scholarly journals Capturing a crucial 'disorder-to-order transition' at the heart of the coronavirus molecular pathology – triggered by highly persistent, interchangeable salt-bridges

2021 ◽  
Author(s):  
Sourav Roy ◽  
Prithwi Ghosh ◽  
Abhirup Bandyapadhyay ◽  
Sankar Basu
Keyword(s):  
Molecular Pathology ◽  
Salt Bridge ◽  
Catalytic Triad ◽  
Order Transition ◽  
Genome Comparison ◽  
Salt Bridges ◽  
Furin Cleavage ◽  
Characteristic Features ◽  
Proteolytic Cleavages ◽  
Cationic Residues

The COVID-19 origin debate has greatly been influenced by Genome comparison studies of late, revealing the seemingly sudden emergence of the Furin-Like Cleavage Site at the S1/S2 junction of the SARS-CoV-2 Spike (FLCS_Spike) containing its 681_PRRAR_685 motif, absent in other related respiratory viruses. Being the rate-limiting (i.e., the slowest) step, the host Furin cleavage is instrumental in the abrupt increase in transmissibility in COVID-19, compared to earlier onsets of respiratory viral diseases. In such a context, the current paper entraps a disorder-to-order transition of the FLCS_Spike (concomitant to an entropy arrest) upon binding to Furin. The interaction clearly seems to be optimized for a more efficient proteolytic cleavage in SARS-CoV-2. The study further shows the formation of dynamically interchangeable and persistent networks of salt-bridges at the Spike-Furin interface in SARS-CoV-2 involving the three arginines (R682, R683, R685) of the FLCS_Spike with several anionic residues (E230, E236, D259, D264, D306) coming from Furin, strategically distributed around its catalytic triad. Multiplicity and structural degeneracy of plausible salt-bridge network archetypes seems the other key characteristic features of the Spike-Furin binding in SARS-CoV-2 allowing the system to breathe - a trademark of protein disorder transitions. Interestingly, with respect to the homologous interaction in SARS-CoV (2002/2003) taken as a baseline, the Spike-Furin binding events generally in the coronavirus lineage seems to have a preference for ionic bond formation, even with lesser number of cationic residues at their potentially polybasic FLCS_Spike patches. The interaction energies are suggestive of a characteristic metastabilities attributed to Spike-Furin interactions generally to the coronavirus lineage - which appears to be favorable for proteolytic cleavages targeted at flexible protein loops. The current findings not only offer novel mechanistic insights into the coronavirus molecular pathology and evolution but also add substantially to the existing theories of proteolytic cleavages.

Salt bridges in model peptides

1988 ◽  
Vol 53 (11) ◽  
pp. 2810-2824 ◽  
Author(s):  
Ilmars Sekacis ◽  
Mark Shenderovich ◽  
Gregory Nikiforovich ◽  
Edvards Liepinš ◽  
Ludmila Polevaya ◽  
...  
Keyword(s):  
Synthetic Peptides ◽  
Salt Bridge ◽  
Peptide Bond ◽  
Space Structure ◽  
Side Chain ◽  
Amino Group ◽  
Salt Bridges ◽  
Ionic Bond ◽  
Theoretical Conformational Analysis ◽  
H Nmr

A group of synthetic peptides including Boc-Lys-Phe-X-Y, X = Ala (I, III) or Thr (II), Y = Pro (I, II) or Ala (III) was studied by means of 1H NMR spectroscopy and theoretical conformational analysis. Compound I in DMSO shows two conformers with the trans- and cis-configuration of the peptide bond Ala-Pro. The salt bridge between the Lys ε-amino group and the C-terminal carboxyl is featured by magnetic nonequivalence of the Lys CεH2 protons. The space structure of I and II was found to possess a salt bridge fixed by an unusual turn in the chain formed by the Lys side chain and the C-terminal dipeptide with the trans-peptide bond X-Pro. Since a stable ionic bond in III and in the cis-conformer of I has not been observed, its contribution to stabilization of the space structure of the peptides in DMSO appears rather small.

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 A random first-order transition theory for an active glass

2018 ◽  
Vol 115 (30) ◽  
pp. 7688-7693 ◽  
Author(s):  
Saroj Kumar Nandi ◽  
Rituparno Mandal ◽  
Pranab Jyoti Bhuyan ◽  
Chandan Dasgupta ◽  
Madan Rao ◽  
...  
Keyword(s):  
Configurational Entropy ◽  
Simulation Models ◽  
Order Transition ◽  
Analytical Treatment ◽  
Apparent Contradiction ◽  
First Order ◽  
Active Particles ◽  
Propulsion Force ◽  
First Order Transition ◽  
Characteristic Features

How does nonequilibrium activity modify the approach to a glass? This is an important question, since many experiments reveal the near-glassy nature of the cell interior, remodeled by activity. However, different simulations of dense assemblies of active particles, parametrized by a self-propulsion force, f0, and persistence time, τp, appear to make contradictory predictions about the influence of activity on characteristic features of glass, such as fragility. This calls for a broad conceptual framework to understand active glasses; here, we extend the random first-order transition (RFOT) theory to a dense assembly of self-propelled particles. We compute the active contribution to the configurational entropy through an effective model of a single particle in a caging potential. This simple active extension of RFOT provides excellent quantitative fits to existing simulation results. We find that whereas f0 always inhibits glassiness, the effect of τp is more subtle and depends on the microscopic details of activity. In doing so, the theory automatically resolves the apparent contradiction between the simulation models. The theory also makes several testable predictions, which we verify by both existing and new simulation data, and should be viewed as a step toward a more rigorous analytical treatment of active glass.

scholarly journals Pathological turret mutations in the cardiac sodium channel cause long-range pore disruption

2021 ◽  
Author(s):  
Zaki F Habib ◽  
Manas Kohli ◽  
Samantha C Salvage ◽  
Taufiq Rahman ◽  
Christopher L-H Huang ◽  
...  
Keyword(s):  
Sodium Channel ◽  
Salt Bridge ◽  
Complex Salt ◽  
Site Directed Mutagenesis ◽  
Salt Bridges ◽  
Ion Permeability ◽  
Aromatic Residues ◽  
Functional Roles ◽  
Cardiac Sodium Channel ◽  
Channel Structures

AbstractThe voltage-gated sodium channel Nav1.5 initiates the cardiac action potential. Germline mutations that disrupt Nav1.5 activity predispose affected individuals to inherited cardiopathologies. Some of these Nav1.5 mutations alter amino acids in extracellular turret domains DII and DIII. Yet the mechanism is unclear. In the rat Nav1.5 structure determined by cryogenic electron microscopy, the wild-type residues corresponding to these mutants form a complex salt-bridge between the DII and DIII turret interface. Furthermore, adjacent aromatic residues form cation-π interactions with the complex salt-bridge. Here, we examine this region using site-directed mutagenesis, electrophysiology and in silico modeling. We confirm functional roles for the salt-bridges and the aromatic residues. We show that their disruption perturbs the geometry of both the DEKA selectivity ring and the inner pore vestibule that are crucial for sodium ion permeability. Our findings provide insights into a class of pathological mutations occurring not only in Nav1.5 but also in other sodium channel isoforms too. Our work illustrates how the sodium channel structures now being reported can be used to formulate and guide novel functional hypotheses.

scholarly journals Electrostatics in the stability and misfolding of the prion protein: salt bridges, self energy, and solvationThis paper is one of a selection of papers published in this special issue entitled “Canadian Society of Biochemistry, Molecular & Cellular Biology 52nd Annual Meeting — Protein Folding: Principles and Diseases” and has undergone the Journal's usual peer review process.

2010 ◽  
Vol 88 (2) ◽  
pp. 371-381 ◽  
Author(s):  
Will C. Guest ◽  
Neil R. Cashman ◽  
Steven S. Plotkin
Keyword(s):  
Prion Protein ◽  
Electrostatic Potential ◽  
Peer Review Process ◽  
Salt Bridge ◽  
Salt Bridges ◽  
Self Energy ◽  
Low Dielectric ◽  
The Stability ◽  
Α Helix ◽  
Electrostatic Potential Energy

Using a recently developed mesoscopic theory of protein dielectrics, we have calculated the salt bridge energies, total residue electrostatic potential energies, and transfer energies into a low dielectric amyloid-like phase for 12 species and mutants of the prion protein. Salt bridges and self energies play key roles in stabilizing secondary and tertiary structural elements of the prion protein. The total electrostatic potential energy of each residue was found to be invariably stabilizing. Residues frequently found to be mutated in familial prion disease were among those with the largest electrostatic energies. The large barrier to charged group desolvation imposes regional constraints on involvement of the prion protein in an amyloid aggregate, resulting in an electrostatic amyloid recruitment profile that favours regions of sequence between α helix 1 and β strand 2, the middles of helices 2 and 3, and the region N-terminal to α helix 1. We found that the stabilization due to salt bridges is minimal among the proteins studied for disease-susceptible human mutants of prion protein.

scholarly journals Intra-helical salt bridge contribution to membrane protein insertion

2021 ◽  
Author(s):  
Gerard Duart ◽  
John Lamb ◽  
Arne Elofsson ◽  
Ismael Mingarro
Keyword(s):  
Amino Acids ◽  
Membrane Protein ◽  
Electrostatic Interactions ◽  
Salt Bridge ◽  
Protein Stabilization ◽  
Membrane Insertion ◽  
Salt Bridges ◽  
Protein Insertion

ABSTRACTSalt bridges between negatively (D, E) and positively charged (K, R, H) amino acids play an important role in protein stabilization. This has a more prevalent effect in membrane proteins where polar amino acids are exposed to a very hydrophobic environment. In transmembrane (TM) helices the presence of charged residues can hinder the insertion of the helices into the membrane. This can sometimes be avoided by TM region rearrangements after insertion, but it is also possible that the formation of salt bridges could decrease the cost of membrane integration. However, the presence of intra-helical salt bridges in TM domains and their effect on insertion has not been properly studied yet. In this work, we use an analytical pipeline to study the prevalence of charged pairs of amino acid residues in TM α-helices, which shows that potentially salt-bridge forming pairs are statistically over-represented. We then selected some candidates to experimentally determine the contribution of these electrostatic interactions to the translocon-assisted membrane insertion process. Using both in vitro and in vivo systems, we confirm the presence of intra-helical salt bridges in TM segments during biogenesis and determined that they contribute between 0.5-0.7 kcal/mol to the apparent free energy of membrane insertion (ΔGapp). Our observations suggest that salt bridge interactions can be stabilized during translocon-mediated insertion and thus could be relevant to consider for the future development of membrane protein prediction software.

scholarly journals Long-lasting salt bridges provide the anchoring mechanism of oncogenic KRas-4B proteins at cell membranes

2020 ◽  
Author(s):  
Huixia Lu ◽  
Jordi Martí
Keyword(s):  
Cell Membrane ◽  
Cell Membranes ◽  
Animal Cell ◽  
Hypervariable Region ◽  
Salt Bridge ◽  
Missense Mutations ◽  
Salt Bridges ◽  
Cellular Processes ◽  
Atom Level ◽  
Related Proteins

Ras is a family of related proteins participating in all animal cell lineages and organs. Ras proteins work as GDP-GTP binary switches and regulate cytoplasmic signalling networks that are able to control several cellular processes, playing an essential role in signal transduction pathways involved in cell growth, differentiation and survival so that overacting Ras signalling can lead to cancer. One of the hardest challenges to face is, with more than hundred different missense mutations found in cancer, the design of mutation-selective therapeutic strategies. In this work, a G12D mutated farnesylated GTP bound KRas-4B protein has been simulated at the interface of a DOPC/DOPS/cholesterol model anionic cell membrane at the all-atom level. A specific long-lasting salt bridge connection between farnesyl and the hypervariable region of the protein has been identified as the main mechanism responsible of the binding of oncogenic farnesylated KRas-4B to the cell membrane, since this particular bond is absent in both wild-type and oncogenic methylated species of KRas-4B. This finding may lead to a deeper understanding of the mechanisms of protein binding and eventual growing and spreading inside cell membranes. From free energy landscapes obtained by well-tempered metadynamics simulations, we have characterised local and global minima of KRas-4B binding to the cell membrane revealing the main pathways between anchored and released states.

scholarly journals Refinement of a Cryo-EM Structure of hERG: Bridging Structure and Function

2020 ◽  
Author(s):  
H.M. Khan ◽  
J. Guo ◽  
H.J. Duff ◽  
D. P. Tieleman ◽  
S. Y. Noskov
Keyword(s):  
Molecular Dynamics ◽  
High Resolution ◽  
Salt Bridge ◽  
Structure And Function ◽  
Channel Structure ◽  
Salt Bridges ◽  
Voltage Sensing ◽  
Chain Conformations ◽  
And Function ◽  
Voltage Sensing Domain

AbstractThe human ether-a-go-go-related gene (hERG) encodes the voltage gated potassium channel (KCNH2 or Kv11.1, commonly known as hERG). This channel plays a pivotal role in the stability of phase 3 repolarization of the cardiac action potential. Although a high-resolution cryo-EM structure is available for its depolarized (open) state, the structure surprisingly did not feature many functionally important interactions established by previous biochemical and electrophysiology experiments. Using Molecular Dynamics Flexible Fitting (MDFF), we refined the structure and recovered the missing functionally relevant salt bridges in hERG in its depolarized state. We also performed electrophysiology experiments to confirm the functional relevance of a novel salt bridge predicted by our refinement protocol. Our work shows how refinement of a high-resolution cryo-EM structure helps to bridge the existing gap between the structure and function in the voltage-sensing domain (VSD) of hERG.Statement of SignificanceCryo-EM has emerged as a major breakthrough technique in structural biology of membrane proteins. However, even high-resolution Cryo-EM structures contain poor side chain conformations and interatomic clashes. A high-resolution cryo-EM structure of hERG1 has been solved in the depolarized (open) state. The state captured by Cryo-EM surprisingly did not feature many functionally important interactions established by previous experiments. Molecular Dynamics Flexible Fitting (MDFF) used to enable refinement of the hERG1 channel structure in complex membrane environment re-establishing key functional interactions in the voltage sensing domain.

scholarly journals Quantifying the Strength of a Salt Bridge by Neutron Scattering and Molecular Dynamics

2019 ◽  
Author(s):  
Philip E. Mason ◽  
Pavel Jungwirth ◽  
Elise Duboué-Dijon
Keyword(s):  
Molecular Dynamics ◽  
Force Field ◽  
Neutron Scattering ◽  
Salt Bridge ◽  
Ion Pairing ◽  
Structural Features ◽  
Quantitative Agreement ◽  
Salt Bridges ◽  
Hydrophobic Contact ◽  
Guanidinium Cation

The molecular structure and strength of a model salt bridge between a guanidinium cation as the charged side chain group of arginine and the carboxylic group of acetate in an aqueous solutions is characterized by a combination of neutron diffraction with isotopic substitution and molecular dynamics simulations. Being able to recover the second order difference signal, the present neutron scattering experiments provide direct information about ion pairing in the investigated solution. At the same time, these measurements serve as benchmarks for assessing the quality of the force field employed in the simulation. We show that a standard non-polarizable force field, which tends to overestimate the strength of salt bridges, does not reproduce the structural features from neutron scattering pertinent to ion pairing. In contrast, a quantitative agreement with experiment is obtained when electronic polarization effects are accounted for in a mean-field way via charge scaling. Such simulations are then used to quantify the weak character of a fully hydrated salt bridge. Finally, on top of the canonical hydrogen-bonding binding mode between guanidinium and acetate, these simulations also point to another interaction motif involving an out-of-plane hydrophobic contact of the methyl group of acetate with the guanidinium cation.

scholarly journals How well do force fields capture the strength of salt bridges in proteins?

2018 ◽  
Author(s):  
Mustapha Carab Ahmed ◽  
Elena Papaleo ◽  
Kresten Lindorff-Larsen
Keyword(s):  
Molecular Dynamics ◽  
Molecular Dynamics Simulations ◽  
Force Fields ◽  
Salt Bridge ◽  
Salt Bridges ◽  
Enhanced Sampling ◽  
Important Interaction ◽  
Close Proximity ◽  
The Stability ◽  
Dynamics Simulations

AbstractSalt bridges form between pairs of ionisable residues in close proximity and are important interactions in proteins. While salt bridges are known to be important both for protein stability, recognition and regulation, we still do not have fully accurate predictive models to assess the energetic contributions of salt bridges. Molecular dynamics simulations is one technique that may be used study the complex relationship between structure, solvation and energetics of salt bridges, but the accuracy of such simulations depend on the force field used. We have used NMR data on the B1 domain of protein G (GB1) to benchmark molecular dynamics simulations. Using enhanced sampling simulations, we calculated the free energy of forming a salt bridge for three possible ionic interactions in GB1. The NMR experiments showed that these interactions are either not formed, or only very weakly formed, in solution. In contrast, we show that the stability of the salt bridges is slightly overestimated in simulations of GB1 using six commonly used combinations of force fields and water models. We therefore conclude that further work is needed to refine our ability to model quantitatively the stability of salt bridges through simulations, and that comparisons between experiments and simulations will play a crucial role in furthering our understanding of this important interaction.

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