scholarly journals Elucidating the Molecular Basis of pH Activation of an Engineered Mechanosensitive Channel

2019 ◽  
Author(s):  
Kalyan Immadisetty ◽  
Adithya Polasa ◽  
Reid Shelton ◽  
Mahmoud Moradi
Keyword(s):  
Mechanical Energy ◽  
Salt Bridge ◽  
Md Simulations ◽  
Pressure Profile ◽  
Chemical Signals ◽  
Activation Mechanism ◽  
Activation Process ◽  
Ph Change ◽  
Non Equilibrium Molecular Dynamics ◽  
First Time

AbstractMechanosensitive (MS) channels detect and respond to changes in the pressure profile of cellular membranes and transduce the mechanical energy into electrical and/or chemical signals. By re-engineering, however, the activation of some MS channels can be triggered by chemical signals such as pH change. Here, for the first time, we have elucidated, at an atomic level, the activation mechanism of an engineered MscL channel in response to the pH changes of the environment through a combination of equilibrium and non-equilibrium molecular dynamics (MD) simulations. The key highlights of our proposed activation mechanism are that: (1) periplasmic loops play a key role in activation, (2) loss of various hydrogen bonding and salt bridge interactions in the engineered MscL channel causes the opening of the channel, and (3) the most significant interactions lost during the activation process are those between the transmembrane (TM) helices 1 and 2 (TM1 and TM2). The orientation-based method in this work for generating and optimizing an open model of engineered MscL is a promising method for generating unknown states of proteins and for studying the activation processes in ion channels. This work facilitates the studies aimed at designing pH-triggered drug delivery liposomes (DDL), which embed MscL as a nanovalve.

scholarly journals Activation mechanism of Drosophila cryptochrome through an allosteric switch

2021 ◽  
Vol 7 (25) ◽  
pp. eabg3815
Author(s):  
Yingjie Wang ◽  
Gianluigi Veglia ◽  
Dongping Zhong ◽  
Jiali Gao
Keyword(s):  
Computational Models ◽  
Dynamic Network ◽  
Salt Bridge ◽  
Structural Features ◽  
Activation Mechanism ◽  
Radius Of Gyration ◽  
Activation Process ◽  
Amino Terminal ◽  
Global Dynamic ◽  
Carboxyl Terminal

Cryptochromes are signaling proteins activated by photoexcitation of the flavin adenine dinucleotide (FAD) cofactor. Although extensive research has been performed, the mechanism for this allosteric process is still unknown. We constructed three computational models, corresponding to different redox states of the FAD cofactor in Drosophila cryptochrome (dCRY). Analyses of the dynamics trajectories reveal that the activation process occurs in the semiquinone state FAD−●, resulting from excited-state electron transfer. The Arg381-Asp410 salt bridge acts as an allosteric switch, regulated by the change in the redox state of FAD. In turn, Asp410 forms new hydrogen bonds, connecting allosteric networks of the amino-terminal and carboxyl-terminal domains initially separated in the resting state. The expansion to a global dynamic network leads to enhanced protein fluctuations, an increase in the radius of gyration, and the expulsion of the carboxyl-terminal tail. These structural features are in accord with mutations and spectroscopic experiments.

Sensitivity of Thermal Conductivity of Carbon Nanotubes to Defect Concentrations and Heat-Treatment

2012 ◽  
Author(s):  
Michael F. P. Bifano ◽  
Jungkyu Park ◽  
Vikas Prakash
Keyword(s):  
Thermal Conductivity ◽  
Heat Treatment ◽  
Interatomic Potential ◽  
Side Wall ◽  
Chemical Vapor ◽  
Md Simulations ◽  
Heat Treated ◽  
Side Walls ◽  
Non Equilibrium Molecular Dynamics ◽  
Vacancy Concentrations

In the present study, classical MD simulations using reverse non-equilibrium molecular dynamics with the AIREBO interatomic potential are used to investigate the sensitivity of thermal conductivity in SWCNTs to side-wall defect concentration and heat-treatment. Two types of defects are investigated. First, the thermal conductivity of (6,6) SWCNTs is obtained as a function of concentration of chemisorbed hydrogen adatoms. Secondly, the thermal conductivity is obtained as a function of point-vacancy concentrations. The results of the studies show that 2 atom% of hydrogenation and 1.5–2% vacancy concentrations have very similar detrimental effects on the thermal conductivity of SWCNT. Vacancy repair is evident with heat treatment, and heat-treatments at 3000°C for up to 22 ns are found to transform point vacancies into various types of non-hexagonal side-wall defects; this vacancy repair is accompanied by a ca. 10% increase in thermal conductivity. Thermal conductivity measurements in both heat-treated and non-heat treated chemical vapor deposition grown MWCNTs are also reviewed. The results suggest that CNT thermal conductivity can be drastically increased if measures are taken to remove common defects from the SWCNT side-walls.

scholarly journals All-Atom MD Simulations of the HBV Capsid Complexed with AT130 Reveal Secondary and Tertiary Structural Changes and Mechanisms of Allostery

2021 ◽  
Author(s):  
Carolina Pérez Segura ◽  
Boon Chong Goh ◽  
Jodi A. Hadden-Perilla
Keyword(s):  
Small Molecules ◽  
Drug Target ◽  
Structural Changes ◽  
Salt Bridge ◽  
Md Simulations ◽  
Health Concern ◽  
Protein Dimer ◽  
B Virus ◽  
Flexible Protein ◽  
Dynamics Simulations

AbstractThe hepatitis B virus (HBV) capsid is an attractive drug target, relevant to combating viral hepatitis as a major public health concern. Among small molecules known to interfere with capsid assembly, the phenylpropenamides, including AT130, represent an important anti-viral paradigm based on disrupting the timing of genome encapsulation. Crystallographic studies of AT130-bound complexes have been essential in explaining the effects of the small molecule on HBV capsid structure; however, computational examination reveals that key changes attributed to AT130 were erroneous, likely a consequence of interpreting poor resolution arising from a highly flexible protein. Here, all-atom molecular dynamics simulations of an intact AT130-bound HBV capsid reveal that, rather than damaging spike helicity, AT130 enhances the capsid’s ability to recover it. A new conformational state is identified, which can lead to dramatic opening of the intradimer interface and disruption of communication within the spike tip. A novel salt bridge is also discovered, which can mediate contact between the spike tip and fulcrum even in closed conformations, revealing a mechanism of direct communication across these domains. Combined with dynamical network analysis, results describe a connection between the intra- and interdimer interfaces and enable mapping of allostery traversing the entire capsid protein dimer.

scholarly journals Exploration of inositol 1,4,5-trisphosphate (IP3) regulated dynamics of N-terminal domain of IP3 receptor reveals early phase molecular events during receptor activation

2018 ◽  
Author(s):  
Aneesh Chandran ◽  
Xavier Chee ◽  
David L. Prole ◽  
Taufiq Rahman
Keyword(s):  
Conformational Dynamics ◽  
Md Simulations ◽  
Receptor Activation ◽  
Activation Mechanism ◽  
Ip3 Receptor ◽  
Dynamic Correlation ◽  
Molecular Events ◽  
Binding Core ◽  
Domain Dynamics ◽  
Phosphate Groups

Inositol 1, 4, 5-trisphosphate (IP3) binding at the N-terminus (NT) of IP3 receptor (IP3R) allosterically triggers the opening of a Ca2+-conducting pore located ~ 100 Å away from the IP3-binding core (IBC). However, the precise mechanism of IP3 binding and correlated domain dynamics in the NT that are central to the IP3R activation, remains unknown. Our all-atom molecular dynamics (MD) simulations recapitulate the characteristic twist motion of the suppresser domain (SD) and reveal correlated ‘clam closure’ dynamics of IBC with IP3-binding, complementing existing suggestions on IP3R activation mechanism. Our study further reveals the existence of inter-domain dynamic correlation in the NT and establishes the SD to be critical for the conformational dynamics of IBC. Also, a tripartite interaction involving Glu283-Arg54-Asp444 at the SD – IBC interface seemed critical for IP3R activation. Intriguingly, during the sub-microsecond long simulation, we observed Arg269 undergoing an SD-dependent flipping of hydrogen bonding between the first and fifth phosphate groups of IP3. This seems to play a major role in determining the IP3 binding affinity of IBC in the presence/absence of the SD. Our study thus provides atomistic details of early molecular events occurring within the NT during and following IP3 binding that lead to channel gating.

scholarly journals Butyl Isocyanide as a Probe of the Activation Mechanism of Soluble Guanylate Cyclase

2007 ◽  
Vol 282 (49) ◽  
pp. 35741-35748 ◽  
Author(s):  
Emily R. Derbyshire ◽  
Michael A. Marletta
Keyword(s):  
Nitric Oxide ◽  
Binding Site ◽  
Guanylate Cyclase ◽  
Electronic Absorption ◽  
Soluble Guanylate Cyclase ◽  
Activation Mechanism ◽  
Activation Process ◽  
Absorbance Maximum ◽  
No Activation ◽  
Allosteric Activator

Nitric oxide (NO) is a physiologically relevant activator of the hemoprotein soluble guanylate cyclase (sGC). In the presence of NO, sGC is activated several hundredfold above the basal level by a mechanism that remains to be elucidated. The heme ligand n-butyl isocyanide (BIC) was used to probe the mechanism of NO activation of sGC. Electronic absorption spectroscopy was used to show that BIC binds to the sGC heme, forming a 6-coordinate complex with an absorbance maximum at 429 nm. BIC activates sGC 2-5-fold, and synergizes with the allosteric activator YC-1, to activate the enzyme 15-25-fold. YC-1 activates the sGC-BIC complex, and leads to an increase in both the Vmax and Km. BIC was also used to probe the mechanism of NO activation. The activity of the sGC-BIC complex increases 15-fold in the presence of NO, without displacing BIC at the heme, which is consistent with previous reports that proposed the involvement of a non-heme NO binding site in the activation process.

AN ANALYSIS OF THE THZ FREQUENCY SIGNATURES IN THE CELLULAR COMPONENTS OF BIOLOGICAL AGENTS

2007 ◽  
Vol 17 (02) ◽  
pp. 225-237 ◽  
Author(s):  
ALEXEI BYKHOVSKI ◽  
TATIANA GLOBUS ◽  
TATYANA KHROMOVA ◽  
BORIS GELMONT ◽  
DWIGHT WOOLARD
Keyword(s):  
Molecular Structure ◽  
Structural Similarity ◽  
Md Simulations ◽  
Detection Capability ◽  
Dna Structures ◽  
E Coli ◽  
Cellular Components ◽  
First Time ◽  
Insight Into ◽  
Specific Contribution

The development of an effective biological (bio) agent detection capability based upon terahertz (THz) frequency absorption spectra will require insight into how the constituent cellular components contribute to the overall THz signature. In this work, the specific contribution of ribonucleic acid (RNA) to THz spectra is analyzed in detail. Previously, it has only been possible to simulate partial fragments of the RNA (or DNA) structures due to the excessive computational demands. For the first time, the molecular structure of the entire transfer RNA (tRNA) molecule of E. coli was simulated and the associated THz signature was derived theoretically. The tRNA that binds amino acid tyrosine (tRNAtyr) was studied. Here, the molecular structure was optimized using the potential energy minimization and molecular dynamical (MD) simulations. Solvation effects (water molecules) were also included explicitly in the MD simulations. To verify that realistic molecular signatures were simulated, a parallel experimental study of tRNAs of E. coli was also conducted. Two very similar molecules, valine and tyrosine tRNA were investigated experimentally. Samples were prepared in the form of water solutions with the concentrations in the range 0.01-1 mg/ml. A strong correlation of the measured THz signatures associated with valine tRNA and tyrosine tRNA was observed. These findings are consistent with the structural similarity of the two tRNAs. The calculated THz signature of the tyrosine tRNA of E. coli reproduces many features of our measured spectra, and, therefore, provides valuable new insights into bio-agent detection.

Absorption of Mechanical Energy via Formation of Ice Nanotubes in Zeolite

2021 ◽  
Author(s):  
Kenji Mochizuki
Keyword(s):  
Molecular Dynamics ◽  
Molecular Dynamics Simulations ◽  
Heterogeneous System ◽  
Mechanical Energy ◽  
Bulk Water ◽  
Pure Silica ◽  
Dynamics Simulations ◽  
First Time

Abstract Molecular dynamics simulations are carried out for a heterogeneous system composed of bulk water and pure-silica zeolites of the AFI type. Our simulations show, for the first time, the...

scholarly journals Computational Study of C-X-C Chemokine Receptor (CXCR)3 Binding with Its Natural Agonists Chemokine (C-X-C Motif) Ligand (CXCL)9, 10 and 11 and with Synthetic Antagonists: Insights of Receptor Activation towards Drug Design for Vitiligo

Molecules ◽  
2020 ◽  
Vol 25 (19) ◽  
pp. 4413
Author(s):  
Giovanny Aguilera-Durán ◽  
Antonio Romo-Mancillas
Keyword(s):  
Molecular Dynamics ◽  
Computational Study ◽  
Md Simulations ◽  
Receptor Activation ◽  
Activation Mechanism ◽  
Coarse Grained ◽  
Dimensional Structure ◽  
Cytotoxic Lymphocytes ◽  
Ligand Interaction ◽  
Α Subunit

Vitiligo is a hypopigmentary skin pathology resulting from the death of melanocytes due to the activity of CD8+ cytotoxic lymphocytes and overexpression of chemokines. These include CXCL9, CXCL10, and CXCL11 and its receptor CXCR3, both in peripheral cells of the immune system and in the skin of patients diagnosed with vitiligo. The three-dimensional structure of CXCR3 and CXCL9 has not been reported experimentally; thus, homology modeling and molecular dynamics could be useful for the study of this chemotaxis-promoter axis. In this work, a homology model of CXCR3 and CXCL9 and the structure of the CXCR3/Gαi/0βγ complex with post-translational modifications of CXCR3 are reported for the study of the interaction of chemokines with CXCR3 through all-atom (AA-MD) and coarse-grained molecular dynamics (CG-MD) simulations. AA-MD and CG-MD simulations showed the first activation step of the CXCR3 receptor with all chemokines and the second activation step in the CXCR3-CXCL10 complex through a decrease in the distance between the chemokine and the transmembrane region of CXCR3 and the separation of the βγ complex from the α subunit in the G-protein. Additionally, a general protein–ligand interaction model was calculated, based on known antagonists binding to CXCR3. These results contribute to understanding the activation mechanism of CXCR3 and the design of new molecules that inhibit chemokine binding or antagonize the receptor, provoking a decrease of chemotaxis caused by the CXCR3/chemokines axis.

Influence of mixing energy on the solid-state behavior and clay fraction threshold of PA12/C30B® nanocomposites

2019 ◽  
Vol 39 (6) ◽  
pp. 565-572
Author(s):  
Nourredine Aït Hocine ◽  
Pascal Médéric ◽  
Hanaya Hassan
Keyword(s):  
Solid State ◽  
Mechanical Energy ◽  
Three Dimensional ◽  
Clay Fraction ◽  
Critical Value ◽  
Processing Conditions ◽  
State Behavior ◽  
Mixing Energy ◽  
End Use ◽  
First Time

Abstract This study focuses on the influence of mixing energy on the solid-state behavior and clay fraction threshold of nanocomposites. Thus, three polyamide12/clay (PA12/C30B®) nanocomposites exhibiting different nanostructures were prepared from three sets of processing conditions. Then, thermal and dynamical viscoelastic properties of these nanocomposites were analyzed, in relationship with the material nanostructure and processing conditions. For the first time, the solid-state properties of the nanocomposites revealed the existence of a critical specific mixing mechanical energy. Below this critical value, an increase of mechanical energy refines the structure, improving some end-use properties of the nanocomposite. Above this value, a high mixing energy supply is necessary in order to significantly modify the structure. They also highlighted that the clay fraction threshold, which is commonly attributed to the formation of a three-dimensional percolated network, decreases with increasing specific mixing energy, less significantly when this energy is superior to its critical value.

scholarly journals The allosteric activation mechanism of a phospholipase A2-like toxin from Bothrops jararacussu venom: a dynamic description

2020 ◽  
Vol 10 (1) ◽  
Author(s):  
Antoniel A. S. Gomes ◽  
Fabio F. Cardoso ◽  
Maximilia F. Souza ◽  
Cristiano L. P. Oliveira ◽  
David Perahia ◽  
...  
Keyword(s):  
Conformational Changes ◽  
Activation Mechanism ◽  
Activation Process ◽  
Structural Determinants ◽  
Allosteric Activation ◽  
Bothrops Jararacussu ◽  
Inactive State ◽  
Dynamic Description ◽  
Comprehensive Study

Abstract The activation process of phospholipase A2-like (PLA2-like) toxins is a key step in their molecular mechanism, which involves oligomeric changes leading to the exposure of specific sites. Few studies have focused on the characterization of allosteric activators and the features that distinguish them from inhibitors. Herein, a comprehensive study with the BthTX-I toxin from Bothrops jararacussu venom bound or unbound to α-tocopherol (αT) was carried out. The oligomerization state of BthTX-I bound or unbound to αT in solution was studied and indicated that the toxin is predominantly monomeric but tends to oligomerize when complexed with αT. In silico molecular simulations showed the toxin presents higher conformational changes in the absence of αT, which suggests that it is important to stabilize the structure of the toxin. The transition between the two states (active/inactive) was also studied, showing that only the unbound BthTX-I system could migrate to the inactive state. In contrast, the presence of αT induces the toxin to leave the inactive state, guiding it towards the active state, with more regions exposed to the solvent, particularly its active site. Finally, the structural determinants necessary for a molecule to be an inhibitor or activator were analyzed in light of the obtained results.

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