Structural implications for the transformation of the Bacillus thuringiensis δ-endotoxins from water-soluble to membrane-inserted forms

Crystal structures combined with biochemical data show that the δ-endotoxins from Bacillus thuringiensis are structurally poised towards large-scale, irreversible conformational changes that transform them from the soluble protein bound at the cell surface into a membrane-embedded form causing lysis of susceptible insect cells. Cry δ-endotoxins are made of a helix bundle, a β-prism and a β-sandwich. The conformational change involves an umbrella-like opening between the helix-4,5-hairpin and the remaining helices, and between the helical domain and the two sheet domains. Comparison of Cry1Ac structures with and without the bound receptor ligand GalNAc associates occupation of the high-affinity site on the β-sandwich with an increase of temperature factors in the helical, pore-forming domain, which may indicate how receptor binding could trigger the required major conformational change. The structure of Cyt δ-endotoxins indicates that the surface helix hairpins must peel away to expose the β-strands for membrane attack. Single amino acid substitutions in hinge residues or the core can restore activity following an inhibitory mutation.

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A Molecular View of Lipid-mediated Activation Process of Apolipoprotein E

10.1101/2020.08.18.255299 ◽

2020 ◽

Author(s):

Dube Dheeraj Prakashchand ◽

Jagannath Mondal

Keyword(s):

Apolipoprotein E ◽

Conformational Change ◽

Conformational Changes ◽

Large Scale ◽

Dynamics Simulation ◽

Lipid Transport ◽

Activation Process ◽

Rapid Separation ◽

Terminal Domain ◽

Complexation Process

AbstractApolipoprotein E (ApoE) is a major determinant protein of lipid-metabolism and actively participates in lipid transport in plasma and central nervous system. As a part of its lipid-transport activity, low-density-lipid receptor (LDLR) needs to recognise apoE as a ligand. But, all prior evidences point to the fact that the recognition of apoE by LDLR only takes place in presence of lipid molecules which are assumed to play an important role in conformationally activating apoE upon binding. However, the molecular mechanism underlying the complexation process of apoE with lipid molecules and associated lipid-induced conformational change of apoE are currently elusive. Here we capture the spontaneous complexation process of monomeric apoE3 and phospholipid molecules by employing molecular dynamics simulation at multiple resolution. In particular, our multi scale simulations demonstrate a large-scale conformational change of the full-length apoE3, triggered by two-stage apoE-lipid complexation process. At first stage, lipid molecules assemble close to C-terminal domain of the protein and induce a rapid separation of C-terminal domain of monomeric apoE3 from rest of its tertiary fold. In the second and final stage, long-time scale simulation captures a slow on-the-fly lipid-induced inter-helix separation process in N-terminal domain of the protein. The resultant equilibrated complex, as obtained in the current work resembles an ‘open conformation’ of lipid-stabilised apoE, previously hypothesised based on small-angle X-ray scattering experiments. Taken together, the simulations provide a molecular view of kinetic interplay of apoE and lipid complexation multi-stage process leading to conformational changes in protein, potentially making it conducive for recognising LDLR.

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Large-Scale, pH-Dependent, Quaternary Structure Changes in an RNA Virus Capsid Are Reversible in the Absence of Subunit Autoproteolysis

Journal of Virology ◽

10.1128/jvi.76.19.9972-9980.2002 ◽

2002 ◽

Vol 76 (19) ◽

pp. 9972-9980 ◽

Cited By ~ 45

Author(s):

Derek J. Taylor ◽

Neel K. Krishna ◽

Mary A. Canady ◽

Anette Schneemann ◽

John E. Johnson

Keyword(s):

Coat Protein ◽

Conformational Change ◽

Conformational Changes ◽

Large Scale ◽

Quaternary Structure ◽

Rna Virus ◽

Expression System ◽

Recombinant Baculovirus ◽

Baculovirus Expression System ◽

Ph Dependent

ABSTRACT The assembly and maturation of the coat protein of a T=4, nonenveloped, single-stranded RNA virus, Nudaurelia capensis ω virus (NωV), was examined by using a recombinant baculovirus expression system. At pH 7.6, the coat protein assembles into a stable particle called the procapsid, which is 450 Å in diameter and porous. Lowering the pH to 5.0 leads to a concerted reorganization of the subunits into a 410-Å-diameter particle called the capsid, which has no obvious pores. This conformational change is rapid but reversible until slow, autoproteolytic cleavage occurs in at least 15% of the subunits at the lower pH. In this report, we show that expression of subunits with replacement of Asn-570, which is at the cleavage site, with Thr results in assembly of particles with expected morphology but that are cleavage defective. The conformational change from procapsid to capsid is reversible in N570T mutant virus-like particles, in contrast to wild-type particles, which are locked into the capsid conformation after cleavage of the coat protein. The reexpanded procapsids display slightly different properties than the original procapsid, suggesting hysteretic effects. Because of the stability of the procapsid under near-neutral conditions and the reversible properties of the cleavage-defective mutant, NωV provides an excellent model for the study of pH-induced conformational changes in macromolecular assemblies. Here, we identify the relationship between cleavage and the conformational change and propose a pH-dependent helix-coil transition that may be responsible for the structural rearrangement in NωV.

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Coupling of ATPase activity, microtubule binding and mechanics in the dynein motor domain

10.1101/309179 ◽

2018 ◽

Cited By ~ 1

Author(s):

Stefan Niekamp ◽

Nicolas Coudray ◽

Nan Zhang ◽

Ronald D. Vale ◽

Gira Bhabha

Keyword(s):

Atpase Activity ◽

Conformational Change ◽

Conformational Changes ◽

Large Scale ◽

Atp Hydrolysis ◽

Molecular Motor ◽

Coiled Coil ◽

Microtubule Binding ◽

Dynein Motor ◽

In The Wild

The movement of a molecular motor protein along a cytoskeletal track requires communication between enzymatic, polymer-binding, and mechanical elements. Such communication is particularly complex and not well understood in the dynein motor, an ATPase that is comprised of a ring of six AAA domains, a large mechanical element (linker) spanning over the ring, and a microtubule-binding domain (MTBD) that is separated from the AAA ring by a ~135 Å coiled-coil stalk. We identified mutations in the stalk that disrupt directional motion, have microtubule-independent hyperactive ATPase activity, and nucleotide-independent low affinity for microtubules. Cryo-electron microscopy structures of a mutant that uncouples ATPase activity from directional movement reveal that nucleotide-dependent conformational changes occur normally in one half of the AAA ring, but are disrupted in the other half. The large-scale linker conformational change observed in the wild-type protein is also inhibited, revealing that this conformational change is not required for ATP hydrolysis. These results demonstrate an essential role of the stalk in regulating motor activity and coupling conformational changes across the two halves of the AAA ring.

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Faculty Opinions recommendation of A large-scale conformational change couples membrane recruitment to cargo binding in the AP2 clathrin adaptor complex.

Faculty Opinions – Post-Publication Peer Review of the Biomedical Literature ◽

10.3410/f.4093956.3870054 ◽

2010 ◽

Author(s):

Eileen Lafer

Keyword(s):

Conformational Change ◽

Large Scale ◽

Membrane Recruitment ◽

Clathrin Adaptor ◽

Cargo Binding

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The Effect of Extraction Conditions on the Barrier and Mechanical Properties of Kefiran Films

Coatings ◽

10.3390/coatings11050602 ◽

2021 ◽

Vol 11 (5) ◽

pp. 602

Author(s):

Carmen Rodica Pop ◽

Teodora Emilia Coldea ◽

Liana Claudia Salanţă ◽

Alina Lăcrămioara Nistor ◽

Andrei Borşa ◽

...

Keyword(s):

Water Vapor ◽

Conformational Changes ◽

Water Vapor Permeability ◽

Edible Films ◽

Film Structure ◽

Water Soluble ◽

Vapor Permeability ◽

Water Molecules ◽

Compact Structure ◽

Technology Applications

Kefiran is an exopolysaccharide classified as a heteropolysaccharide comprising glucose and galactose in equimolar quantities, and it is classified as a water-soluble glucogalactan. This work aimed to investigate the effect of different extraction conditions of kefiran on the structural and physical properties of the edible films obtained. Fourier-transform infrared spectroscopy and scanning electron microscopy were performed, together with a determinations of moisture content, solubility, water vapor permeability and degree of swelling. The kefiran films presented values of the water vapor permeability between 0.93 and 4.38 × 10−11 g/m.s.Pa. These results can be attributed to the development of a more compact structure, where glycerol had no power to increase the free volume and the water vapor diffusion through their structure. The possible conformational changes in the kefiran film structure, due to the interspersing of the plasticizers and water molecules that they absorb, could be the reason for producing flexible kefiran films in the case of using glycerol as a plasticizer at 7.5% w/w. Moreover, it was observed that the extraction conditions are a significant factor in the properties of these films and their food technology applications.

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Solubilization of Charged Porphyrins in Interpolyelectrolyte Complexes: A Computer Study

Polymers ◽

10.3390/polym13040502 ◽

2021 ◽

Vol 13 (4) ◽

pp. 502

Author(s):

Karel Šindelka ◽

Zuzana Limpouchová ◽

Karel Procházka

Keyword(s):

Dissipative Particle Dynamics ◽

Water Soluble ◽

Coarse Grained ◽

Core Shell ◽

Computer Study ◽

Interpolyelectrolyte Complex ◽

The Core ◽

Porphyrin Derivatives ◽

Oppositely Charged ◽

Positively Charged

Using coarse-grained dissipative particle dynamics (DPD) with explicit electrostatics, we performed (i) an extensive series of simulations of the electrostatic co-assembly of asymmetric oppositely charged copolymers composed of one (either positively or negatively charged) polyelectrolyte (PE) block A and one water-soluble block B and (ii) studied the solubilization of positively charged porphyrin derivatives (P+) in the interpolyelectrolyte complex (IPEC) cores of co-assembled nanoparticles. We studied the stoichiometric mixtures of 137 A10+B25 and 137 A10−B25 chains with moderately hydrophobic A blocks (DPD interaction parameter aAS=35) and hydrophilic B blocks (aBS=25) with 10 to 120 P+ added (aPS=39). The P+ interactions with other components were set to match literature information on their limited solubility and aggregation behavior. The study shows that the moderately soluble P+ molecules easily solubilize in IPEC cores, where they partly replace PE+ and electrostatically crosslink PE− blocks. As the large P+ rings are apt to aggregate, P+ molecules aggregate in IPEC cores. The aggregation, which starts at very low loadings, is promoted by increasing the number of P+ in the mixture. The positively charged copolymers repelled from the central part of IPEC core partially concentrate at the core-shell interface and partially escape into bulk solvent depending on the amount of P+ in the mixture and on their association number, AS. If AS is lower than the ensemble average ⟨AS⟩n, the copolymer chains released from IPEC preferentially concentrate at the core-shell interface, thus increasing AS, which approaches ⟨AS⟩n. If AS>⟨AS⟩n, they escape into the bulk solvent.

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A Large-Scale Conformational Change Couples Membrane Recruitment to Cargo Binding in the AP2 Clathrin Adaptor Complex

Cell ◽

10.1016/j.cell.2010.05.006 ◽

2010 ◽

Vol 141 (7) ◽

pp. 1220-1229 ◽

Cited By ~ 224

Author(s):

Lauren P. Jackson ◽

Bernard T. Kelly ◽

Airlie J. McCoy ◽

Thomas Gaffry ◽

Leo C. James ◽

...

Keyword(s):

Conformational Change ◽

Large Scale ◽

Membrane Recruitment ◽

Clathrin Adaptor ◽

Cargo Binding

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Metastable Intermediates as Stepping Stones on the Maturation Pathways of Viral Capsids

mBio ◽

10.1128/mbio.02067-14 ◽

2014 ◽

Vol 5 (6) ◽

Cited By ~ 10

Author(s):

Giovanni Cardone ◽

Robert L. Duda ◽

Naiqian Cheng ◽

Lili You ◽

James F. Conway ◽

...

Keyword(s):

Conformational Changes ◽

Large Scale ◽

Structural Changes ◽

Energy Landscape ◽

Potential Hazard ◽

Stepping Stones ◽

Scanning Calorimetry ◽

Conformational Effects ◽

Capsid Maturation ◽

Capsid Integrity

ABSTRACT As they mature, many capsids undergo massive conformational changes that transform their stability, reactivity, and capacity for DNA. In some cases, maturation proceeds via one or more intermediate states. These structures represent local minima in a rich energy landscape that combines contributions from subunit folding, association of subunits into capsomers, and intercapsomer interactions. We have used scanning calorimetry and cryo-electron microscopy to explore the range of capsid conformations accessible to bacteriophage HK97. To separate conformational effects from those associated with covalent cross-linking (a stabilization mechanism of HK97), a cross-link-incompetent mutant was used. The mature capsid Head I undergoes an endothermic phase transition at 60°C in which it shrinks by 7%, primarily through changes in its hexamer conformation. The transition is reversible, with a half-life of ~3 min; however, >50% of reverted capsids are severely distorted or ruptured. This observation implies that such damage is a potential hazard of large-scale structural changes such as those involved in maturation. Assuming that the risk is lower for smaller changes, this suggests a rationalization for the existence of metastable intermediates: that they serve as stepping stones that preserve capsid integrity as it switches between the radically different conformations of its precursor and mature states. IMPORTANCE Large-scale conformational changes are widespread in virus maturation and infection processes. These changes are accompanied by the release of conformational free energy as the virion (or fusogenic glycoprotein) switches from a precursor state to its mature state. Each state corresponds to a local minimum in an energy landscape. The conformational changes in capsid maturation are so radical that the question arises of how maturing capsids avoid being torn apart. Offering proof of principle, severe damage is inflicted when a bacteriophage HK97 capsid reverts from the (nonphysiological) state that it enters when heated past 60°C. We suggest that capsid proteins have been selected in part by the criterion of being able to avoid sustaining collateral damage as they mature. One way of achieving this—as with the HK97 capsid—involves breaking the overall transition down into several smaller steps in which the risk of damage is reduced.

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