A5006975149- Receptor Mechanisms and Signaling
- Protein Structure and Dynamics
- Protein Kinase Regulation and GTPase Signaling
- Computational Drug Discovery Methods
- RNA and protein synthesis mechanisms
- Retinal Development and Disorders
- Machine Learning in Bioinformatics
- Lipid Membrane Structure and Behavior
- Characterization and Applications of Magnetic Nanoparticles
- Molecular Communication and Nanonetworks
- Gold and Silver Nanoparticles Synthesis and Applications
- Enzyme Structure and Function
- Spectroscopy and Quantum Chemical Studies
- Protein purification and stability
- Surface Chemistry and Catalysis
- Synthesis and biological activity
- Cellular transport and secretion
- Cholesterol and Lipid Metabolism
- Chemistry and Chemical Engineering
- Surfactants and Colloidal Systems
- Machine Learning in Materials Science
- Ion channel regulation and function
- Inorganic and Organometallic Chemistry
- Genetics, Bioinformatics, and Biomedical Research
Academy of Athens
2018-2024
National and Kapodistrian University of Athens
2018-2023
Biomedical Research Foundation of the Academy of Athens
2021-2022
Abstract Recent advances in structural biology and computational techniques have revealed allosteric mechanisms for an abundance of targets leading to the establishment rational design modulators as a new avenue drug discovery. Considering that allostery is intrinsic property protein conformational ensemble, has potential develop into innovative approach modulate dysregulation therapeutic are considered be undruggable at their orthosteric site, explore strategic opportunities tackle chemical...
Citizen Observatories (COs) empower residents to become active contributors the observation and management of their local environments. Instrumented with low-cost sensors, communities can monitor environment. However, data insights from COs do not always contribute policy development. To address this challenge, CitiObs project (www.citiobs.eu) is developing tools, methodologies approaches enhance in observing, monitoring, protecting urban environment, a focus on air...
Modeling of nanoparticles is an essential first step to assess their capacities for different uses such as energy storage and drug delivery. However, creating initial starting conformation modeling simulation tedious because every crystalline material grows with a crystal habit. In this application note, we describe NanoCrystal, novel web-based crystallographic tool that creates nanoparticle models from any structure guided by preferred equilibrium shape under standard conditions according...
Abstract Abnormal protein–membrane attachment is involved in deregulated cellular pathways and disease. Therefore, the possibility to modulate interactions represents a new promising therapeutic strategy for peripheral membrane proteins that have been considered so far undruggable. A major obstacle this drug design membrane-binding domains of are usually unknown. The development fast efficient algorithms predicting interface would shed light into accessibility membrane–protein interfaces by...
Relative binding free energy calculations in drug design are becoming a useful tool facilitating lead affinity optimization cost- and time-efficient manner. However, they have been limited by technical challenges such as the manual creation of large numbers input files to set up, run, analyze simulations. In this Application Note, we describe FEPrepare, novel web-based tool, which automates setup procedure for relative FEP dual-topology scheme NAMD, one major MD engines, using OPLS-AA force...
The allosteric modulation of peripheral membrane proteins (PMPs) by targeting protein-membrane interactions with drug-like molecules represents a new promising therapeutic strategy for currently considered undruggable. However, the accessibility interfaces small has been so far unexplored, possibly due to complexity interface, limited structural information and lack computational workflows study it. Herein, we present pipeline drugging using DREAMM (Drugging pRotein mEmbrAne Machine learning...
Abstract Motivation Characterizing interactions at the protein–membrane interface is crucial as abnormal peripheral attachment involved in onset of many diseases. However, a limiting factor studying and understanding that membrane-binding domains membrane proteins (PMPs) are typically unknown. By applying artificial intelligence techniques context natural language processing (NLP), accuracy prediction time for analysis can be significantly improved compared to existing methods. Here, we...
Ras proteins are membrane-anchored GTPases that regulate key cellular signaling networks. It has been recently shown different anionic lipid types can affect the properties of in terms dimerization/clustering on cell membrane. To understand effects lipids spatiotemporal dimeric K-Ras4B, we perform all-atom molecular dynamics simulations dimer K-Ras4B presence and absence Raf[RBD/CRD] effectors two model membranes: one containing 78% mol DOPC, 20% DOPS, 2% PIP2 another with enhanced...
<p>Modeling nanoparticles is an essential first step to assess their capacity in different uses such as energy storage or drug delivery. However, creating initial starting conformation for modeling and simulation tedious because every crystalline material grows with a crystal habit. In this application note, we describe Nano-Crystal, novel web-based crystallographic tool, which creates nanoparticle models from any structure guided by preferred equilibrium shape under standard...
RAS proteins are membrane-anchored GTPases that regulate key cellular signaling networks. It has been recently shown different anionic lipid types can affect the properties of in terms dimerization/clustering on cell membrane. To understand effects lipids spatiotemporal dimeric K-Ras4B, we perform all-atom molecular dynamics simulations dimer K-Ras4B presence and absence Raf[CRD/RBD] effectors two model membranes: one containing 78% mol. DOPC, 20% DOPS, 2% PIP2 another with enhanced...
AlphaFold2 (AF2) and RoseTTaFold (RF) have revolutionized structural biology, serving as highly reliable effective methods for predicting protein structures. This article explores their impact limitations, focusing on integration into experimental pipelines application in diverse classes, including membrane proteins, intrinsically disordered proteins (IDPs), oligomers.In pipelines, AF2 models aid X-ray crystallography resolving the phase problem, while complementarity with Mass Spectrometry...
Modeling nanoparticles is an essential first step to assess their capacity in different uses such as energy storage or drug delivery. However, creating initial starting conformation for modeling and simulation tedious because every crystalline material grows with a crystal habit. In this application note, we describe Nano-Crystal, novel web-based crystallographic tool, which creates nanoparticle models from any structure guided by preferred equilibrium shape under standard conditions...
Ras proteins are membrane-anchored GTPases that regulate key cellular signaling networks. It has been recently shown different anionic lipid types can affect the properties of in terms dimerization/clustering on cell membrane. To understand effects lipids spatiotemporal dimeric K-Ras4B, we perform all-atom molecular dynamics simulations dimer K-Ras4B presence and absence Raf[RBD/CRD] effectors two model membranes: one containing 78% mol DOPC, 20% DOPS, 2% PIP2 another with enhanced...
ABSTRACT K-Ras4B is one the most frequently mutated proteins in cancer, yet mechanistic details of its activation such as homodimerization on membrane remain elusive. The structural determinants have been debated with different conformations being proposed literature. Here, we perform microsecond all-atom Molecular Dynamics (MD) simulations monomer solution, membrane, and two experimentally-based dimer models α4-α5 interface to investigate stability these structures bound GTP a model cell...
Abstract Abnormal protein-membrane attachment is involved in deregulated cellular pathways and disease. Therefore, the possibility to modulate interactions represents a new promising therapeutic strategy for peripheral membrane proteins that have been considered so far undruggable. A major obstacle this drug design binding domains of are usually not known. The development fast efficient algorithms predicting interface would shed light into accessibility membrane-protein interfaces by...
RAS proteins are membrane-anchored GTPases that regulate key cellular signaling networks. It has been recently shown different anionic lipid types can affect the properties of in terms dimerization/clustering on cell membrane. To understand effects lipids spatiotemporal dimeric K-Ras4B, we perform all-atom molecular dynamics simulations dimer K-Ras4B presence and absence Raf[CRD/RBD] effectors two model membranes: one containing 78% mol. DOPC, 20% DOPS, 2% PIP2 another with enhanced...