Our Work

Publications

57 publications from the lab: 49 peer-reviewed journal articles, 7 book chapters and reviews, and 1 conference proceeding.

2026

01

A dual gating mechanism controls target-strand cleavage in Cas12j: implications for engineering efficient nickases

Karvounis IG, Daskalakis V (2026) Protein Science 35(10): e70792. doi.org/10.1002/pro.70792

02

Role of Small Membrane Proteins in the Green Sulfur Bacterial Reaction Center

Lyratzakis A, Konstantopoulou A, Fragkaki EV, Sousani TI, Karvounis IG, Tsiotis G, Daskalakis V (2026) ACS Phys. Chem. Au. doi.org/10.1021/acsphyschemau.5c00142 — selected for the ACS 150th-anniversary journal cover.

03

Structural insights into an engineered feruloyl esterase with improved MHET degrading properties

Karampa P, Makryniotis K, Sousani TI, Topakas E, Daskalakis V, Dimarogona M (2026) FEBS Letters. doi.org/10.1002/1873-3468.70322

BC

A Practical Guide to Investigating Biomolecular Condensates: A Comment from the Plant Community

Peng J, Agudo-Canalejo J, Chodasiewicz M, Van Damme D, Daskalakis V, et al. (2026) Sci China Life Sci. doi.org/10.1007/s11427-026-3459-x

2025

04

Conformational plasticity enables functional switching in diatom light-harvesting complexes

Sousani TI, Zender B, Maity S, Kleinekathöfer U, Daskalakis V (2025) Commun Chem 8, 392. doi.org/10.1038/s42004-025-01774-x

05

An Unexpected Water Channel in the Light-Harvesting Complex of a Diatom: Implications for the Switch between Light Harvesting and Photoprotection

Daskalakis V, Maity S, Kleinekathöfer U (2025) ACS Phys. Chem. Au 5(1), 47–61. doi.org/10.1021/acsphyschemau.4c00069 — January 2025 journal cover.

2024

06

Hydrophobic mismatch in the thylakoid membrane regulates photosynthetic light harvesting

Wilson S, Clarke C, Carbajal MA, Buccafusca R, Fleck R, Daskalakis V, Ruban A (2024) J. Am. Chem. Soc. 146(21), 14905–14914. doi.org/10.1021/jacs.4c05220

07

Acclimation mechanism of microalgal photosynthetic apparatus under low atmospheric pressures – New astrobiological perspectives in a Mars-like atmosphere

Gritsi CS, Sarmas E, Daskalakis V, Kotzabasis K (2024) Functional Plant Biology 51, FP24058. doi.org/10.1071/FP24058

08

Electric Field Susceptibility of Chlorophyll c Leads to Unexpected Excitation Dynamics in the Major Light-Harvesting Complex of Diatoms

Maity S, Daskalakis V, Jansen LCT, Kleinekathöfer U (2024) J. Phys. Chem. Lett. 15(9), 2499–2510.

09

The synergy between the PscC subunits for electron transfer to the P840 special pair in Chlorobaculum tepidum

Daskalakis V, Lyratzakis A, Xie H, Tsiotis G (2024) Photosynth Res 160, 87–96. doi.org/10.1007/s11120-024-01093-7

2023

10

Engineering salt-tolerant Cas12f1 variants for gene-editing applications

Daskalakis V, Papapetros S (2023) J. Biomolecular Struct. and Dynamics. doi.org/10.1080/07391102.2023.2240418

2022

11

Recognition motifs for Importin 4 [(L)PPRS(G/P)P] and Importin 5 [KP(K/Y)LV] binding, identified by bio-informatic simulation and experimental in vitro validation

Panagiotopoulos AA, Kalyvianaki K, Tsodoulou PK, Darivianaki MN, Dellis D, Notas G, Daskalakis V, Theodoropoulos PA, Panagiotidis CA, Castanas E, Kampa M (2022) Comp. Struct. Biotechnol. J. doi.org/10.1016/j.csbj.2022.10.015

12

Deciphering the QR code of the CRISPR-Cas9 system: Synergy between Gln768 (Q) and Arg976 (R)

Daskalakis V (2022) Journal of Physical Chemistry Au. doi.org/10.1021/acsphyschemau.2c00041

13

Trivial Excitation Energy Transfer to Carotenoids is an Unlikely Mechanism for Non-Photochemical Quenching in LHCII

Gray C, Wei T, Polívka T, Daskalakis V, Duffy CDP (2022) Front. Plant Sci. 12: 797373.

BC

From Traditional Ethnopharmacology to Modern Natural Drug Discovery: A Methodology Discussion and Specific Examples

Pirintsos S, Panagiotopoulos A, Bariotakis M, Daskalakis V, Lionis C, Sourvinos G, Karakasiliotis I, Kampa M, Castanas E (2022) MDPI Molecules 27(13), 4060.

BC

A perspective on the Major Light Harvesting Complex Dynamics Under the Effect of pH, Salts and the Photoprotective PsbS Protein

Navakoudis E, Stergiannakos T, Daskalakis V (2022) Photosynthesis Research — book chapter.

2021

14

Natural polyphenols inhibit the dimerization of the SARS-CoV-2 main protease: the case of fortunellin and its structural analogs

Panagiotopoulos AA, Karakasiliotis I, Kotzampasi D-M, Dimitriou M, Sourvinos G, Kampa M, Pirintsos S, Castanas E, Daskalakis V (2021) Molecules (MDPI), 26, 6068.

15

Robust Strategy for Photoprotection in the Light-Harvesting Antenna of Diatoms: A Molecular Dynamics Study

Chrysafoudi A, Maity S, Kleinekathöfer U, Daskalakis V (2021) J. Phys. Chem. Lett. 12, 9626–9633.

16

Time-Dependent Atomistic Simulations of the CP29 Light-Harvesting Complex

Maity S, Sarngadharan P, Daskalakis V, Kleinekathöfer U (2021) J. Chem. Phys. 155, 055103.

17

Hydrogen gas as a central on-off functional switch of reversible metabolic arrest – New perspectives for biotechnological applications

Zerveas S, Kydonakis E, Mente M-S, Daskalakis V, Kotzabasis K (2021) J. Biotechnology 335: 9–18.

18

p-cymene impairs SARS-CoV-2 and Influenza A (H1N1) viral replication: In silico predicted interaction with SARS-CoV-2 nucleocapsid protein and H1N1 nucleoprotein

Panagiotopoulos A, Tseliou M, Karakasiliotis I, Kotzampasi D-M, Daskalakis V, Kesesidis N, Notas G, Lionis C, Kampa M, Pirintsos S, Sourvinos G, Castanas E (2021) Pharmacol Res Perspect. 9:e00798.

19

Multiscale QM/MM Molecular Dynamics Simulations of the Trimeric Major Light-Harvesting Complex II

Maity S, Daskalakis V, Elstner M, Kleinekathöfer U (2021) Phys. Chem. Chem. Phys. 23, 7407–7417.

2020

20

The conformational phase space of the photoprotective switch in the major Light Harvesting Complex II

Daskalakis V, Papadatos S, Stergiannakos T (2020) Chem. Commun. 56, 11215–11218.

21

Structure and Dynamics of a Thermostable Alcohol Dehydrogenase from the Antarctic Psychrophile Moraxella sp. TAE123

Petratos K, Gessmann R, Daskalakis V, Papadovasilaki M, Papanikolau Y, Tsigos I, Bouriotis V (2020) ACS Omega 5(24), 14523–14534.

2019

22

Structural Basis for Allosteric Regulation in the Major Antenna Trimer of Photosystem II

Daskalakis V, Maity S, Hart CL, Stergiannakos T, Duffy CDP, Kleinekathöfer U (2019) J. Phys. Chem. B 123(45), 9609–9615.

23

Fine tuning of the photosystem II major antenna mobility within the thylakoid membrane of higher plants

Daskalakis V, Papadatos S, Kleinekathoefer U (2019) Biochim. Biophys. Acta – Biomembranes 1861, 183059.

24

On a Chlorophyll-Carotenoid Coupling in LHCII

Maity S, Gelessus A, Daskalakis V, Kleinekathoefer U (2019) Chem. Phys. 526, 110439.

2018

25

Protein-Protein Interactions within Photosystem II under Photoprotection: The Synergy between CP29 Minor Antenna, Subunit S (PsbS) and Zeaxanthin at all-atom resolution

Daskalakis V (2018) Phys. Chem. Chem. Phys. 20, 11843–11855.

2017

26

The Photosystem II Subunit S under Stress

Daskalakis V, Papadatos S (2017) Biophys. J. (Cell) 113(11), 2364–2372.

27

A pathway for protective quenching in antenna proteins of Photosystem II

Papadatos S, Charalambous CA, Daskalakis V (2017) Scientific Reports (NPG) 7, 2523. doi.org/10.1038/s41598-017-02892-w

28

Detection of Maillard reaction products by a coupled HPLC-Fraction collector technique and FTIR characterization of Cu(II)-complexation with the isolated species

Ioannou A, Daskalakis V, Varotsis C (2017) J. Mol. Struct. 1141, 634–642.

29

Coupling of helix E-F motion with the O-nitrito and 2-nitrovinyl coordination in myoglobin

Ioannou A, Lambrou A, Daskalakis V, Pinakoulaki E (2017) Biophys. Chem. 221, 10–16.

30

Nitrite coordination in myoglobin

Ioannou A, Lambrou A, Daskalakis V, Pinakoulaki E (2017) J. Inorg. Biochemistry 166, 49–54.

BC

Atmospheric Ice Nucleation by Glassy Organic Compounds: A Review

Salameh A, Daskalakis V (2017) Chem. Comp. J 1(1), 13–23.

2016

31

Energizing the Light Harvesting Antenna: Insight from CP29

Ioannidis NE, Papadatos S, Daskalakis V (2016) BBA – Bioenergetics 1857(10), 1643–1650.

32

Correlation Between Surface Tension and the Bulk Dynamics in Salty Atmospheric Aquatic Droplets

Salameh A, Vorka F, Daskalakis V (2016) J. Phys. Chem. C 120(21), 11508–11518.

2015

33

Structure and properties of the catalytic site of nitric oxide reductase at ambient temperature

Daskalakis V, Ohta T, Kitagawa T, Varotsis C (2015) Biochim. Biophys. Acta – Bioenergetics 1847(10), 1240–1244.

34

Surface-Active Organic Matter induces salt morphology transitions during new atmospheric particle formation and growth

Daskalakis V, Charalambous F, Demetriou DC, Georgiou AG (2015) RSC Adv. 5, 63240–63251.

2014

35

Effects of Surface Activity on Carbon Dioxide Nucleation in Atmospheric Wet Aerosols: A Molecular Dynamics Study

Daskalakis V, Charalambous F, Panagiotou F, Nearchou I (2014) Phys. Chem. Chem. Phys. 16, 23723–23734.

36

Hexagonal Ice Stability and Growth in the presence of Glyoxal and Secondary Organic Aerosols

Daskalakis V, Hadjicharalambous M (2014) Phys. Chem. Chem. Phys. 16(33), 17799–17810.

BC

Probing the Action of Cytochrome c Oxidase

Daskalakis V, Varotsis C (2014) Advances in Photosynthesis and Respiration 39(10). The Structural Basis of Biological Energy Generation.

2013

37

The protein effect in the structure of two ferryl-oxo intermediates at the same oxidation level in the heme-copper binuclear center of cytochrome c oxidase

Pinakoulaki E, Daskalakis V, Ohta T, Richter OM, Budiman K, Kitagawa T, Ludwig B, Varotsis C (2013) J. Biol. Chem. 288(28), 20261–20266.

2012

38

Exploring the Topography of Free Energy Surfaces and Kinetics of Cytochrome c Oxidases interacting with small ligands

Porrini M, Daskalakis V, Farantos SC (2012) RSC Adv. 2, 5828–5836.

39

Non-Linear Vibrational Modes in Biomolecules: a periodic orbits description

Kampanarakis A, Farantos SC, Daskalakis V, Varotsis C (2012) Chem. Phys. 399, 258–263.

40

The origin of the FeIV=O intermediates in cytochrome aa3 oxidase

Pinakoulaki E, Daskalakis V, Varotsis C (2012) BBA Bioenergetics 1817, 552–557.

BC

Tuning heme functionality: the cases of Cytochrome c Oxidase and Myoglobin Oxidation

Daskalakis V, Farantos SC, Varotsis C (2012) LNCS, Springer-Verlag Berlin Heidelberg, p. 304–315.

2011

41

Regulation of Electron and Proton Transfer by the Protein Matrix of Cytochrome c Oxidase

Daskalakis V, Farantos SC, Guallar V, Varotsis C (2011) J. Phys. Chem. B 115(13), 3648–3655.

BC

Grid Computing Multiple Shooting Algorithms for Extended Phase Space Sampling and Long Time Propagation in Molecular Dynamics

Daskalakis V, Giatromanolakis M, Porrini M, Farantos SC, Gervasi O (2011) Computer Physics, Chapter 4, pp. 1–18, Nova Science Publishers.

2010

42

Vibrational Resonances and CuB displacement controlled by proton motion in Cytochrome c Oxidase

Daskalakis V, Farantos SC, Guallar V, Varotsis C (2010) J. Phys. Chem. B 114(2), 1136–1143.

2009

43

Binding and Docking Interactions of NO, CO and O2 in Heme Proteins as Probed by Density Functional Theory

Daskalakis V, Varotsis C (2009) Int. J. Mol. Sci. 10, 4137–4156. Review.

44

Heme Cavity Dynamics of Photodissociated CO from ba3-Cytochrome c Oxidase: The Role of Ring-D Propionate

Porrini M, Daskalakis V, Farantos SC, Varotsis C (2009) J. Phys. Chem. B 113(35), 12129–12135.

2008

45

Assigning vibrational spectra of ferryl-oxo intermediates of cytochrome c oxidase by periodic orbits and Molecular Dynamics

Daskalakis V, Farantos SC, Varotsis C (2008) J. Am. Chem. Soc. 130(37), 12385–12393.

2007

46

Probing the environment of CuB in heme-copper oxidases

Daskalakis V, Pinakoulaki E, Stavrakis S, Varotsis C (2007) J. Phys. Chem. B 111, 10502–10509.

CNF

Protein Dynamics and Spectroscopy for Ferryl Intermediate of Cytochrome c Oxidase: A Molecular Dynamics Approach

Daskalakis V, Farantos SC, Varotsis C (2007) AIP Computation in Modern Science and Engineering, Proc. 963(2), 31–34.

2006

47

Two ligand binding sites in the O2-sensing signal transducer HemAT: Implications for ligand recognition/discrimination and signaling

Pinakoulaki E, Yoshimura H, Daskalakis V, Yoshioka S, Aono S, Varotsis C (2006) Proc. Natl. Acad. Sci. USA 103, 14796–14801.

2005

48

Structural dynamics of Heme-copper oxidases and Nitric oxide reductases: Time-Resolved step-scan FTIR and Time-resolved Resonance Raman studies

Pinakoulaki E, Koutsoupakis C, Stavrakis S, Marialena A, Papadopoulos G, Daskalakis V, Varotsis C (2005) J. Raman Spec. 36, 337–349.

2004

49

Time-resolved step-scan Fourier transform infrared investigation of heme-copper oxidases: implications for O2 input and H2O/H+ output channels

Koutsoupakis C, Pinakoulaki E, Stavrakis S, Daskalakis V, Varotsis C (2004) Bioch. Biophys. Acta 1655, 347–352.