scholarly journals Molecular Determinants of μ-Conotoxin KIIIA Interaction with the Voltage-Gated Sodium Channel Nav1.7

2019 ◽  
Author(s):  
Ian H. Kimball ◽  
Phuong T. Nguyen ◽  
Baldomero M. Olivera ◽  
Jon T. Sack ◽  
Vladimir Yarov-Yarovoy
Keyword(s):  
Computational Modeling ◽  
Rational Design ◽  
Structural Model ◽  
Critical Role ◽  
Structural Data ◽  
Molecular Probes ◽  
Integrative Approach ◽  
In Silico Docking ◽  
Voltage Gated ◽  
Dynamics Simulations

AbstractThe voltage-gated sodium (Nav) channel subtype Nav1.7 plays a critical role in pain signaling, making it an important drug target. Here we studied the molecular interactions between μ-conotoxin KIIIA (KIIIA) and the human Nav1.7 channel (hNav1.7). We developed a structural model of hNav1.7 using Rosetta computational modeling and performed in silico docking of KIIIA using RosettaDock to predict residues forming specific pairwise contacts between KIIIA and hNav1.7. We experimentally validated these contacts using mutant cycle analysis. Comparison between our KIIIA-hNav1.7 model and the recently published cryo-EM structure of KIIIA-hNav1.2 revealed key similarities and differences between channel subtypes with potential implications for the molecular mechanism of toxin block. Our integrative approach, combining structural data with computational modeling, experimental validation, and molecular dynamics simulations will be useful for engineering molecular probes to study Nav channel function, and for rational design of novel biologics targeting specific Nav channels.

scholarly journals Braiding topology and the energy landscape of chromosome organization proteins

2019 ◽  
Vol 117 (3) ◽  
pp. 1468-1477 ◽  
Author(s):  
Dana Krepel ◽  
Aram Davtyan ◽  
Nicholas P. Schafer ◽  
Peter G. Wolynes ◽  
José N. Onuchic
Keyword(s):  
Structural Information ◽  
Protein Complexes ◽  
Energy Landscape ◽  
Critical Role ◽  
Coiled Coil ◽  
Structural Data ◽  
Atomic Scale ◽  
Integrative Approach ◽  
Chromosome Organization ◽  
Conformational Ensemble

Assemblies of structural maintenance of chromosomes (SMC) proteins and kleisin subunits are essential to chromosome organization and segregation across all kingdoms of life. While structural data exist for parts of the SMC−kleisin complexes, complete structures of the entire complexes have yet to be determined, making mechanistic studies difficult. Using an integrative approach that combines crystallographic structural information about the globular subdomains, along with coevolutionary information and an energy landscape optimized force field (AWSEM), we predict atomic-scale structures for several tripartite SMC−kleisin complexes, including prokaryotic condensin, eukaryotic cohesin, and eukaryotic condensin. The molecular dynamics simulations of the SMC−kleisin protein complexes suggest that these complexes exist as a broad conformational ensemble that is made up of different topological isomers. The simulations suggest a critical role for the SMC coiled-coil regions, where the coils intertwine with various linking numbers. The twist and writhe of these braided coils are coupled with the motion of the SMC head domains, suggesting that the complexes may function as topological motors. Opening, closing, and translation along the DNA of the SMC−kleisin protein complexes would allow these motors to couple to the topology of DNA when DNA is entwined with the braided coils.

scholarly journals Discovery of a hidden transient state in all bromodomain families

2021 ◽  
Vol 118 (4) ◽  
pp. e2017427118
Author(s):  
Lluís Raich ◽  
Katharina Meier ◽  
Judith Günther ◽  
Clara D. Christ ◽  
Frank Noé ◽  
...  
Keyword(s):  
Posttranslational Modifications ◽  
Rational Design ◽  
General Structure ◽  
Transient State ◽  
Structural Data ◽  
Binding Mode ◽  
Dynamical Features ◽  
The One ◽  
Markov State Modeling ◽  
Dynamics Simulations

Bromodomains (BDs) are small protein modules that interact with acetylated marks in histones. These posttranslational modifications are pivotal to regulate gene expression, making BDs promising targets to treat several diseases. While the general structure of BDs is well known, their dynamical features and their interplay with other macromolecules are poorly understood, hampering the rational design of potent and selective inhibitors. Here, we combine extensive molecular dynamics simulations, Markov state modeling, and available structural data to reveal a transiently formed state that is conserved across all BD families. It involves the breaking of two backbone hydrogen bonds that anchor the ZA-loop with the αA helix, opening a cryptic pocket that partially occludes the one associated to histone binding. By analyzing more than 1,900 experimental structures, we unveil just two adopting the hidden state, explaining why it has been previously unnoticed and providing direct structural evidence for its existence. Our results suggest that this state is an allosteric regulatory switch for BDs, potentially related to a recently unveiled BD-DNA–binding mode.

scholarly journals Discovery of a hidden transient state in all bromodomain families

2020 ◽  
Author(s):  
Lluís Raich ◽  
Katharina Meier ◽  
Judith Günther ◽  
Clara D. Christ ◽  
Frank Noé ◽  
...  
Keyword(s):  
Rational Design ◽  
General Structure ◽  
Transient State ◽  
Structural Data ◽  
Binding Mode ◽  
Post Translational Modifications ◽  
Dynamical Features ◽  
The One ◽  
Markov State Modeling ◽  
Dynamics Simulations

ABSTRACTBromodomains (BDs) are small protein modules that interact with acetylated marks in histones. These post-translational modifications are pivotal to regulate gene expression, making BDs promising targets to treat several diseases. While the general structure of BDs is well known, their dynamical features and their interplay with other macromolecules are poorly understood, hampering the rational design of potent and selective inhibitors. Here we combine extensive molecular dynamics simulations, Markov state modeling and structural data to reveal a novel and transiently formed state that is conserved across all BD families. It involves the breaking of two backbone hydrogen bonds that anchor the ZA-loop with the αA helix, opening a cryptic pocket that partially occludes the one associated with histone binding. Our results suggest that this novel state is an allosteric regulatory switch for BDs, potentially related to a recently unveiled BD-DNA binding mode.

scholarly journals Deciphering the structure of the condensin protein complex

2018 ◽  
Vol 115 (47) ◽  
pp. 11911-11916 ◽  
Author(s):  
Dana Krepel ◽  
Ryan R. Cheng ◽  
Michele Di Pierro ◽  
José N. Onuchic
Keyword(s):  
Protein Complexes ◽  
Structural Data ◽  
Atomic Scale ◽  
Integrative Approach ◽  
Protein Subunit ◽  
Entire Complex ◽  
Domains Of Life ◽  
Function Relationship ◽  
Dynamics Simulations ◽  
Opening And Closing

Protein assemblies consisting of structural maintenance of chromosomes (SMC) and kleisin subunits are essential for the process of chromosome segregation across all domains of life. Prokaryotic condensin belonging to this class of protein complexes is composed of a homodimer of SMC that associates with a kleisin protein subunit called ScpA. While limited structural data exist for the proteins that comprise the (SMC)–kleisin complex, the complete structure of the entire complex remains unknown. Using an integrative approach combining both crystallographic data and coevolutionary information, we predict an atomic-scale structure of the whole condensin complex, which our results indicate being composed of a single ring. Coupling coevolutionary information with molecular-dynamics simulations, we study the interaction surfaces between the subunits and examine the plausibility of alternative stoichiometries of the complex. Our analysis also reveals several additional configurational states of the condensin hinge domain and the SMC–kleisin interaction domains, which are likely involved with the functional opening and closing of the condensin ring. This study provides the foundation for future investigations of the structure–function relationship of the various SMC–kleisin protein complexes at atomic resolution.

scholarly journals Rational design of ASCT2 inhibitors using an integrated experimental-computational approach

2021 ◽  
Vol 118 (37) ◽  
pp. e2104093118
Author(s):  
Rachel-Ann A. Garibsingh ◽  
Elias Ndaru ◽  
Alisa A. Garaeva ◽  
Yueyue Shi ◽  
Laura Zielewicz ◽  
...  
Keyword(s):  
Amino Acid ◽  
Computational Modeling ◽  
Binding Site ◽  
Rational Design ◽  
Cancer Therapeutics ◽  
Integrated Analysis ◽  
Peripheral Tissues ◽  
Ligand Discovery ◽  
Potential Strategy ◽  
Dynamics Simulations

ASCT2 (SLC1A5) is a sodium-dependent neutral amino acid transporter that controls amino acid homeostasis in peripheral tissues. In cancer, ASCT2 is up-regulated where it modulates intracellular glutamine levels, fueling cell proliferation. Nutrient deprivation via ASCT2 inhibition provides a potential strategy for cancer therapy. Here, we rationally designed stereospecific inhibitors exploiting specific subpockets in the substrate binding site using computational modeling and cryo-electron microscopy (cryo-EM). The final structures combined with molecular dynamics simulations reveal multiple pharmacologically relevant conformations in the ASCT2 binding site as well as a previously unknown mechanism of stereospecific inhibition. Furthermore, this integrated analysis guided the design of a series of unique ASCT2 inhibitors. Our results provide a framework for future development of cancer therapeutics targeting nutrient transport via ASCT2, as well as demonstrate the utility of combining computational modeling and cryo-EM for solute carrier ligand discovery.

scholarly journals An emerging consensus on voltage-dependent gating from computational modeling and molecular dynamics simulations

2012 ◽  
Vol 140 (6) ◽  
pp. 587-594 ◽  
Author(s):  
Ernesto Vargas ◽  
Vladimir Yarov-Yarovoy ◽  
Fatemeh Khalili-Araghi ◽  
William A. Catterall ◽  
Michael L. Klein ◽  
...  
Keyword(s):  
Molecular Dynamics ◽  
Computational Modeling ◽  
Md Simulations ◽  
Missing Information ◽  
Voltage Gated ◽  
Voltage Dependent ◽  
Voltage Gated Channels ◽  
Voltage Gated Ion Channels ◽  
Dynamics Simulations ◽  
Resolution Structure

Developing an understanding of the mechanism of voltage-gated ion channels in molecular terms requires knowledge of the structure of the active and resting conformations. Although the active-state conformation is known from x-ray structures, an atomic resolution structure of a voltage-dependent ion channel in the resting state is not currently available. This has motivated various efforts at using computational modeling methods and molecular dynamics (MD) simulations to provide the missing information. A comparison of recent computational results reveals an emerging consensus on voltage-dependent gating from computational modeling and MD simulations. This progress is highlighted in the broad context of preexisting work about voltage-gated channels.

scholarly journals Atomic Constraints between the Voltage Sensor and the Pore Domain in a Voltage-gated K+ Channel of Known Structure

2008 ◽  
Vol 131 (6) ◽  
pp. 549-561 ◽  
Author(s):  
Anthony Lewis ◽  
Vishwanath Jogini ◽  
Lydia Blachowicz ◽  
Muriel Lainé ◽  
Benoît Roux
Keyword(s):  
Structural Model ◽  
Voltage Sensor ◽  
K Channel ◽  
Structural Reorganization ◽  
Voltage Gated ◽  
Transmembrane Segments ◽  
Close Physical Proximity ◽  
Activated State ◽  
Dynamics Simulations ◽  
Pore Domain

In voltage-gated K+ channels (Kv), membrane depolarization promotes a structural reorganization of each of the four voltage sensor domains surrounding the conducting pore, inducing its opening. Although the crystal structure of Kv1.2 provided the first atomic resolution view of a eukaryotic Kv channel, several components of the voltage sensors remain poorly resolved. In particular, the position and orientation of the charged arginine side chains in the S4 transmembrane segments remain controversial. Here we investigate the proximity of S4 and the pore domain in functional Kv1.2 channels in a native membrane environment using electrophysiological analysis of intersubunit histidine metallic bridges formed between the first arginine of S4 (R294) and residues A351 or D352 of the pore domain. We show that histidine pairs are able to bind Zn2+ or Cd2+ with high affinity, demonstrating their close physical proximity. The results of molecular dynamics simulations, consistent with electrophysiological data, indicate that the position of the S4 helix in the functional open-activated state could be shifted by ∼7–8 Å and rotated counterclockwise by 37° along its main axis relative to its position observed in the Kv1.2 x-ray structure. A structural model is provided for this conformation. The results further highlight the dynamic and flexible nature of the voltage sensor.

Structural model of a voltage-gated potassium channel based on spectroscopic data

2001 ◽  
Vol 29 (4) ◽  
pp. 589-593 ◽  
Author(s):  
P. I. Haris
Keyword(s):  
Potassium Channel ◽  
Structural Model ◽  
Structural Data ◽  
Theoretical Models ◽  
Shaker Potassium Channel ◽  
Voltage Gated ◽  
Folded Structure ◽  
Membrane Spanning ◽  
Voltage Gated Ion Channels ◽  
Pore Domain

It is estimated that membrane proteins comprise as much as 30% of most genomes. Yet our knowledge of membrane-protein folding is still in its infancy. Consequently, there is a great need for developing approaches that can further advance our understanding of how peptides and proteins interact with membranes and thereby attain their folded structure. An approach that we have been exploring involves dissecting voltage-gated ion channels into simple peptide domains for the purpose of determining their structure in different media using physical techniques. We have synthesized peptides corresponding to the six membrane-spanning segments, as well as the pore domain, of the Shaker channel and characterized their secondary structures. From these studies we have developed a model for the transmembrane structure of the Shaker potassium channel that is constructed from α-helices. The hard structural data obtained from these studies lends support to the recent theoretical models of this channel protein that have been developed by others.

Hierarchy of π-Stacking Determines the Conformational Preference of Bis-Squaraines

2020 ◽  
Author(s):  
Abhishek Singh ◽  
Reman K. Singh ◽  
G Naresh Patwari
Keyword(s):  
Hydrogen Bonding ◽  
Rational Design ◽  
Biological Molecules ◽  
Conformational Space ◽  
X Ray Crystallography ◽  
Simple Strategy ◽  
Induced Folding ◽  
Π Stacking ◽  
Varying Length ◽  
Dynamics Simulations

The rational design of conformationally controlled foldable modules can lead to a deeper insight into the conformational space of complex biological molecules where non-covalent interactions such as hydrogen bonding and π-stacking are known to play a pivotal role. Squaramides are known to have excellent hydrogen bonding capabilities and hence, are ideal molecules for designing foldable modules that can mimic the secondary structures of bio-molecules. The π-stacking induced folding of bis-squaraines tethered using aliphatic primary and secondary-diamine linkers of varying length is explored with a simple strategy of invoking small perturbations involving the length linkers and degree of substitution. Solution phase NMR investigations in combination with molecular dynamics simulations suggest that bis-squaraines predominantly exist as extended conformations. Structures elucidated by X-ray crystallography confirmed a variety of folded and extended secondary conformations including hairpin turns and 𝛽-sheets which are determined by the hierarchy of π-stacking relative to N–H···O hydrogen bonds.

Hierarchy of π-Stacking Determines the Conformational Preference of Bis-Squaraines

2020 ◽  
Author(s):  
Abhishek Singh ◽  
Reman K. Singh ◽  
G Naresh Patwari
Keyword(s):  
Hydrogen Bonding ◽  
Rational Design ◽  
Biological Molecules ◽  
Conformational Space ◽  
X Ray Crystallography ◽  
Simple Strategy ◽  
Induced Folding ◽  
Π Stacking ◽  
Varying Length ◽  
Dynamics Simulations

The rational design of conformationally controlled foldable modules can lead to a deeper insight into the conformational space of complex biological molecules where non-covalent interactions such as hydrogen bonding and π-stacking are known to play a pivotal role. Squaramides are known to have excellent hydrogen bonding capabilities and hence, are ideal molecules for designing foldable modules that can mimic the secondary structures of bio-molecules. The π-stacking induced folding of bis-squaraines tethered using aliphatic primary and secondary-diamine linkers of varying length is explored with a simple strategy of invoking small perturbations involving the length linkers and degree of substitution. Solution phase NMR investigations in combination with molecular dynamics simulations suggest that bis-squaraines predominantly exist as extended conformations. Structures elucidated by X-ray crystallography confirmed a variety of folded and extended secondary conformations including hairpin turns and 𝛽-sheets which are determined by the hierarchy of π-stacking relative to N–H···O hydrogen bonds.

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