Conformational stability and order of Hoogsteen base pair induced by protein binding

Several experimental studies have shown that Hoogsteen (HG) base pair (bp) stabilizes in the presence of proteins. The molecular mechanism underlying this stabilization is not well known. This leads us to examine the stability of the HG bp in duplex DNA using all-atom molecular dynamics simulation in both the absence and presence of proteins. We use conformational thermodynamics to investigate the stability of a HG bp in duplex DNA at the molecular level. We compute the changes in the conformational free energy and entropy of DNA when DNA adopts a HG bp in its bp sequence rather than a Watson-Crick (WC) bp in both naked DNA and protein-bound DNA complex. We observe that the presence of proteins stabilizes and organizes the HG bp and the entire DNA duplex. Sugar-phosphate, sugar-base, and sugar-pucker torsion angles play key roles in stabilizing and ordering the HG bp in the protein-bound DNA complex.

Effect on the conformations of the spike protein of SARS-CoV-2 due to mutation

The spike protein of SARS-CoV-2 mediates receptor binding and cell entry and is the key immunogenic target for virus neutralization and the present attention of many vaccine layouts. It exhibits significant conformational flexibility. We study the structural fluctuations of spike protein among the most common mutations that appeared in the variant of concerns (VOC). We report the thermodynamics of conformational changes in mutant spike protein with respect to the wild-type from the distributions of the dihedral angles obtained from the equilibrium configurations generated via all-atom molecular dynamics simulations. We find that the mutation causes the increase in distance between the N-terminal domain and receptor binding domain, leading to an obtuse angle cosine θ distribution in the trimeric structure in spike protein. Thus, an increase in open state is conferred to the more infectious variants of SARS-CoV-2. The thermodynamically destabilized and disordered residues of receptor binding motif among the mutant variants of spike protein are proposed to serve as better binding sites for the host factor. We identify a short stretch of region connecting the N-terminal domain and receptor binding domain forming a linker loop where many residues undergo stabilization in the open state compared to the closed one.

Effect of biphosphate salt on dipalmitoylphosphatidylcholine bilayer deformation by Tat polypeptide

Translocation of positively charged cell penetrating peptides (CPP) through cell membrane is important in drug delivery. Here we report all-atom molecular dynamics simulations to investigate how a biphosphate salt in a solvent affects the interaction of a CPP, HIV-1 Tat peptide with model dipalmitoylphosphatidylcholine (DPPC) lipid bilayer. Tat peptide has a large number of basic arginines and a couple of polar glutamines. We observe that in absence of salt, the basic residues of the polypeptide get localized in the vicinity of the membrane without altering the bilayer properties much; polypeptide induce local thinning of the bilayer membrane at the area of localization. In presence of biphosphate salt, the basic residues, dressed by the biphosphate ions, are repelled by the phosphate head groups of the lipid molecules. However, polar glutamine prefers to stay in the vicinity of the bilayer. This leads to larger local bilayer thickness at the contact point by the polar residue and non-uniform bilayer thickness profile. The thickness deformation of bilayer structure disappears upon mutating the polar residue, suggesting importance of the polar residue in bilayer deformation. Our studies point to control bilayer deformation by appropriate peptide sequence and solvent conditions.

Structural and dynamic responses of calcium ion binding loop residues in metallo-proteins

Conformational changes in bio-molecular systems are fundamental to several biological processes. It is important to study changes in responses of underlying microscopic variables, like dihedral angles as conformational change takes place. We perform all-atom simulations and modelling via Langevin equation to illustrate the changes in structural and dynamic responses of dihedral angles of calcium ion binding residues of different proteins in metal ion free (apo) and bound (holo) states. The equilibrium distributions of dihedral angles in apo- and holo-states represent structural response. Our studies show the presence of dihedrals with multiple peaks (isomeric states) separated by barrier heights is more frequent in apo- than in holo-state. The relaxation time-scale of dihedral fluctuations is found to increase linearly with decreasing barrier height due to more frequent barrier re-crossing events. The slow kinetic response of the dihedrals also contributes to slowing down of macro-scale fluctuations, which may be useful to understand kinetics of various bio-molecular processes.

Allostery in Orai1 binding to calmodulin revealed from conformational thermodynamics

Here, we study microscopic mechanism of complex formation between Ca²⁺-bound calmodulin (holoCaM) and Orai1 that regulates Ca²⁺-dependent inactivation process in eukaryotic cells. We compute conformational thermodynamic changes in holoCaM with respect to complex of Orai1 bound to C-terminal domain of holoCaM using histograms of dihedral angles of the proteins over trajectories from molecular dynamics simulations. Our analysis shows that the N-terminal domain residues L4, T5, Q41, N42, T44 and E67 of holoCaM get destabilized and disordered due to Orai1 binding to C-terminal domain of calmodulin affect the N-terminal domain residues. Among these residues, polar T44, having maximum destabilization and disorder via backbone fluctuations, shows the largest change in solvent exposure. This suggests that N-terminal domain is allosterically regulated via T44 by the binding of Orai1 to the C-terminal domain.

Molecular dynamics simulations on interaction between bacterial proteins: Implication on pathogenic activities

We perform molecular dynamics simulation studies on interaction between bacterial proteins: an outer-membrane protein STY3179 and a yfdX protein STY3178 of Salmonella Typhi. STY3179 has been found to be involved in bacterial adhesion and invasion. STY3178 is recently biophysically characterized. It is a soluble protein having antibiotic binding and chaperon activity capabilities. These two proteins co-occur and are from neighboring gene in Salmonella Typhi-occurrence of homologs of both STY3178 and STY3179 are identified in many Gram-negative bacteria. We show using homology modeling, docking followed by molecular dynamics simulation that they can form a stable complex. STY3178 belongs to aqueous phase, while the beta barrel portion of STY3179 remains buried in DPPC bilayer with extra-cellular loops exposed to water. To understand the molecular basis of interaction between STY3178 and STY3179, we compute the conformational thermodynamics which indicate that these two proteins interact through polar and acidic residues belonging to their interfacial region. Conformational thermodynamics results further reveal instability of certain residues in extra-cellular loops of STY3179 upon complexation with STY3178 which is an indication for binding with host cell protein laminin.

Chain-chain complexation and heme binding in haemoglobin with respect to the hydrophobic core structure

Heme binding by proteins and protein-protein complexation are the processes strongly related to the biological activity of proteins. The mechanism of these processes has not been still recognised. These phenomena are presented using haemoglobin as the example. Half of the mature haemoglobin (one α-chain and one β-chain) treated as a dissociation step in haemoglobin degradation reveals a specific change in heme binding after dissociation. This phenomenon is the object of analysis that interprets the structure of both complexes (tetramer and dimer) with respect to their hydrophobic core structure. The results suggest the higher stability of the complex in the form of one α-chain and one β-chain with respect to the hydrophobic core.

Molecular dynamics studies on conformational thermodynamics of Orai1-calmodulin complex

Molecular understanding of bio-macromolecular binding is a challenging task due to large sizes of the molecules and presence of variety of interactions. Here, we study the molecular mechanism of calmodulin (CaM) binding to Orai1 that regulates Ca²⁺-dependent inactivation process in eukaryotic cells. Although experimental observations indicate that Orai1 binds to the C-terminal of Ca²⁺-loaded CaM, it is not decisive if N-domain of CaM interacts with Orai1. We address the issue of interaction of different domains of CaM with Orai1 using conformational thermodynamic changes, computed from histograms of dihedral angles over simulated trajectories of CaM, CaM-binding domain of Orai1 and complexes of CaM with Orai1. The changes for all residues of both C and N terminal domains of CaM upon Orai1 binding are compared. Our analysis shows that Orai1binds to both C-terminal and N-terminal domains of CaM, indicating 1:2 stoichiometry. The Orai1 binding to N-terminal domain of CaM is less stable than that to the C-terminal domain. The binding residues are primarily hydrophobic. These observations are in qualitative agreement to the experiments. The conformational thermodynamic changes thus provide a useful computational tool to provide atomic details of interactions in bio-macromolecular binding.

Anion induced conformational preference of Cα NN motif residues in functional proteins

Among different ligand binding motifs, anion binding C^α NN motif consisting of peptide backbone atoms of three consecutive residues are observed to be important for recognition of free anions, like sulphate or biphosphate and participate in different key functions. Here we study the interaction of sulphate and biphosphate with C^α NN motif present in different proteins. Instead of total protein, a peptide fragment has been studied keeping C^α NN motif flanked in between other residues. We use classical force field based molecular dynamics simulations to understand the stability of this motif. Our data indicate fluctuations in conformational preferences of the motif residues in absence of the anion. The anion gives stability to one of these conformations. However, the anion induced conformational preferences are highly sequence dependent and specific to the type of anion. In particular, the polar residues are more favourable compared to the other residues for recognising the anion.

SDS induced dissociation of STY3178 oligomer: experimental and molecular dynamics studies

STY3178 the yfdX Salmonella Typhi protein dissociates reversibly in presence of sodium dodecyl sulphate from trimer to monomer.

Conformational thermodynamics guided structural reconstruction of biomolecular fragments

Conformational thermodynamics compares the modeling protocols to identify the conformation of the missing region leading to a suitable model for metal ion free (apo) skeletal muscle Troponin C.

A microscopic insight from conformational thermodynamics to functional ligand binding in proteins

We show that the thermodynamics of metal ion-induced conformational changes aid to understand the functions of protein complexes. This is illustrated in the case of a metalloprotein, alpha-lactalbumin (aLA), a divalent metal ion binding protein. We use the histograms of dihedral angles of the protein, generated from all-atom molecular dynamics simulations, to calculate conformational thermodynamics. The thermodynamically destabilized and disordered residues in different conformational states of a protein are proposed to serve as binding sites for ligands. This is tested for β-1,4-galactosyltransferase (β4GalT) binding to the Ca(2+)-aLA complex, in which the binding residues are known. Among the binding residues, the C-terminal residues like aspartate (D) 116, glutamine (Q) 117, tryptophan (W) 118 and leucine (L) 119 are destabilized and disordered and can dock β4GalT onto Ca(2+)-aLA. No such thermodynamically favourable binding residues can be identified in the case of the Mg(2+)-aLA complex. We apply similar analysis to oleic acid binding and predict that the Ca(2+)-aLA complex can bind to oleic acid through the basic histidine (H) 32 of the A2 helix and the hydrophobic residues, namely, isoleucine (I) 59, W60 and I95, of the interfacial cleft. However, the number of destabilized and disordered residues in Mg(2+)-aLA are few, and hence, the oleic acid binding to Mg(2+)-bound aLA is less stable than that to the Ca(2+)-aLA complex. Our analysis can be generalized to understand the functionality of other ligand bound proteins.