Biology subjects

Prakashchand, D. D.

Publications and source records attributed to Prakashchand, D. D..

5 recordsLinked to original sources

bioRxiv2022

Serine-129 phosphorylation of α-synuclein is a trigger for physiologic protein-protein interactions and synaptic function

Phosphorylation of -synuclein at the Serine-129 site (-syn Ser129P) is an established pathologic hallmark of synucleinopathies, and also a therapeutic target. In physiologic states, only a small fraction of total -syn is phosphorylated at this site, and consequently, almost all studies to date have focused on putative pathologic roles of this post-translational modification. We noticed that unlike native (total) -syn that is widely expressed throughout the brain, the overall pattern of -syn Ser129P is restricted, suggesting intrinsic regulation and putative physiologic roles. Surprisingly, preventing phosphorylation at the Ser-129 site blocked the ability of -syn to attenuate activity-dependent synaptic vesicle (SV) recycling - widely thought to reflect its normal function. Exploring mechanisms, we found that neuronal activity augments -syn Ser-129P, and this phosphorylation is required for -syn binding to VAMP2 and synapsin - two functional binding-partners that are necessary for -syn function. AlphaFold2-driven modeling suggests a scenario where Ser129P induces conformational changes in the C-terminus that stabilizes this region and facilitates protein-protein interactions. Our experiments indicate that the pathology-associated Ser129P is an unexpected physiologic trigger of -syn function, which has broad implications for pathophysiology and drug-development.

neuroscience↗

bioRxiv2021

Molecular View of Biomimetic Peptide in Action with Membrane

Amphiphilic {beta}-peptides, which are synthetically designed short-chain helical foldamer of {beta}-amino acids, are established potent biomimetic alternatives of natural antimicrobial peptides. An intriguing question is: how does the distinct molecular architecture of these short-chain and rigid synthetic peptides translates to its potent membrane disruption ability? Here, we address this question via a combination of all atom and coarse-grained molecular dynamics simulations of the interaction of mixed phospholipid bilayer with an antimicrobial 10-residue globally amphiphilic helical {beta}-peptide at wide range of concentrations. The simulation demonstrates that multiple copies of this synthetic peptide, initially placed in aqueous solution, readily self-assemble and adsorb at membrane interface. Subsequently, beyond a threshold peptide-to-lipid ratio, the surface-adsorbed oligomeric aggregate moves inside the membrane and spontaneously forms stable water-filled transmembrane pore via a cooperative mechanism. The defects induced by these pores lead to the dislocation of interfacial lipid head groups, membrane thinning and substantial water leakage inside the hydrophobic core of the membrane. A molecular analysis reveals that, despite having a short architecture, these synthetic peptides, once inside the membrane, would stretch themselves towards the distal leaflet in favour of potential contact with polar head groups and interfacial water layer. The pore formed in coarse-grained simulation was found to be resilient upon structural refinement. Interestingly, the pore-inducing ability was found to be elusive in a non-globally amphiphilic sequence isomer of the same {beta}-peptide, indicating strong sequence dependence. Taken together, this work put forward key perspectives of membrane-activity of minimally designed synthetic biomimetic oligomers relative to the natural antimicrobial peptides. STATEMENT OF SIGNIFICANCEThe development of bacterial resistance to conventional antibiotics is a major concern towards public health. Antimicrobial peptides, which provide a natural defence against a large range of pathogens, including bacteria and fungi, are emerging as a sustainable substitute of antibiotics. However, serious issues with the naturally occurring antimicrobial peptides which have prevented their wide-spread appreciations are their susceptibility to degradation and lack of specificity for microbial targets. In this regard, synthetic biomimetic peptides are coming up as a viable alternative. In this work we provide clarity on how these synthetic antimicrobial peptides, which often involves distinctly short architecture, acts on the membrane. We show that despite its short architecture, a 10-residue biomimetic peptide, {beta}-peptide, can spontaneously form stable membrane-spanning pore and induce water-leakage inside the membrane.

biophysics↗

bioRxiv2020

A Molecular View of Lipid-mediated Activation Process of Apolipoprotein E

Apolipoprotein E (ApoE), a major determinant protein for lipid-metabolism, actively participates in lipid transport in central nervous system via high-affinity interaction with lipoprotein receptor LDLR. Prior evidences indicate that the phospholipids first need to assemble around apoE, before the protein can recognise its receptor. However, despite multiple attempts via spectroscopic and biochemical investigations, it is unclear what are the impact of lipid assembly on globular structure of apoE. Here, using a combination of all-atom and coarse-grained molecular dynamics simulations, we demonstrate that, an otherwise compact tertiary fold of monomeric apoE3 spontaneously unwraps in an aqueous phospholipid solution in two distinct stages. Interestingly, these structural reorganizations are triggered by an initial localised binding of lipid molecules to the C-terminal domain of the protein, which induce a rapid separation of C-terminal domain of apoE3 from the rest of its tertiary fold. This is followed by a slow lipid-induced inter-helix separation event within the N-terminal domain of the protein, as seen in an extensively long coarse-grained simulation. Remarkably, the resultant complex takes the shape of an open conformation of lipid-stabilised unwrapped protein, which intriguingly coincides with an earlier proposal by small-angle X-ray scattering (SAXS) experiment. The lipid-binding activity and the lipid-induced protein conformation are found to be robust across a monomeric mutant and wild-type sequence of apoE3. The open complex derived in coarse-grained simulation retains its structural morphology after reverse-mapping to all-atom representation. Collectively, the investigation puts forward a plausible structure of currently elusive conformationally activated state of apoE3, which is primed for recognition by lipoprotein receptor and can be exploited for eventual lipid transport. Table of Content O_FIG O_LINKSMALLFIG WIDTH=199 HEIGHT=200 SRC="FIGDIR/small/255299v2_ufig1.gif" ALT="Figure 1"> View larger version (67K): org.highwire.dtl.DTLVardef@1551278org.highwire.dtl.DTLVardef@2f85fdorg.highwire.dtl.DTLVardef@5c90aorg.highwire.dtl.DTLVardef@1d1ddb2_HPS_FORMAT_FIGEXP M_FIG C_FIG

biophysics↗

bioRxiv2019

Non-affine displacements encode collective conformational fluctuations in proteins

Identifying subtle conformational fluctuations underlying the dynamics of bio macro-molecules is crucial for resolving their free energy landscape. We show that a collective variable, originally proposed for crystalline solids, is able to filter out essential macro-molecular motions more efficiently than other approaches. While homogenous or affine deformations of the biopolymer are trivial, biopolymer conformations are complicated by the occurrence of in-homogenous or non-affine displacements of atoms relative to their positions in the native structure. We show that these displacements encode functionally relevant conformations of macromolecule and, in combination with a formalism based upon time-structured independent component analysis, quantitatively resolve the free energy landscape of a number of macromolecules of hierarchical complexity. The kinetics of conformational transitions among the basins can now be mapped within the framework of a Markov state model. The non-affine modes, obtained by projecting out homogenous fluctuations from the local displacements, are found to be responsible for local structural changes required for transitioning between pairs of macro states.

biophysics↗

bioRxiv2018

On identifying collective displacements in apo-proteins that reveal eventual binding pathways

Binding of small molecules to proteins often involves large conformational changes in the latter, which open up pathways to the binding site. Observing and pinpointing these rare events in large scale, all-atom, computations of specific protein-ligand complexes, is expensive and to a great extent serendipitous. Further, relevant collective variables which characterise specific binding or un-binding scenarios are still difficult to identify despite the large body of work on the subject. Here, we show that possible primary and secondary binding pathways can be discovered from short simulations of the apo-protein without waiting for an actual binding event to occur. We use a projection formalism, introduced earlier to study deformation in solids, to analyse local atomic displacements into two mutually orthogonal subspaces -- those which are \"affine\" i.e. expressible as a homogeneous deformation of the native structure, and those which are not. The susceptibility to non-affine displacements among the various residues in the apo-protein is then shown to correlate with typical binding pathways and sites crucial for allosteric modifications. We validate our observation with all-atom computations of three proteins, T4-Lysozyme, Src kinase and Cytochrome P450.

biophysics↗