scholarly journals Investigating the opening mechanism of topoisomerase I B in complex with DNA by means of metadynamics

2016 ◽  
Author(s):  
Blasco Morozzo della Rocca ◽  
Andrea Coletta ◽  
Federico Iacovelli ◽  
Alessandro Desideri
Keyword(s):  
Conformational Changes ◽  
Topoisomerase I ◽  
Specific Activity ◽  
Dimensional Space ◽  
Center Of Mass ◽  
Minimum Energy ◽  
Salt Bridge ◽  
Computational Techniques ◽  
Salt Bridges ◽  
Collective Variables

Motivations: Topoisomerases play a central role in DNA homeostasis and act on them through a catalytic cycle that comprises the opening of the protein clamp to embrace the DNA (at the beginning of the cycle) and opening to allow the release of the topologically relaxed substrate. Protein opening is hard to follow experimentally thus computational techniques are very handy in dealing with this transitions, although classical molecular dynamics is limited in following big conformational changes and slowly occurring transitions. Therefore we present a well-tempered Metadynamics study of hToP1 clamp opening in presence of a 22-bp long ds-DNA substrate. Methods: The protein structure of wild type hTopIB in complex with DNA has been obtained as previously reported. The hTopIB clamp around the DNA molecule has been destabilized by means of metadynamics using Gromacs-4.5.5 with the PLUMEDv1.3 patch. In the simulation, two Collective Variables have been used to describe the clamp opening: the distance between the center of mass of Cα atoms of the lip1 and of the lip2; and the number of hydrogen bonds between the protein and DNA.Free-energy surface (FES) and the minimum energy path (MEP) connecting different minima were reconstructed using in-house written codes in Python. Salt bridge analysis was conducted via Salt bridges extension of the VMD program and other analyses were performed with the tools of the GROMACS package. Results: Results indicate that the lobes of the protein retain their domain structure during the opening that is characterized by an energy barrier of about 50 Kjoul/mole. Furthermore the DNA remains in contact with the Cap lobe, a fact that would enable the protein to perform 1D-diffusion in the DNA strand to enhance the specific activity by reducing the dimensional space it has to search between relaxation events.

scholarly journals Investigating the opening mechanism of topoisomerase I B in complex with DNA by means of metadynamics

2016 ◽  
Author(s):  
Blasco Morozzo della Rocca ◽  
Andrea Coletta ◽  
Federico Iacovelli ◽  
Alessandro Desideri
Keyword(s):  
Conformational Changes ◽  
Topoisomerase I ◽  
Specific Activity ◽  
Dimensional Space ◽  
Center Of Mass ◽  
Minimum Energy ◽  
Salt Bridge ◽  
Computational Techniques ◽  
Salt Bridges ◽  
Collective Variables

Motivations: Topoisomerases play a central role in DNA homeostasis and act on them through a catalytic cycle that comprises the opening of the protein clamp to embrace the DNA (at the beginning of the cycle) and opening to allow the release of the topologically relaxed substrate. Protein opening is hard to follow experimentally thus computational techniques are very handy in dealing with this transitions, although classical molecular dynamics is limited in following big conformational changes and slowly occurring transitions. Therefore we present a well-tempered Metadynamics study of hToP1 clamp opening in presence of a 22-bp long ds-DNA substrate. Methods: The protein structure of wild type hTopIB in complex with DNA has been obtained as previously reported. The hTopIB clamp around the DNA molecule has been destabilized by means of metadynamics using Gromacs-4.5.5 with the PLUMEDv1.3 patch. In the simulation, two Collective Variables have been used to describe the clamp opening: the distance between the center of mass of Cα atoms of the lip1 and of the lip2; and the number of hydrogen bonds between the protein and DNA.Free-energy surface (FES) and the minimum energy path (MEP) connecting different minima were reconstructed using in-house written codes in Python. Salt bridge analysis was conducted via Salt bridges extension of the VMD program and other analyses were performed with the tools of the GROMACS package. Results: Results indicate that the lobes of the protein retain their domain structure during the opening that is characterized by an energy barrier of about 50 Kjoul/mole. Furthermore the DNA remains in contact with the Cap lobe, a fact that would enable the protein to perform 1D-diffusion in the DNA strand to enhance the specific activity by reducing the dimensional space it has to search between relaxation events.

scholarly journals Controlling membrane barrier during bacterial type-III protein secretion

2020 ◽  
Author(s):  
Svenja Hüsing ◽  
Ulf van Look ◽  
Alina Guse ◽  
Eric J. C. Gálvez ◽  
Emmanuelle Charpentier ◽  
...  
Keyword(s):  
Conformational Changes ◽  
High Speed ◽  
Membrane Integrity ◽  
Salt Bridge ◽  
High Rate ◽  
Salt Bridges ◽  
Secretion Systems ◽  
Bacterial Flagellum ◽  
Type Iii ◽  
Membrane Barrier

Type-III secretion systems (T3SSs) of the bacterial flagellum and the evolutionarily related injectisome are capable of translocating proteins with a remarkable speed of several thousand amino acids per second. Here, we investigated how T3SSs are able to transport proteins at such a high rate while preventing the leakage of small molecules. Our mutational and evolutionary analyses demonstrate that an ensemble of conserved methionine residues at the cytoplasmic side of the T3SS channel create a deformable gasket (M-gasket) around fast-moving substrates undergoing export. The unique physicochemical features of the M-gasket are crucial to preserve the membrane barrier, to accommodate local conformational changes during active secretion, and to maintain stability of the secretion pore in cooperation with a plug domain (R-plug) and a network of salt-bridges. The conservation of the M-gasket, R-plug, and salt-bridge network suggests a universal mechanism by which the membrane integrity is maintained during high-speed protein translocation in all T3SSs.

scholarly journals Salt bridges gate α-catenin activation at intercellular junctions

2018 ◽  
Vol 29 (2) ◽  
pp. 111-122 ◽  
Author(s):  
Samantha Barrick ◽  
Jing Li ◽  
Xinyu Kong ◽  
Alokananda Ray ◽  
Emad Tajkhorshid ◽  
...  
Keyword(s):  
Molecular Dynamics ◽  
Mechanical Activation ◽  
Conformational Changes ◽  
Intercellular Junctions ◽  
Salt Bridge ◽  
Salt Bridges ◽  
Equilibrium Binding ◽  
Binding Data ◽  
Dynamics Simulations ◽  
Intercellular Adhesions

Molecular dynamics simulations, equilibrium binding measurements, and fluorescence imaging reveal the influence of a key salt bridge in the mechanical activation of α-catenin at intercellular adhesions. Simulations reveal possible α-catenin conformational changes underlying experimental fluorescence and equilibrium binding data.

scholarly journals Access to the Complement Factor B Scissile Bond Is Facilitated by Association of Factor B with C3b Protein

2011 ◽  
Vol 286 (41) ◽  
pp. 35725-35732 ◽  
Author(s):  
Dennis E. Hourcade ◽  
Lynne M. Mitchell
Keyword(s):  
Conformational Changes ◽  
Metal Ion ◽  
Alternative Pathway ◽  
Salt Bridge ◽  
Single Amino Acid ◽  
Complement Factor ◽  
Salt Bridges ◽  
Complement Alternative Pathway ◽  
Factor B ◽  
Scissile Bond

Factor B is a zymogen that carries the catalytic site of the complement alternative pathway C3 convertase. During convertase assembly, factor B associates with C3b and Mg2+ forming a pro-convertase C3bB(Mg2+) that is cleaved at a single factor B site by factor D. In free factor B, a pair of salt bridges binds the Arg234 side chain to Glu446 and to Glu207, forming a double latch structure that sequesters the scissile bond (between Arg234 and Lys235) and minimizes its unproductive cleavage. It is unknown how the double latch is released in the pro-convertase. Here, we introduce single amino acid substitutions into factor B that preclude one or both of the Arg234 salt bridges, and we examine their impact on several different pro-convertase complexes. Our results indicate that loss of the Arg234-Glu446 salt bridge partially stabilizes C3bB(Mg2+). Loss of the Arg234-Glu207 salt bridge has lesser effects. We propose that when factor B first associates with C3b, it bears two intact Arg234 salt bridges. The complex rapidly dissociates unless the Arg234-Glu446 salt bridge is released whereupon conformational changes occur that activate the metal ion-dependent adhesion site and partially stabilize the complex. The remaining salt bridge is then released, exposing the scissile bond and permitting factor D cleavage.

Modelling and expression studies of two novel mutations causing factor V deficiency

2008 ◽  
Vol 100 (05) ◽  
pp. 766-772 ◽  
Author(s):  
Anna Pavlova ◽  
Stefan Heinz ◽  
Mathias Blaise ◽  
Tamir Chandra ◽  
Bernd Poetsch ◽  
...  
Keyword(s):  
Short Duration ◽  
Conformational Changes ◽  
Structural Integrity ◽  
Specific Activity ◽  
Coagulation Factor ◽  
Salt Bridge ◽  
Factor V ◽  
Wild Type ◽  
Novel Mutations ◽  
Human Embryonic Kidney Cells

SummaryHuman coagulation factor V (FV), a non-enzymatic cofactor of the prothrombinase complex, is required for the rapid generation of thrombin. FV deficiency is a rare autosomal recessive bleeding disorder. We describe two novel mutations,Tyr91Asn and Asp2098Tyr,found in two probands with a residual FV activity of 51% and 4%, respectively. Modelling and structural analysis of these mutations were performed following short-duration molecular dynamics (MD) simulation.Asp2098Tyr lead to abolishment of the highly conserved salt bridge Asp2098-Arg2171 presumably required for structural integrity of the C2 domain. MD studies suggest that additional conformational changes resulting from this mutation involve local rearrangements at Tyr2063 and Tyr2064 and so affect the phospholipid-membrane binding. MD modelling of the Try91Asn mutant revealed a conformational change nearby the Cu2+ binding site that could affect overall stabilization of the heavy and light chains. These findings suggest that both mutations influence the structural integrity of FV protein. Transient expression data of wild-type and mutant FV variants in 293T human embryonic kidney cells showed FV-specific activity reduced to 26% for Asp2098Tyr and 56% for Tyr91Asn compared to that of wild-type. Thus, both the data from the short duration molecular dynamic simulation and from expression analysis indicate alterations of the FV protein variants that explain the clinical phenotype.

scholarly journals Control of membrane barrier during bacterial type-III protein secretion

2021 ◽  
Vol 12 (1) ◽  
Author(s):  
Svenja Hüsing ◽  
Manuel Halte ◽  
Ulf van Look ◽  
Alina Guse ◽  
Eric J. C. Gálvez ◽  
...  
Keyword(s):  
Conformational Changes ◽  
High Speed ◽  
Membrane Integrity ◽  
Salt Bridge ◽  
High Rate ◽  
Salt Bridges ◽  
Secretion Systems ◽  
Bacterial Flagellum ◽  
Type Iii ◽  
Membrane Barrier

AbstractType-III secretion systems (T3SSs) of the bacterial flagellum and the evolutionarily related injectisome are capable of translocating proteins with a remarkable speed of several thousand amino acids per second. Here, we investigate how T3SSs are able to transport proteins at such a high rate while preventing the leakage of small molecules. Our mutational and evolutionary analyses demonstrate that an ensemble of conserved methionine residues at the cytoplasmic side of the T3SS channel create a deformable gasket (M-gasket) around fast-moving substrates undergoing export. The unique physicochemical features of the M-gasket are crucial to preserve the membrane barrier, to accommodate local conformational changes during active secretion, and to maintain stability of the secretion pore in cooperation with a plug domain (R-plug) and a network of salt-bridges. The conservation of the M-gasket, R-plug, and salt-bridge network suggests a universal mechanism by which the membrane integrity is maintained during high-speed protein translocation in all T3SSs.

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.

scholarly journals Hyperbolic Center of Mass for a System of Particles in a Two-Dimensional Space with Constant Negative Curvature: An Application to the Curved 2-Body Problem

Mathematics ◽  
2021 ◽  
Vol 9 (5) ◽  
pp. 531
Author(s):  
Pedro Pablo Ortega Palencia ◽  
Ruben Dario Ortiz Ortiz ◽  
Ana Magnolia Marin Ramirez
Keyword(s):  
Negative Curvature ◽  
Dimensional Space ◽  
Center Of Mass ◽  
Simple Expression ◽  
Two Dimensional ◽  
Constant Negative Curvature ◽  
Euclidean Case ◽  
System Of Particles ◽  
Material Points ◽  
The One

In this article, a simple expression for the center of mass of a system of material points in a two-dimensional surface of Gaussian constant negative curvature is given. By using the basic techniques of geometry, we obtained an expression in intrinsic coordinates, and we showed how this extends the definition for the Euclidean case. The argument is constructive and serves to define the center of mass of a system of particles on the one-dimensional hyperbolic sphere LR1.

ALPHA-HELIX FORMATION IN C-PEPTIDE RNASE-A INVESTIGATED BY PARALLEL TEMPERING SIMULATIONS

2007 ◽  
Vol 18 (01) ◽  
pp. 91-98 ◽  
Author(s):  
GÖKHAN GÖKOĞLU ◽  
TARIK ÇELİK
Keyword(s):  
Energy State ◽  
Minimum Energy ◽  
Alpha Helix ◽  
Salt Bridge ◽  
Rnase A ◽  
Parallel Tempering ◽  
Implicit Solvent ◽  
C Peptide ◽  
Helix Formation ◽  
Α Helix

We have performed parallel tempering simulations of a 13-residue peptide fragment of ribonuclease-A, c-peptide, in implicit solvent with constant dielectric permittivity. This peptide has a strong tendency to form α-helical conformations in solvent as suggested by circular dichroism (CD) and nuclear magnetic resonance (NMR) experiments. Our results demonstrate that 5th and 8–12 residues are in the α-helical region of the Ramachandran map for global minimum energy state in solvent environment. Effects of salt bridge formation on stability of α-helix structure are discussed.

Dynamics of a composite system in a point source-induced space–time

2021 ◽  
pp. 2150144
Author(s):  
Abdullah Guvendi
Keyword(s):  
Point Source ◽  
Composite System ◽  
Dimensional Space ◽  
Energy Levels ◽  
Center Of Mass ◽  
Three Dimensional ◽  
Space Time ◽  
Spin Coupling ◽  
Quantum Oscillator ◽  
Dimensional Space Time

We investigate the dynamics of a composite system ([Formula: see text]) consisting of an interacting fermion–antifermion pair in the three-dimensional space–time background generated by a static point source. By considering the interaction between the particles as Dirac oscillator coupling, we analyze the effects of space–time topology on the energy of such a [Formula: see text]. To achieve this, we solve the corresponding form of a two-body Dirac equation (fully-covariant) by assuming the center-of-mass of the particles is at rest and locates at the origin of the spatial geometry. Under this assumption, we arrive at a nonperturbative energy spectrum for the system in question. This spectrum includes spin coupling and depends on the angular deficit parameter [Formula: see text] of the geometric background. This provides a suitable basis to determine the effects of the geometric background on the energy of the [Formula: see text] under consideration. Our results show that such a [Formula: see text] behaves like a single quantum oscillator. Then, we analyze the alterations in the energy levels and discuss the limits of the obtained results. We show that the effects of the geometric background on each energy level are not same and there can be degeneracy in the energy levels for small values of the [Formula: see text].

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