Biology subjects

Niemela, A.

Publications and source records attributed to Niemela, A..

5 recordsLinked to original sources

bioRxiv2025

Exploring Peptide-Based Nanodiscs Structure and Dynamics through Synergistic Approach of NMR Spectroscopy, SAS and MD Simulations

Peptide nanodiscs are promising anti-atherosclerosis therapeutics, drug delivery particles and structural biology tools. However, the lack of experimental methods for structural and dynamical characterization of these particles hinders their further development. Here we integrated nuclear magnetic resonance (NMR), small-angle x-ray scattering, and small-angle neutron scattering experiments with molecular dynamics (MD) simulations to investigate the structure and dynamics of peptide nanodiscs stabilized by the apolipoprotein A-I mimetic peptide 22A with therapeutic activity against atherosclerosis. This multi-technique approach takes advantage of combining average size and shape information from small-angle scattering, peptide site-specific information from NMR spectroscopy, and interpretative power of MD simulations. Our results reveal the intrinsic polydispersity in size of peptide nanodiscs, highlighting the importance of careful interpretation when using averaged experimental parameters. Our consensus model suggests that 22A peptides are predominantly in -helical configuration with a disordered inter-helical orientation around the lipid matrix. The terminal regions of the peptides display greater flexibility relative to the peptide core and an enhanced C-terminal exposure to solvent, which could facilitate interaction with the enzyme LCAT. Interestingly, our results indicate that peptides and lipids rotate together as a rigid body. The methodological approach described in this paper paves the way for the design of more stable and effective therapeutic nanodiscs and for the characterization of other biomolecular aggregates that are beyond the scope of current structural biology techniques. Significance StatementNanodiscs stabilized by 22A apoA-I mimetic peptides hold significant pharmaceutical potential for treating cardiovascular diseases by mimicking HDL functions, yet their development is hindered by the difficulty of characterizing disordered biomolecular systems. Standard structural biology techniques cannot readily resolve the structure and dynamics of these peptide nanodiscs, which is essential for rational therapeutic design. Here, we integrate complementary biophysical experiments with MD simulations to establish a consensus model of 22A peptide nanodisc structure, dynamics, and interactions with biological partners at molecular resolution. Beyond advancing peptide nanodisc design, our integrative methodology provides a generalizable framework for characterizing other disordered biomolecular assemblies that are similarly challenging to conventional structural approaches.

biochemistry↗

bioRxiv2025

Modifications of the 22A apoA-I mimetic peptide sequence improve the anti-atherosclerotic properties of synthetic HDL

Synthetic high-density lipoprotein (sHDL) constituted of apolipoprotein A-I (apoA-I) mimetic peptides and phospholipids are nanometer-scale particles designed to recreate biological functions of HDL particles in the context of cardiovascular disease. Particularly, the therapeutic efficacy of sHDL particles is attributed to their ability to promote reverse cholesterol transport (RCT), a process where accumulated cholesterol is transported from peripheral tissues to the liver for elimination. Here, we designed two novel apoA-I mimetic peptides (22A-F and 22A-P-18A) by modifying the sequence of the well-studied apoA-I mimetic peptide 22A. These modifications were intended to improve cholesterol efflux from macrophages in vitro and structural stability of sHDL particles in human plasma while preserving their ability to activate lecithin-cholesterol acyltransferase (LCAT). We performed a systematic examination of the potency of sHDL particles made with these peptides in cellular cholesterol efflux, activation of LCAT, plasma HDL remodeling and proteolytic stability. Our study highlights that these modifications improve cholesterol efflux and, in the case of 22A-P-18A, also cholesterol esterification rate by LCAT but they do not appear to influence HDL remodeling in human plasma. Nonetheless, the LCAT activity assay conducted in human plasma suggest that intact sHDL particles are present and are likely the primary contributors to the increased cholesterol esterification rate, rather than the pre-{beta} HDL fraction generated through HDL remodeling. These findings offer new mechanistic insights into how specific peptide modifications affect key steps in RCT, laying the groundwork for future studies to explore their functional relevance in atherosclerosis and HDL-based drug delivery applications.

pharmacology and toxicology↗

bioRxiv2023

Systematic Evaluation of Lecithin:Cholesterol Acyltransferase Binding Sites in Apolipoproteins via Peptide Based Nanodiscs: Regulatory Role of Charged Residues at Positions 4 and 7

Lecithin:cholesterol acyltransferase (LCAT) exhibits -activity on high-density and {beta}-activity on low-density lipoproteins. However, the molecular determinants governing LCAT activation by different apolipoproteins remain elusive. Uncovering these determinants would offer the opportunity to design and explore advanced therapies against dyslipidemias. Here, we have conducted coarse-grained and all-atom molecular dynamics simulations of LCAT with nanodiscs made with -helical amphiphilic peptides either derived from apolipoproteins A1 and E (apoA1 and apoE) or apoA1 mimetic peptide 22A that was optimized to activate LCAT. This study aims to explore what drives the binding of peptides to our previously identified interaction site in LCAT. We hypothesized that this approach could be used to screen for binding sites of LCAT in different apolipoproteins and would provide insights to differently localized LCAT activities. Our screening approach was able to discriminate apoA1 helixes 4, 6, and 7 as key contributors to the interaction with LCAT supporting the previous research data. The simulations provided detailed molecular determinants driving the interaction with LCAT: the formation of hydrogen bonds or salt bridges between peptides E4 or D4 and LCAT S236 or K238 residues. Additionally, salt bridging between R7 and D73 was observed, depending on the availability of R7. Expanding our investigation to diverse plasma proteins, we detected novel LCAT binding helixes in apoL1, apoB100, and serum amyloid A. Our findings suggest that the same binding determinants, involving E4 or D4 -S236 and R7-D73 interactions, influence LCAT {beta}-activity on low-density lipoproteins, where apoE and or apoB100 are hypothesized to interact with LCAT.

molecular biology↗

bioRxiv2022

Mechanistic insights into the activation of lecithin-cholesterol acyltransferase in therapeutic nanodiscs composed of apolipoprotein A-I mimetic peptides and phospholipids

The mechanistic details behind the activation of lecithin-cholesterol acyltransferase (LCAT) by apolipoprotein A-I (apoA-I) and its mimetic peptides are still enigmatic. Resolving the fundamental principles behind the LCAT activation will facilitate the design of advanced HDL-mimetic therapeutic nanodiscs for LCAT deficiencies and coronary heart disease, and for several targeted drug delivery applications. Here, we have combined coarse-grained molecular dynamics simulations with complementary experiments to gain mechanistic insight into how apoA-I mimetic peptide 22A and its variants attune LCAT activity in peptide-lipid nanodiscs. Results highlight that peptide 22A forms transient antiparallel dimers in the rim of nanodiscs. The dimerization tendency considerably decreases with the removal of C-terminal lysine K22, which has also been shown to reduce the cholesterol esterification activity of LCAT. In addition, our simulations revealed that LCAT prefers to localize to the rim of nanodiscs in a manner that shields the membrane-binding domain (MBD), A-A, and the lid amino acids from the water phase, following the previous experimental evidence. Meanwhile, the location and conformation of LCAT in the rim of nanodisc are spatially more restricted when the active site covering lid of LCAT is in the open form. The average location and spatial dimensions of LCAT in its open form were highly compatible with the electron microscopy images. All peptide 22A variants studied here had a specific interaction site in the open LCAT structure flanked by the lid and MBD domain. The bound peptides showed different tendencies to form antiparallel dimers and, interestingly, the temporal binding site occupancies of the peptide variants affected their in vitro ability to promote LCAT-mediated cholesterol esterification.

biophysics↗

bioRxiv2020

Positive allosteric modulators of lecithin:cholesterol acyltransferase adjust the orientation of the membrane-binding domain and alter its spatial free energy profile

Lecithin:cholesterol acyltransferase protein (LCAT) promotes the esterification reaction between cholesterol and phospholipid derived acyl chains. Positive allosteric modulators have been developed to treat LCAT deficiencies and, plausibly, also cardiovascular diseases in the future. The mechanism of action of these compounds is poorly understood. Here computational docking and atomistic molecular dynamics simulations were utilized to study the interactions between LCAT and the activating compounds. Results indicate that all drugs bind to the allosteric binding pocket in the membrane-binding domain in a similar fashion. The presence of the compounds in the allosteric site results in a distinct spatial orientation and sampling of the membrane-binding domain (MBD). The MBDs different spatial arrangement plausibly affects the lids movement from closed to open state and vice versa, as suggested by steered molecular dynamics simulations.

biophysics↗