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

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.

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

2001 ◽  
Vol 29 (4) ◽  
pp. 571-577 ◽  
Author(s):  
J. Li ◽  
D. J. Derbyshire ◽  
B. Promdonkoy ◽  
D. J. Ellar
Keyword(s):  
Bacillus Thuringiensis ◽  
Conformational Change ◽  
Conformational Changes ◽  
Large Scale ◽  
Insect Cells ◽  
Water Soluble ◽  
Single Amino Acid ◽  
The Core ◽  
High Affinity Site ◽  
Temperature Factors

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.

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

2002 ◽  
Vol 76 (19) ◽  
pp. 9972-9980 ◽  
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.

scholarly journals Molecular dynamics simulations of nucleotide release from the circadian clock protein KaiC reveal atomic-resolution functional insights

2018 ◽  
Vol 115 (49) ◽  
pp. E11475-E11484 ◽  
Author(s):  
Lu Hong ◽  
Bodhi P. Vani ◽  
Erik H. Thiede ◽  
Michael J. Rust ◽  
Aaron R. Dinner
Keyword(s):  
Molecular Dynamics ◽  
Conformational Changes ◽  
Bound States ◽  
Large Scale ◽  
Nucleotide Exchange ◽  
Terminal Domain ◽  
Nucleotide Exchange Factor ◽  
Nucleotide Release ◽  
Dynamics Simulations

The cyanobacterial clock proteins KaiA, KaiB, and KaiC form a powerful system to study the biophysical basis of circadian rhythms, because an in vitro mixture of the three proteins is sufficient to generate a robust ∼24-h rhythm in the phosphorylation of KaiC. The nucleotide-bound states of KaiC critically affect both KaiB binding to the N-terminal domain (CI) and the phosphotransfer reactions that (de)phosphorylate the KaiC C-terminal domain (CII). However, the nucleotide exchange pathways associated with transitions among these states are poorly understood. In this study, we integrate recent advances in molecular dynamics methods to elucidate the structure and energetics of the pathway for Mg·ADP release from the CII domain. We find that nucleotide release is coupled to large-scale conformational changes in the KaiC hexamer. Solvating the nucleotide requires widening the subunit interface leading to the active site, which is linked to extension of the A-loop, a structure implicated in KaiA binding. These results provide a molecular hypothesis for how KaiA acts as a nucleotide exchange factor. In turn, structural parallels between the CI and CII domains suggest a mechanism for allosteric coupling between the domains. We relate our results to structures observed for other hexameric ATPases, which perform diverse functions.

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

2018 ◽  
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.

scholarly journals Structure and assembly of the diiron cofactor in the heme-oxygenase-like domain of the N-nitrosourea-producing enzyme SznF

2020 ◽  
Author(s):  
Molly J. McBride ◽  
Sarah R. Pope ◽  
Kai Hu ◽  
Jeffrey W. Slater ◽  
C. Denise Okafor ◽  
...  
Keyword(s):  
Conformational Change ◽  
Heme Oxygenase ◽  
Conformational Changes ◽  
Functional Characterization ◽  
Tight Binding ◽  
Dynamics Simulation ◽  
Structural Basis ◽  
Cancer Drug ◽  
Enzymatic Function ◽  
Iron Deficient

AbstractIn biosynthesis of the pancreatic cancer drug streptozotocin, the tri-domain nonheme-iron oxygenase, SznF, hydroxylates Nδ and Nω’ of Nω-methyl-L-arginine before oxidatively rearranging the triply modified guanidine to the N-methyl-N-nitrosourea pharmacophore. A previously published structure visualized the mono-iron cofactor in the enzyme’s C-terminal cupin domain, which effects the final rearrangement, but exhibited disorder and minimal metal occupancy in the site of the proposed diiron cofactor in the N-hydroxylating heme-oxygenase-like (HO-like) central domain. Here we leverage our recent report of an intensely absorbing µ-peroxodiiron(III/III) intermediate formed from the Fe2(II/II) complex and O2 to understand assembly of the diiron cofactor in the HO-like domain and to obtain structures with both SznF iron cofactors bound. Tight binding at one diiron subsite is associated with a conformational change, which is followed by weak binding at the second subsite and rapid capture of O2 by the Fe2(II/II) complex. Differences between iron-deficient and iron-replete structures reveal both the conformational change required to form the O2-reactive Fe2(II/II) complex and the structural basis for cofactor instability, showing that a ligand-harboring core helix dynamically refolds during metal acquisition and release. The cofactor also coordinates an unanticipated Glu ligand contributed by an auxiliary helix implicated in substrate binding by docking and molecular dynamics simulation. The additional ligand is conserved in another experimentally validated HO-like N-oxygenase but not in two known HO-like diiron desaturases. Among ∼9600 sequences identified bioinformatically as belonging to the emerging HO-like diiron protein (HDO) superfamily, ∼25% have this carboxylate residue and are thus tentatively assigned as N-oxygenases.Significance statementThe enzyme SznF assembles the N-nitrosourea pharmacophore of the drug streptozotocin. Its central N-oxygenase domain resembles heme-oxygenase (HO) and belongs to an emerging superfamily of HO-like diiron enzymes (HDOs) with unstable metallocofactors that have resisted structural characterization. We investigated assembly of the O2-reactive diiron complex from metal-free SznF and Fe(II) and leveraged this insight to obtain the first structure of a functionally assigned HDO with intact cofactor. Conformational changes accompanying cofactor acquisition explain its instability, and the observation of an unanticipated glutamate ligand that is conserved in only a subset of the HDO sequences provides a potential basis for top-level assignment of enzymatic function. Our results thus provide a roadmap for structural and functional characterization of novel HDOs.

scholarly journals Structure of monomeric full-length ARC sheds light on molecular flexibility, protein interactions, and functional modalities

2018 ◽  
Author(s):  
Erik I. Hallin ◽  
Maria S. Eriksen ◽  
Sergei Baryshnikov ◽  
Oleksii Nikolaienko ◽  
Sverre Grødem ◽  
...  
Keyword(s):  
Conformational Changes ◽  
Protein Interaction ◽  
Protein Interactions ◽  
Large Scale ◽  
Lipid Membrane ◽  
Hippocampal Slices ◽  
Coiled Coil ◽  
Full Length ◽  
Dimensional Structure ◽  
Terminal Domain

AbstractThe activity-regulated cytoskeleton-associated protein (ARC) is critical for long-term synaptic plasticity and memory formation. Acting as a protein interaction hub, ARC regulates diverse signalling events in postsynaptic neurons. A protein interaction site is present in the ARC C-terminal domain (CTD), a bilobar structure homologous to the retroviral Gag capsid domain. However, knowledge of the 3-dimensional structure of full-length ARC is required to elucidate its molecular function. We purified recombinant monomeric full-length ARC and analyzed its structure using small-angle X-ray scattering and synchrotron radiation circular dichroism spectroscopy. In solution, monomeric ARC has a compact, closed structure, in which the oppositely charged N-terminal domain (NTD) and CTD are juxtaposed, and the flexible linker between them is not extended. The modelled structure of ARC is supported by intramolecular live-cell FRET imaging in rat hippocampal slices. Peptides from several postsynaptic proteins, including stargazin, bind to the N-lobe, but not to the C-lobe, of the bilobar CTD. This interaction does not induce large-scale conformational changes in the CTD or flanking unfolded regions. The ARC NTD contains long helices, predicted to form an anti-parallel coiled coil; binding of ARC to phospholipid membranes requires the NTD. Our data support a role for the ARC NTD in oligomerization as well as lipid membrane binding. These findings have important implications for the structural organization of ARC in distinct functional modalities, such as postsynaptic signal transduction and virus-like capsid formation.

Crystal structures of Magnaporthe oryzae trehalose-6-phosphate synthase (MoTps1) suggest a model for catalytic process of Tps1

2019 ◽  
Vol 476 (21) ◽  
pp. 3227-3240 ◽  
Author(s):  
Shanshan Wang ◽  
Yanxiang Zhao ◽  
Long Yi ◽  
Minghe Shen ◽  
Chao Wang ◽  
...  
Keyword(s):  
Crystal Structures ◽  
Conformational Changes ◽  
Magnaporthe Oryzae ◽  
Structural Information ◽  
Complex Structure ◽  
Critical Role ◽  
Catalytic Process ◽  
Structural Basis ◽  
Salt Bridges ◽  
Terminal Domain

Trehalose-6-phosphate (T6P) synthase (Tps1) catalyzes the formation of T6P from UDP-glucose (UDPG) (or GDPG, etc.) and glucose-6-phosphate (G6P), and structural basis of this process has not been well studied. MoTps1 (Magnaporthe oryzae Tps1) plays a critical role in carbon and nitrogen metabolism, but its structural information is unknown. Here we present the crystal structures of MoTps1 apo, binary (with UDPG) and ternary (with UDPG/G6P or UDP/T6P) complexes. MoTps1 consists of two modified Rossmann-fold domains and a catalytic center in-between. Unlike Escherichia coli OtsA (EcOtsA, the Tps1 of E. coli), MoTps1 exists as a mixture of monomer, dimer, and oligomer in solution. Inter-chain salt bridges, which are not fully conserved in EcOtsA, play primary roles in MoTps1 oligomerization. Binding of UDPG by MoTps1 C-terminal domain modifies the substrate pocket of MoTps1. In the MoTps1 ternary complex structure, UDP and T6P, the products of UDPG and G6P, are detected, and substantial conformational rearrangements of N-terminal domain, including structural reshuffling (β3–β4 loop to α0 helix) and movement of a ‘shift region' towards the catalytic centre, are observed. These conformational changes render MoTps1 to a ‘closed' state compared with its ‘open' state in apo or UDPG complex structures. By solving the EcOtsA apo structure, we confirmed that similar ligand binding induced conformational changes also exist in EcOtsA, although no structural reshuffling involved. Based on our research and previous studies, we present a model for the catalytic process of Tps1. Our research provides novel information on MoTps1, Tps1 family, and structure-based antifungal drug design.

Combustion Driven by Fragment-based Ab Initio Molecular Dynamics Simulation

2019 ◽  
Author(s):  
Liqun Cao ◽  
Jinzhe Zeng ◽  
Mingyuan Xu ◽  
Chih-Hao Chin ◽  
Tong Zhu ◽  
...  
Keyword(s):  
Molecular Dynamics ◽  
Ab Initio ◽  
Large Scale ◽  
Methane Combustion ◽  
Combustion Method ◽  
Dynamics Simulation ◽  
Ab Initio Molecular Dynamics ◽  
Computational Time ◽  
Combustion Mechanism ◽  
Daily Lives

Combustion is a kind of important reaction that affects people's daily lives and the development of aerospace. Exploring the reaction mechanism contributes to the understanding of combustion and the more efficient use of fuels. Ab initio quantum mechanical (QM) calculation is precise but limited by its computational time for large-scale systems. In order to carry out reactive molecular dynamics (MD) simulation for combustion accurately and quickly, we develop the MFCC-combustion method in this study, which calculates the interaction between atoms using QM method at the level of MN15/6-31G(d). Each molecule in systems is treated as a fragment, and when the distance between any two atoms in different molecules is greater than 3.5 Å, a new fragment involved two molecules is produced in order to consider the two-body interaction. The deviations of MFCC-combustion from full system calculations are within a few kcal/mol, and the result clearly shows that the calculated energies of the different systems using MFCC-combustion are close to converging after the distance thresholds are larger than 3.5 Å for the two-body QM interactions. The methane combustion was studied with the MFCC-combustion method to explore the combustion mechanism of the methane-oxygen system.

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