, consistent with its observed positive membrane curvature generation. Laterally interacting helical spirals of I-BAR dimers on tube interiors are stable and have an enhanced binding energy that is sufficient for membrane bending to experimentally observed tubule diameters at a reasonable surface density.

BAR domains and membrane curvature: bringing your curves to the BAR.

2005 ◽  
Vol 72 ◽  
pp. 223-231 ◽  
Author(s):  
Jennifer L. Gallop ◽  
Harvey T. McMahon
Keyword(s):  
Membrane Binding ◽  
Membrane Curvature ◽  
Protein Activity ◽  
Bar Domain ◽  
Additional Layer ◽  
Binding Interface ◽  
Binding Function ◽  
Dimerization Interface ◽  
Curved Membranes ◽  
Lipid Tubules

BAR (bin, amphiphysin and Rvs161/167) domains are a unique class of dimerization domains, whose dimerization interface is edged by a membrane-binding surface. In its dimeric form, the membrane-binding interface is concave, and this gives the ability to bind better to curved membranes, i.e. to sense membrane curvature. When present at higher concentrations, the domain can stabilize membrane curvature, generating lipid tubules. This domain is found in many contexts in a wide variety of proteins, where the dimerization and membrane-binding function of this domain is likely to have a profound effect on protein activity. If these proteins function as predicted, then there will be membrane subdomains based on curvature, and thus there is an additional layer of compartmentalization on membranes. These and other possible functions of the BAR domain are discussed.

scholarly journals Endophilin Recruitment via GPCR Interactions Enables Membrane Curvature Generation in the Absence of Anionic Lipids

2020 ◽  
Author(s):  
Samsuzzoha Mondal ◽  
Imania Powers ◽  
Karthik Narayan ◽  
Samuel Botterbusch ◽  
Tobias Baumgart
Keyword(s):  
Electrostatic Interactions ◽  
Membrane Lipids ◽  
Direct Interaction ◽  
Sh3 Domain ◽  
Membrane Curvature ◽  
Receptor Internalization ◽  
Intracellular Loop ◽  
Bar Domain ◽  
Src Homology ◽  
Anionic Lipids

AbstractThe Bin/Amphiphysin/Rvs (BAR) family protein endophilin plays key roles in membrane curvature generation during endocytosis of cellular receptors. The Src homology 3 (SH3) domain of endophilin interacts with the proline rich third intracellular loop (TIL) of various G-protein coupled receptors (GPCRs). While electrostatic interactions between BAR domain and anionic membrane lipids have been considered to be the major driving force in curvature generation, it is unclear how the direct interaction between TIL and SH3 affects this function and its coupling with receptor internalization. Here we show that TIL mediated interactions alone not only recruit endophilin to the membrane but also facilitate curvature sorting and curvature generating behavior of endophilin. To demonstrate this, we designed model membranes with covalently lipid-conjugated TIL and lipids without net negative charge so that endophilin was recruited exclusively via SH3/TIL interactions. We find curvature generation and curvature sorting under those conditions. Furthermore, we show that TIL interacts electrostatically with membranes in the presence of anionic lipids and that this interaction can interfere with binding of SH3. Overall, our study suggests that an interplay between TIL, charged membranes, BAR domain, and SH3 domain mediate membrane curvature generation to regulate receptor endocytosis following receptor stimulation.

scholarly journals Endophilin recruitment drives membrane curvature generation through coincidence detection of GPCR loop interactions and negative lipid charge

2020 ◽  
pp. jbc.RA120.016118
Author(s):  
Samsuzzoha Mondal ◽  
Karthik B. Narayan ◽  
Imania Powers ◽  
Samuel Botterbusch ◽  
Tobias Baumgart
Keyword(s):  
Electrostatic Interactions ◽  
Membrane Lipids ◽  
Sh3 Domain ◽  
Membrane Curvature ◽  
Coincidence Detection ◽  
Intracellular Loop ◽  
Direct Role ◽  
Cellular Receptors ◽  
Bar Domain ◽  
Anionic Lipids

Endophilin plays key roles during endocytosis of cellular receptors, including generating membrane curvature to drive internalization. Electrostatic interactions between endophilin’s BAR domain and anionic membrane lipids have been considered the major driving force in curvature generation. However, the SH3 domain of endophilin also interacts with the proline-rich third intracellular loop (TIL) of various G-protein coupled receptors (GPCRs), and it is unclear whether this interaction has a direct role in generating membrane curvature during endocytosis. To examine this, we designed model membranes with a membrane density of 1400 receptors per µm2 represented by a covalently conjugated TIL region from β1-adrenergic receptor. We observed that TIL recruits endophilin to membranes composed of 95 mol% of zwitterionic lipids via the SH3 domain. More importantly, endophilin recruited via TIL tubulates vesicles and gets sorted onto highly curved membrane tubules. These observations indicate that the cellular membrane bending and curvature sensing activities of endophilin can be facilitated through detection of the TIL of activated GPCRs in addition to binding to anionic lipids. Furthermore, we show that TIL electrostatically interacts with membranes composed of anionic lipids. Therefore, anionic lipids can modulate TIL/SH3 domain binding. Overall, our findings imply that an interplay between TIL, charged membrane lipids, BAR domain, and SH3 domain could exist in the biological system and that these components may act in coordination to regulate the internalization of cellular receptors.

scholarly journals Studies of Conformational Changes of Tubulin Induced by Interaction with Kinesin Using Atomistic Molecular Dynamics Simulations

2021 ◽  
Vol 22 (13) ◽  
pp. 6709
Author(s):  
Xiao-Xuan Shi ◽  
Peng-Ye Wang ◽  
Hong Chen ◽  
Ping Xie
Keyword(s):  
Molecular Dynamics ◽  
High Resolution ◽  
Binding Energy ◽  
Molecular Dynamics Simulations ◽  
Conformational Changes ◽  
Weak Interactions ◽  
Molecular Motor ◽  
Structural Data ◽  
Calculated Binding Energy ◽  
Dynamics Simulations

The transition between strong and weak interactions of the kinesin head with the microtubule, which is regulated by the change of the nucleotide state of the head, is indispensable for the processive motion of the kinesin molecular motor on the microtubule. Here, using all-atom molecular dynamics simulations, the interactions between the kinesin head and tubulin are studied on the basis of the available high-resolution structural data. We found that the strong interaction can induce rapid large conformational changes of the tubulin, whereas the weak interaction cannot. Furthermore, we found that the large conformational changes of the tubulin have a significant effect on the interaction of the tubulin with the head in the weak-microtubule-binding ADP state. The calculated binding energy of the ADP-bound head to the tubulin with the large conformational changes is only about half that of the tubulin without the conformational changes.

scholarly journals Antiviral Resistance against Viral Mutation: Praxis and Policy for SARS-CoV-2

2021 ◽  
Vol 9 (1) ◽  
pp. 81-89
Author(s):  
Robert Penner
Keyword(s):  
Free Energy ◽  
Vaccine Development ◽  
A Priori ◽  
Structural Data ◽  
Medical Sciences ◽  
Spike Glycoprotein ◽  
Mutagenic Potential ◽  
Viral Mutation ◽  
Novel Method ◽  
Antiviral Targets

Abstract Tools developed by Moderna, BioNTech/Pfizer, and Oxford/Astrazeneca, among others, provide universal solutions to previously problematic aspects of drug or vaccine delivery, uptake and toxicity, portending new tools across the medical sciences. A novel method is presented based on estimating protein backbone free energy via geometry to predict effective antiviral targets, antigens and vaccine cargos that are resistant to viral mutation. This method is reviewed and reformulated in light of the recent proliferation of structural data on the SARS-CoV-2 spike glycoprotein and its mutations in multiple lineages. Key findings include: collections of mutagenic residues reoccur across strains, suggesting cooperative convergent evolution; most mutagenic residues do not participate in backbone hydrogen bonds; metastability of the glyco-protein limits the change of free energy through mutation thereby constraining selective pressure; and there are mRNA or virus-vector cargos targeting low free energy peptides proximal to conserved high free energy peptides providing specific recipes for vaccines with greater specificity than the full-spike approach. These results serve to limit peptides in the spike glycoprotein with high mutagenic potential and thereby provide a priori constraints on viral and attendant vaccine evolution. Scientific and regulatory challenges to nucleic acid therapeutic and vaccine development and deployment are finally discussed.

scholarly journals How proteins open fusion pores: insights from molecular simulations

2020 ◽  
Author(s):  
H. Jelger Risselada ◽  
Helmut Grubmüller
Keyword(s):  
Free Energy ◽  
Fusion Proteins ◽  
Graphics Processing Units ◽  
Fusion Reaction ◽  
Molecular Simulations ◽  
Minimum Free Energy ◽  
Free Energy Calculations ◽  
Coarse Grained ◽  
Fusion Pore ◽  
Graphics Processing

AbstractFusion proteins can play a versatile and involved role during all stages of the fusion reaction. Their roles go far beyond forcing the opposing membranes into close proximity to drive stalk formation and fusion. Molecular simulations have played a central role in providing a molecular understanding of how fusion proteins actively overcome the free energy barriers of the fusion reaction up to the expansion of the fusion pore. Unexpectedly, molecular simulations have revealed a preference of the biological fusion reaction to proceed through asymmetric pathways resulting in the formation of, e.g., a stalk-hole complex, rim-pore, or vertex pore. Force-field based molecular simulations are now able to directly resolve the minimum free-energy path in protein-mediated fusion as well as quantifying the free energies of formed reaction intermediates. Ongoing developments in Graphics Processing Units (GPUs), free energy calculations, and coarse-grained force-fields will soon gain additional insights into the diverse roles of fusion proteins.

scholarly journals FAM92A1 is a BAR domain protein required for mitochondrial ultrastructure and function

2018 ◽  
Vol 218 (1) ◽  
pp. 97-111 ◽  
Author(s):  
Liang Wang ◽  
Ziyi Yan ◽  
Helena Vihinen ◽  
Ove Eriksson ◽  
Weihuan Wang ◽  
...  
Keyword(s):  
Mitochondrial Function ◽  
Molecular Mechanisms ◽  
Membrane Curvature ◽  
Mitochondrial Morphology ◽  
Membrane Remodeling ◽  
Mitochondrial Ultrastructure ◽  
Bar Domain ◽  
Bar Domain Proteins ◽  
Domain Protein

Mitochondrial function is closely linked to its dynamic membrane ultrastructure. The mitochondrial inner membrane (MIM) can form extensive membrane invaginations known as cristae, which contain the respiratory chain and ATP synthase for oxidative phosphorylation. The molecular mechanisms regulating mitochondrial ultrastructure remain poorly understood. The Bin-Amphiphysin-Rvs (BAR) domain proteins are central regulators of diverse cellular processes related to membrane remodeling and dynamics. Whether BAR domain proteins are involved in sculpting membranes in specific submitochondrial compartments is largely unknown. In this study, we report FAM92A1 as a novel BAR domain protein localizes to the matrix side of the MIM. Loss of FAM92A1 caused a severe disruption to mitochondrial morphology and ultrastructure, impairing organelle bioenergetics. Furthermore, FAM92A1 displayed a membrane-remodeling activity in vitro, inducing a high degree of membrane curvature. Collectively, our findings uncover a role for a BAR domain protein as a critical organizer of the mitochondrial ultrastructure that is indispensable for mitochondrial function.

scholarly journals Drosophila F-BAR protein Syndapin contributes to coupling the plasma membrane and contractile ring in cytokinesis

Open Biology ◽  
2013 ◽  
Vol 3 (8) ◽  
pp. 130081 ◽  
Author(s):  
Tetsuya Takeda ◽  
Iain M. Robinson ◽  
Matthew M. Savoian ◽  
John R. Griffiths ◽  
Anthony D. Whetton ◽  
...  
Keyword(s):  
Plasma Membrane ◽  
Membrane Curvature ◽  
Cellular Process ◽  
Cleavage Furrow ◽  
Contractile Ring ◽  
Functional Interaction ◽  
Cortical Dynamics ◽  
Central Spindle ◽  
Bar Domain ◽  
Spindle Microtubules

Cytokinesis is a highly ordered cellular process driven by interactions between central spindle microtubules and the actomyosin contractile ring linked to the dynamic remodelling of the plasma membrane. The mechanisms responsible for reorganizing the plasma membrane at the cell equator and its coupling to the contractile ring in cytokinesis are poorly understood. We report here that Syndapin, a protein containing an F-BAR domain required for membrane curvature, contributes to the remodelling of the plasma membrane around the contractile ring for cytokinesis. Syndapin colocalizes with phosphatidylinositol 4,5-bisphosphate (PI(4,5)P 2 ) at the cleavage furrow, where it directly interacts with a contractile ring component, Anillin. Accordingly, Anillin is mislocalized during cytokinesis in Syndapin mutants. Elevated or diminished expression of Syndapin leads to cytokinesis defects with abnormal cortical dynamics. The minimal segment of Syndapin, which is able to localize to the cleavage furrow and induce cytokinesis defects, is the F-BAR domain and its immediate C-terminal sequences. Phosphorylation of this region prevents this functional interaction, resulting in reduced ability of Syndapin to bind to and deform membranes. Thus, the dephosphorylated form of Syndapin mediates both remodelling of the plasma membrane and its proper coupling to the cytokinetic machinery.

The dissociation of nuclear proteins from superhelical DNA

1978 ◽  
Vol 29 (1) ◽  
pp. 103-116
Author(s):  
J.M. Levin ◽  
E. Jost ◽  
P.R. Cook
Keyword(s):  
Molecular Weight ◽  
Free Energy ◽  
Binding Energy ◽  
Apparent Molecular Weight ◽  
Morphological Features ◽  
Nuclear Proteins ◽  
Double Labelling ◽  
Ionic Detergents ◽  
Labelling Procedure ◽  
High Concentrations

Structures retaining many of the morphological features of nuclei may be released by gently lysing human cells in solutions containing non-ionic detergents and high concentrations of salt. These nucleoids contain superhelical DNA. Using a double-labelling procedure we have compared, at different salt concentrations, the amounts and types of protein associated with human nucleoides containings superhelical or relaxed DNA. We find that the slightly lysine-rich histones (H2A and H2B) but not the arginine-rich histones (H3 and H4) dissociate more slowly from nucleoids containing superhelical DNA than from those containing relaxed DNA. A protein of apparent molecular weight of 22000 also binds more tightly to superhelical DNA. We conclude that this protein and the slightly lysine-rich histones transmute free energy of supercoiling into binding energy when they bind to superhelical DNA.

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