scholarly journals The Role of Substrate Mediated Allostery in the Catalytic Competency of the Bacterial Oligosaccharyltransferase PglB

2021 ◽  
Vol 8 ◽  
Author(s):  
Brittany R. Morgan ◽  
Francesca Massi
Keyword(s):  
Structural Changes ◽  
Transmembrane Domain ◽  
Consensus Sequence ◽  
Catalytic Efficiency ◽  
Van Der Waals Interactions ◽  
External Loop ◽  
Allosteric Communication ◽  
Periplasmic Domain ◽  
Campylobacter Lari ◽  
Dynamics Simulations

The oligosaccharyltransferase of Campylobacter lari (PglB) catalyzes the glycosylation of asparagine in the consensus sequence N-X-S/T, where X is any residue except proline. Molecular dynamics simulations of PglB bound to two different substrates were used to characterize the differences in the structure and dynamics of the substrate-enzyme complexes that can explain the higher catalytic efficiency observed for substrates containing threonine at the +2 position rather than serine. We observed that a threonine-containing substrate is more tightly bound than a serine-containing substrate. Because serine lacks a methyl group relative to threonine, the serine-containing peptide cannot stably form simultaneous van der Waals interactions with T316 and I572 as the threonine-containing substrate can. As a result, the peptide-PglB interaction is destabilized and the allosteric communication between the periplasmic domain and external loop EL5 is disrupted. These changes ultimately lead to the reorientation of the periplasmic domain relative to the transmembrane domain such that the two domains are further apart compared to PglB bound to the threonine-containing peptide. The crystal structure of PglB bound to the peptide and a lipid-linked oligosaccharide analog shows a pronounced closing of the periplasmic domain over the transmembrane domain in comparison to structures of PglB with peptide only, indicating that a closed conformation of the domains is needed for catalysis. The results of our studies suggest that lower enzymatic activity observed for serine versus threonine results from a combination of less stable binding and structural changes in PglB that influence the ability to form a catalytically competent state. This study illustrates a mechanism for substrate specificity via modulation of dynamic allosteric pathways.

scholarly journals Dynamic Community Composition Unravels Allosteric Communication in PDZ3

2020 ◽  
Author(s):  
Tandac F. Guclu ◽  
Ali Rana Atilgan ◽  
Canan Atilgan
Keyword(s):  
Community Composition ◽  
Conformational Changes ◽  
Structural Changes ◽  
Distal Segment ◽  
Allosteric Communication ◽  
C Terminus ◽  
N Terminus ◽  
Ligand Interactions ◽  
Binding Cavity ◽  
Dynamics Simulations

ABSTRACTThe third domain of PSD-95 (PDZ3) is a model for investigating allosteric communication in protein and ligand interactions. While motifs contributing to its binding specificity have been scrutinized, a conformational dynamical basis is yet to be established. Despite the miniscule structural changes due to point mutants, the observed significant binding affinity differences have previously been assessed with a focus on two α-helices located at the binding groove (α2) and the C-terminus (α3). Here, we employ a new computational approach to develop a generalized view on the molecular basis of PDZ3 binding selectivity and interaction communication for a set of point mutants of the protein (G330T, H372A, G330T-H372A) and its ligand (CRIPT named L1 and its T-2F variant L2) along with the wild type (WT). To analyze the dynamical aspects hidden in the conformations that are produced by molecular dynamics simulations, we utilize variations in community composition calculated based on the betweenness centrality measure from graph theory. We find that the highly charged N-terminus which is located far from the ligand has the propensity to share the same community with the ligand in the biologically functional complexes, indicating a distal segment might mediate the binding dynamics. N- and C-termini of PDZ3 share communities, and α3 acts as a hub for the whole protein by sustaining the communication with all structural segments, albeit being a trait not unique to the functional complexes. Moreover, α2 which lines the binding cavity frequently parts communities with the ligand and is not a controller of the binding but is rather a slave to the overall dynamics coordinated by the N-terminus. Thus, ligand binding fate in PDZ3 is traced to the population of community compositions extracted from dynamics despite the lack of significant conformational changes.

scholarly journals Mechanistic Insights into the Active Site and Allosteric Communication Pathways in Human Nonmuscle Myosin-2C

2017 ◽  
Author(s):  
Krishna Chinthalapudi ◽  
Sarah M. Heissler ◽  
Matthias Preller ◽  
James R. Sellers ◽  
Dietmar J. Manstein
Keyword(s):  
Active Site ◽  
Structural Changes ◽  
Release Kinetics ◽  
Motor Domain ◽  
Actin Binding ◽  
Nonmuscle Myosin ◽  
Cortical Actin ◽  
Allosteric Communication ◽  
Dynamics Simulations ◽  
Communication Pathway

AbstractThe cyclical interaction of myosin with F-actin and nucleotides is the basis for contractility of the actin cytoskeleton. Despite a generic, highly conserved motor domain, ATP turnover kinetics and their activation by F-actin vary greatly between myosins-2 isoforms. Here, we present a 2.25 Å crystal structure of the human nonmuscle myosin-2C motor domain, one of the slowest myosins characterized. In combination with integrated mutagenesis, ensemble-solution kinetics, and molecular dynamics simulations approaches, this study reveals an allosteric communication pathway that connects the distal end of the motor domain with the active site. Genetic disruption of this pathways reduces nucleotide binding and release kinetics up to 85-fold and abolishes nonmuscle myosin-2 specific kinetic signatures. These results provide insights into structural changes in the myosin motor domain that are triggered upon F-actin binding and contribute critically to the mechanochemical behavior of stress fibers, actin arcs, and cortical actin-based structures.

scholarly journals Mg2+-sensing mechanism of Mg2+ transporter MgtE probed by molecular dynamics study

2008 ◽  
Vol 105 (40) ◽  
pp. 15393-15398 ◽  
Author(s):  
Ryuichiro Ishitani ◽  
Yuji Sugita ◽  
Naoshi Dohmae ◽  
Noritaka Furuya ◽  
Motoyuki Hattori ◽  
...  
Keyword(s):  
Molecular Dynamics ◽  
Structural Changes ◽  
Transmembrane Domain ◽  
Ion Selectivity ◽  
Ion Concentration ◽  
Detailed Model ◽  
Cytosolic Domain ◽  
Ion Conducting ◽  
Dynamics Simulations ◽  
Cbs Domains

Proper regulation of the intracellular ion concentration is essential to maintain life and is achieved by ion transporters that transport their substrates across the membrane in a strictly regulated manner. MgtE is a Mg2+ transporter that may function in the homeostasis of the intracellular Mg2+ concentration. A recent crystallographic study revealed that its cytosolic domain undergoes a Mg2+-dependent structural change, which is proposed to gate the ion-conducting pore passing through the transmembrane domain. However, the dynamics of Mg2+ sensing, i.e., how MgtE responds to the change in the intracellular Mg2+ concentration, remained elusive. Here we performed molecular dynamics simulations of the MgtE cytosolic domain. The simulations successfully reproduced the structural changes of the cytosolic domain upon binding or releasing Mg2+, as well as the ion selectivity. These results suggested the roles of the N and CBS domains in the cytosolic domain and their respective Mg2+ binding sites. Combined with the current crystal structures, we propose an atomically detailed model of Mg2+ sensing by MgtE.

Tuning the Electric Field Response of MOFs by Rotatable Dipolar Linkers

2019 ◽  
Author(s):  
Johannes P. Dürholt ◽  
Babak Farhadi Jahromi ◽  
Rochus Schmid
Keyword(s):  
Electric Field ◽  
Electric Fields ◽  
Structural Changes ◽  
Dielectric Behavior ◽  
Two Dimensions ◽  
Dielectric Constants ◽  
Electric Response ◽  
Dipole Strength ◽  
Metal Organic ◽  
Dynamics Simulations

Recently the possibility of using electric fields as a further stimulus to trigger structural changes in metal-organic frameworks (MOFs) has been investigated. In general, rotatable groups or other types of mechanical motion can be driven by electric fields. In this study we demonstrate how the electric response of MOFs can be tuned by adding rotatable dipolar linkers, generating a material that exhibits paralectric behavior in two dimensions and dielectric behavior in one dimension. The suitability of four different methods to compute the relative permittivity κ by means of molecular dynamics simulations was validated. The dependency of the permittivity on temperature T and dipole strength μ was determined. It was found that the herein investigated systems exhibit a high degree of tunability and substantially larger dielectric constants as expected for MOFs in general. The temperature dependency of κ obeys the Curie-Weiss law. In addition, the influence of dipolar linkers on the electric field induced breathing behavior was investigated. With increasing dipole moment, lower field strength are required to trigger the contraction. These investigations set the stage for an application of such systems as dielectric sensors, order-disorder ferroelectrics or any scenario where movable dipolar fragments respond to external electric fields.

scholarly journals Cofilin is a pH sensor for actin free barbed end formation: role of phosphoinositide binding

2008 ◽  
Vol 183 (5) ◽  
pp. 865-879 ◽  
Author(s):  
Christian Frantz ◽  
Gabriela Barreiro ◽  
Laura Dominguez ◽  
Xiaoming Chen ◽  
Robert Eddy ◽  
...  
Keyword(s):  
Actin Filament ◽  
Structural Changes ◽  
Ph Sensor ◽  
Ph Sensitive ◽  
Actin Binding ◽  
Filamentous Actin ◽  
Filament Dynamics ◽  
Ph Dependent ◽  
Dynamics Simulations

Newly generated actin free barbed ends at the front of motile cells provide sites for actin filament assembly driving membrane protrusion. Growth factors induce a rapid biphasic increase in actin free barbed ends, and we found both phases absent in fibroblasts lacking H+ efflux by the Na-H exchanger NHE1. The first phase is restored by expression of mutant cofilin-H133A but not unphosphorylated cofilin-S3A. Constant pH molecular dynamics simulations and nuclear magnetic resonance (NMR) reveal pH-sensitive structural changes in the cofilin C-terminal filamentous actin binding site dependent on His133. However, cofilin-H133A retains pH-sensitive changes in NMR spectra and severing activity in vitro, which suggests that it has a more complex behavior in cells. Cofilin activity is inhibited by phosphoinositide binding, and we found that phosphoinositide binding is pH-dependent for wild-type cofilin, with decreased binding at a higher pH. In contrast, phosphoinositide binding by cofilin-H133A is attenuated and pH insensitive. These data suggest a molecular mechanism whereby cofilin acts as a pH sensor to mediate a pH-dependent actin filament dynamics.

scholarly journals A Comprehensive Review of Cholinesterase Modeling and Simulation

Biomolecules ◽  
2021 ◽  
Vol 11 (4) ◽  
pp. 580
Author(s):  
Danna De Boer ◽  
Nguyet Nguyen ◽  
Jia Mao ◽  
Jessica Moore ◽  
Eric J. Sorin
Keyword(s):  
Modeling And Simulation ◽  
Binding Site ◽  
Catalytic Efficiency ◽  
Site Location ◽  
Simulation Techniques ◽  
Therapeutic Value ◽  
Docking Calculations ◽  
Computer Based ◽  
Dynamics Simulations ◽  
And Function

The present article reviews published efforts to study acetylcholinesterase and butyrylcholinesterase structure and function using computer-based modeling and simulation techniques. Structures and models of both enzymes from various organisms, including rays, mice, and humans, are discussed to highlight key structural similarities in the active site gorges of the two enzymes, such as flexibility, binding site location, and function, as well as differences, such as gorge volume and binding site residue composition. Catalytic studies are also described, with an emphasis on the mechanism of acetylcholine hydrolysis by each enzyme and novel mutants that increase catalytic efficiency. The inhibitory activities of myriad compounds have been computationally assessed, primarily through Monte Carlo-based docking calculations and molecular dynamics simulations. Pharmaceutical compounds examined herein include FDA-approved therapeutics and their derivatives, as well as several other prescription drug derivatives. Cholinesterase interactions with both narcotics and organophosphate compounds are discussed, with the latter focusing primarily on molecular recognition studies of potential therapeutic value and on improving our understanding of the reactivation of cholinesterases that are bound to toxins. This review also explores the inhibitory properties of several other organic and biological moieties, as well as advancements in virtual screening methodologies with respect to these enzymes.

scholarly journals Two transmembrane dimers of the bovine papillomavirus E5 oncoprotein clamp the PDGF β receptor in an active dimeric conformation

2017 ◽  
Vol 114 (35) ◽  
pp. E7262-E7271 ◽  
Author(s):  
Alexander G. Karabadzhak ◽  
Lisa M. Petti ◽  
Francisco N. Barrera ◽  
Anne P. B. Edwards ◽  
Andrés Moya-Rodríguez ◽  
...  
Keyword(s):  
Transmembrane Domain ◽  
Transmembrane Protein ◽  
Receptor Activation ◽  
Bovine Papillomavirus ◽  
Detailed Model ◽  
E5 Protein ◽  
Membrane Modeling ◽  
E5 Oncoprotein ◽  
Β Receptor ◽  
Dynamics Simulations

The dimeric 44-residue E5 protein of bovine papillomavirus is the smallest known naturally occurring oncoprotein. This transmembrane protein binds to the transmembrane domain (TMD) of the platelet-derived growth factor β receptor (PDGFβR), causing dimerization and activation of the receptor. Here, we use Rosetta membrane modeling and all-atom molecular dynamics simulations in a membrane environment to develop a chemically detailed model of the E5 protein/PDGFβR complex. In this model, an active dimer of the PDGFβR TMD is sandwiched between two dimers of the E5 protein. Biochemical experiments showed that the major PDGFβR TMD complex in mouse cells contains two E5 dimers and that binding the PDGFβR TMD to the E5 protein is necessary and sufficient to recruit both E5 dimers into the complex. These results demonstrate how E5 binding induces receptor dimerization and define a molecular mechanism of receptor activation based on specific interactions between TMDs.

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