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About me

Current position: Associate Professor

Main interests: RNA dynamics, RNA riboswitches, gene regulation and nucleic acids, biomolecular simulation of biological/medical relevant processes, development of atomistic and coarse grained models.

Previous research appointments

Polymer theory group, Max Planck Institute for Polymer Research, Mainz, Germany.

Theoretical chemistry group of Prof. Gerhard Stock, Goethe University, Frankfurt am Main, Germany.
Molecular dynamics group of Prof. Alan E. Mark, University of Groningen, The Netherlands.
 

 

Education

  • 2015 Docent in Biochemistry, Karolinska Institutet, Sweden.
  • 2000 Ph.D. in Physical-Chemistry, University of Milano, Italy.
  • 1998 Master in ’Management of technology’, University of Milano, Italy.
  • 1995 Degree in Chemistry, University of Milano, Italy.
     

 

Research description

My research is focused on understanding the interactions which govern cellular processes. In particular, I am interested in understanding binding and aggregation of biomolecules in medical relevant context. The final aim is to understand the chemistry and the physics of biological processes to successfully develop new synthetic molecules with medical or biotechnological applications.

I use computational chemistry methods and in particular molecular dynamics techniques. Molecular simulations provide a microscopic description of biophysical processes and are performed to verify new hypothesis of binding and/or aggregation mechanisms and to test new molecules or mutations in systems.

Current projects

- Non-coding RNA: interactions and dynamics in bacterial riboswitches.

- Understanding subcellullar processes involved in traumatic brain injuries and dementia

- The role of tautomerism and pH in designing triple forming oligonucleotides: a promise tools to modulate gene expression

- Base tautomerism and modification in ribosome. 

Teaching portfolio

Current teaching activities:

- Course coordinator, lecturer and examiner of “‘Applied communication in biomedicine 4”, master program in Biomedicine, Karolinska Institutet (Sweden).

- Course coordinator, designer and lecturer of Doctoral Course: “Principles of nucleic acid structure” (DEVREG program), Karolinska Institutet (Sweden).

- Lecturer of “Molecular Simulation”, master course in Simulation Methods in Medical Engineering, Kungliga Tekniska Högskolan (Sweden).

- Lecturer of “Structural Biology”, Bachelor program in Biomedicine, Karolinska Institutet (Sweden).

Pedagogical Qualifications

- University Pedagogy 1 and 2  at Stockholm Univesity, Sweden.

- Pedagogy for doctoral supervisors at Karolinska Institutet, Sweden.

 

 

Academic honours, awards and prizes

Individual Marie Curie Fellowship (2000)

Links

Publications

LNA effects on DNA binding and conformation: from single strand to duplex and triplex structures
Pabon-martinez Yv, Xu Y, Villa A, Lundin Ke, Geny S, Nguyen Ch, et al
Scientific reports 2017;7(1):11043-

Sequence dependency of canonical base pair opening in the DNA double helix
Lindahl V, Villa A, Hess B
PLoS computational biology 2017;13(4):e1005463-

Structural Basis of Egg Coat-Sperm Recognition at Fertilization
Raj I, Sadat Al Hosseini H, Dioguardi E, Nishimura K, Han L, Villa A, et al
Cell 2017;169(7):1315-1326.e17

The free energy of locking a ring: Changing a deoxyribonucleoside to a locked nucleic acid
Xu Y, Villa A, Nilsson L
Journal of computational chemistry 2017;38(15):1147-1157

Effect of mutations on internal dynamics of an RNA hairpin from hepatitis B virus
Juneja A, Nilsson L, Villa A
Biophysical chemistry 2016;218():7-13

Structure and stability of DNA duplex upon binding of triplex-forming oligonucleotide
Villa A, Uyar A, Xu Y, Nilsson L
EUROPEAN BIOPHYSICS JOURNAL WITH BIOPHYSICS LETTERS 2015;:S244-S244

Elucidating the Relation between Internal Motions and Dihedral Angles in an RNA Hairpin Using Molecular Dynamics
Juneja A, Villa A, Nilsson L
JOURNAL OF CHEMICAL THEORY AND COMPUTATION 2014;10(8):3532-40

Triple helical DNA in a duplex context and base pair opening
Esguerra M, Nilsson L, Villa A
Nucleic acids research 2014;42(18):11329-38

Loop-loop interaction in an adenine-sensing riboswitch: a molecular dynamics study
Allnér O, Nilsson L, Villa A
RNA (New York, N.Y.) 2013;19(7):916-26

Understanding dynamical differences of Hepatitis B-virus apical stem-loop using MD simulation
Juneja A, Villa A, Nilsson L
EUROPEAN BIOPHYSICS JOURNAL WITH BIOPHYSICS LETTERS 2013;:S192-S192

DNA triplex and the bisLNA construct
Esguerra M, Villa A, Nilsson L
ABSTRACTS OF PAPERS OF THE AMERICAN CHEMICAL SOCIETY 2012;:-

Magnesium Ion-Water Coordination and Exchange in Biomolecular Simulations
Allner O, Nilsson L, Villa A
JOURNAL OF CHEMICAL THEORY AND COMPUTATION 2012;8(4):1493-502

A Challenge for Peptide Coarse Graining: Transferability of Fragment-Based Models
Engin O, Villa A, Peter C, Sayar M
MACROMOLECULAR THEORY AND SIMULATIONS 2011;20(7):451-465

Driving Forces for Adsorption of Amphiphilic Peptides to the Air-Water Interface
Engin O, Villa A, Sayar M, Hess B
JOURNAL OF PHYSICAL CHEMISTRY B 2010;114(34):11093-101

Transferability of Nonbonded Interaction Potentials for Coarse-Grained Simulations: Benzene in Water
Villa A, Peter C, Van Der Vegt Nfa
JOURNAL OF CHEMICAL THEORY AND COMPUTATION 2010;6(8):2434-44

Conformational behaviour determines the low-relaxivity state of a conditional MRI contrast agent
Cosentino U, Pitea D, Moro G, Saracino Gaa, Villa A
PHYSICAL CHEMISTRY CHEMICAL PHYSICS 2009;11(20):3943-50

Dynamics and Structure of Ln(III)-Aqua Ions: A Comparative Molecular Dynamics Study Using ab Initio Based Flexible and Polarizable Model Potentials
Villa A, Hess B, Saint-martin H
JOURNAL OF PHYSICAL CHEMISTRY B 2009;113(20):7270-81

Inclusion of ionization states of ligands in affinity calculations
Donnini S, Villa A, Groenhof G, Mark Ae, Wierenga Rk, Juffer Ah
PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS 2009;76(1):138-50

Molecular dynamics simulation study of the binding of purine bases to the aptamer domain of the guanine sensing riboswitch
Villa A, Wohnert J, Stock G
NUCLEIC ACIDS RESEARCH 2009;37(14):4774-86

Self-assembling dipeptides: conformational sampling in solvent-free coarse-grained simulation
Villa A, Peter C, Van Der Vegt Nfa
PHYSICAL CHEMISTRY CHEMICAL PHYSICS 2009;11(12):2077-86

Self-assembling dipeptides: including solvent degrees of freedom in a coarse-grained model
Villa A, Van Der Vegt Nfa, Peter C
PHYSICAL CHEMISTRY CHEMICAL PHYSICS 2009;11(12):2068-76

Spontaneous beta-helical fold in prion protein: The case of PrP(82-146)
Saracino Gaa, Villa A, Moro G, Cosentino U, Salmona M
PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS 2009;75(4):964-76

Molecular dynamics simulation of the structure, dynamics, and thermostability of the RNA hairpins uCACGg and cUUCGg
Villa A, Widjajakusuma E, Stock G
JOURNAL OF PHYSICAL CHEMISTRY B 2008;112(1):134-42

NMR and MD studies of the temperature-dependent dynamics of RNA YNMG-tetraloops
Ferner J, Villa A, Duchardt E, Widjajakusuma E, Wohnert J, Stock G, et al
NUCLEIC ACIDS RESEARCH 2008;36(6):1928-40

How sensitive are nanosecond molecular dynamics simulations of proteins to changes in the force field?
Villa A, Fan H, Wassenaar T, Mark Ae
JOURNAL OF PHYSICAL CHEMISTRY B 2007;111(21):6015-25

On the characterization of host-guest complexes: Surface tension, calorimetry, and molecular dynamics of cyclodextrins with a non-ionic surfactant
Pineiro A, Banquy X, Perez-casas S, Tovar E, Garcia A, Villa A, et al
JOURNAL OF PHYSICAL CHEMISTRY B 2007;111(17):4383-92

Conformational polymorphism of the PrP106-126 peptide in different environments: A molecular dynamics study
Villa A, Mark Ae, Saracino Gaa, Cosentino U, Pitea D, Moro G, et al
JOURNAL OF PHYSICAL CHEMISTRY B 2006;110(3):1423-8

What NMR relaxation can tell us about the internal motion of an RNA hairpin: A molecular dynamics simulation study
Villa A, Stock G
JOURNAL OF CHEMICAL THEORY AND COMPUTATION 2006;2(5):1228-36

Advanced approaches for the characterization of a de novo designed antiparallel coiled coil peptide
Pagel K, Seeger K, Seiwert B, Villa A, Mark Ae, Berger S, et al
ORGANIC & BIOMOLECULAR CHEMISTRY 2005;3(7):1189-94

A molecular dynamics study of the formation, stability, and oligomerization state of two designed coiled coils: Possibilities and limitations
Pinero A, Villa A, Vagt T, Koksch B, Mark Ae
BIOPHYSICAL JOURNAL 2005;89(6):3701-13

Incorporating the effect of ionic strength in free energy calculations using explicit ions
Donnini S, Mark Ae, Juffer Ah, Villa A
JOURNAL OF COMPUTATIONAL CHEMISTRY 2005;26(2):115-22

Structural basis for the enantioselectivity of an epoxide ring opening reaction catalyzed by halo alcohol dehalogenase HheC
De Jong Rm, Tiesinga Jjw, Villa A, Tang Lx, Janssen Db, Dijkstra Bw
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY 2005;127(38):13338-43

A biomolecular force field based on the free enthalpy of hydration and solvation: The GROMOS force-field parameter sets 53A5 and 53A6
Oostenbrink C, Villa A, Mark Ae, Van Gunsteren Wf
JOURNAL OF COMPUTATIONAL CHEMISTRY 2004;25(13):1656-76

Theoretical investigation into the influence of conformational equilibria on the water-exchange process in magnetic resonance imaging contrast agents
Cosentino U, Pitea D, Moro G, Barone V, Villa A, Muller Rn, et al
THEORETICAL CHEMISTRY ACCOUNTS 2004;111(2-6):204-209

Sampling and convergence in free energy calculations of protein-ligand interactions: The binding of triphenoxypyridine derivatives to factor Xa and trypsin
Villa A, Zangi R, Pieffet G, Mark Ae
JOURNAL OF COMPUTER-AIDED MOLECULAR DESIGN 2003;17(10):673-86

Understanding binding affinity: A combined isothermal titration calorimetry/molecular dynamics study of the binding of a series of hydrophobically modified benzamidinium chloride inhibitors to trypsin
Talhout R, Villa A, Mark Ae, Engberts Jbfn
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY 2003;125(35):10570-9

Calculation of the free energy of solvation for neutral analogs of amino acid side chains
Villa A, Mark Ae
JOURNAL OF COMPUTATIONAL CHEMISTRY 2002;23(5):548-53

Conformational characterization of lanthanide(III)-DOTA complexes by ab initio investigation in vacuo and in aqueous solution
Cosentino U, Villa A, Pitea D, Moro G, Barone V, Maiocchi A
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY 2002;124(17):4901-9

Extension of computational chemistry to the study of lanthanide(III) ions in aqueous solution: Implementation and validation of a continuum solvent approach
Cosentino U, Villa A, Pitea D, Moro G, Barone V
JOURNAL OF PHYSICAL CHEMISTRY B 2000;104(33):8001-8007

Force field parametrization for gadolinium complexes-based on ab initio potential energy surface calculations
Villa A, Cosentino U, Pitea D, Moro G, Maiocchi A
JOURNAL OF PHYSICAL CHEMISTRY A 2000;104(15):3421-3429

Ab initio investigation of gadolinium complexes with polyamino carboxylate ligands and force fields parametrization of metal-ligand interactions
Cosentino U, Moro G, Pitea D, Villa A, Fantucci Pc, Maiocchi A, et al
JOURNAL OF PHYSICAL CHEMISTRY A 1998;102(24):4606-4614

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