Biology subjects

Koivuniemi, A.

Publications and source records attributed to Koivuniemi, A..

5 recordsLinked to original sources

bioRxiv2026

DNA origami uptake in Y-79 retinoblastoma cells driven by oligolysine coating

DNA origami nanoparticles (DONs) are attractive nanocarriers of controllable size, shape and addressability that have potential for treating eye diseases by overcoming ocular barriers. However, suboptimal physiological stability and poor cell uptake due to the negative charge may limit their use. Previous reports show that electrostatic complexation of DONs with cationic PEG-oligolysine block-copolymers like PEG5K-K10 can improve structural integrity and promote cell internalization. Here, we investigated a dual approach of PEG5K-K10 coatings and PL3 targeting peptides to improve uptake of 24-helix bundle (24HB) DONs into Y-79 retinoblastoma cells. Uptake studies revealed that PEG5K-K10 was essential for DON uptake in Y-79 cells, as uptake only occurred upon exceeding a distinct PEG5K-K10 amount. Longer exposure times or increased polymer amounts improved cell association. However, no beneficial effect of PL3 was observed. While free PEG5K-K10 reduced cell viability at higher concentrations (IC50 36.8 {micro}M), coated DONs were well-tolerated. Furthermore, single particle tracking in ex vivo porcine eyes revealed comparable vitreal mobility for uncoated and coated 24HB, with a slight decrease at higher coating amounts. Our findings highlight that PEG5K-K10 can enhance ocular cell uptake without limiting nanoparticle diffusivity in the vitreous, and support further optimization of DONs for ocular drug delivery.

biochemistry↗

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↗

bioRxiv2024

Gliflozins, sucrose and flavonoids are allosteric activators of lecithin:cholesterol acyltransferase

Lecithin:cholesterol acyltransferase (LCAT) serves as a pivotal enzyme in preserving cholesterol homeostasis via reverse cholesterol transport, a process closely associated with the onset of atherosclerosis. Impaired LCAT function can lead to severe LCAT deficiency disorders for which no pharmacological treatment exists. LCAT-based therapies, such as small molecule positive allosteric modulators (PAMs), against LCAT deficiencies and atherosclerosis hold promise, although their efficacy against atherosclerosis remains challenging. Herein we utilized a quantitative in silico metric to predict the activity of novel PAMs and tested their potencies with in vitro enzymatic assays. As predicted, sodium-glucose cotransporter 2 (SGLT2) inhibitors (gliflozins), sucrose and flavonoids activate LCAT. This has intriguing implications for the mechanism of action of gliflozins, which are commonly used in the treatment of type 2 diabetes, and for the endogenous activation of LCAT. Our results underscore the potential of molecular dynamics simulations in rational drug design.

biochemistry↗

bioRxiv2017

Interaction of lecithin-cholesterol acyltransferase with lipid surfaces and apolipoprotein A-I derived peptides: implications for the cofactor mechanism of apolipoprotein A-I

Lecithin-cholesterol acyltransferase (LCAT) is an enzyme responsible for the formation of cholesteryl esters from cholesterol (CHOL) and phospholipid (PL) molecules in high-density lipoprotein (HDL) particles that play a crucial role in the reverse cholesterol transport and the development of coronary heart disease (CHD). However, it is poorly understood how LCAT interacts with lipoprotein surfaces and how apolipoprotein A-I (apoA-I) activates it. Thus, here we have studied the interactions between LCAT and lipids through extensive atomistic and coarse-grained molecular dynamics simulations to reveal mechanistic details behind the cholesterol esterification process catalyzed by LCAT. In addition, we studied the binding of LCAT to apoA-I derived peptides, and their effect on LCAT lipid association utilizing experimental surface sensitive biophysical methods. Our simulations show that LCAT anchors itself to lipoprotein surfaces by utilizing non-polar amino acids located in the membrane-binding domain and the active site tunnel opening. Meanwhile, the membrane anchoring hydrophobic amino acids attract cholesterol molecules next to them. The results also highlight the role of the lid-loop in the lipid binding and conformation of LCAT with respect to the lipid surface. The apoA-I derived peptides from the LCAT activating region bind to LCAT and promote its lipid surface interactions, although some of these peptides do not bind lipids individually. By means of free-energy calculations we provided a hypothetical explanation for this mechanism. We also found that the transfer free-energy of PL to the active site is consistent with the activation energy of LCAT. Furthermore, the entry of CHOL molecules into the active site becomes highly favorable by the acylation of SER181. The results provide substantial mechanistic insights concerning the activity of LCAT that may lead to the development of novel pharmacological agents preventing CHD in the future.

biophysics↗