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Hydration Free Energy Profiles of Amino Acid Side Chains at Water-Air Interface. Lomonosov Moscow State University Faculty of Biology Department of Bioengineering. Alexey Shaytan. alex@molsim.org. MSU. founded 1755 39 faculties and 15 research institutions ~35 000 students

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hydration free energy profiles of amino acid side chains at water air interface
Hydration Free Energy Profiles of Amino Acid Side Chains at Water-Air Interface

Lomonosov Moscow State University

Faculty of Biology

Department of Bioengineering

Alexey Shaytan

alex@molsim.org

slide2
MSU
  • founded 1755
  • 39 faculties and 15 research institutions
  • ~35 000 students
  • ~5 000 PHD students
  • ~10 000 research and faculty staff
molecular simulations group
Molecular Simulations Group

Head – Prof. Konstantin V. Shaitan

Associate Prof. – Nikolai K. Balabaev

Research Staff

Mikhail Antonov

Alexey Shaytan

Valeriy Novoselezkii

PHD students

Philipp

Orekhov

Marine

Bozdaganyan

Ann

Popinako

Tatiyana

Naumenkova

Students

Marina Kasimova, Olesya Volokh, Mikhail Vishnepolskii

outline
Outline
  • ) Free energies in MD simulations
  • ) hydration free energies of amino acids
  • ) validity of forcefields
  • ) hydration of molecules at water/air interface
  • ) free energy profiles
  • ) adsorption free energies
free energies and md simulations
Free energies and MD simulations

F=E-TS

Free energy refers to the amount of work that can be extracted from a system.

Thermodynamics

H(p1,…,pN,x1,…,xN)

Probability~const*exp(-H/kT)

Statistical physics

F=-kT lnZ

biological system are in water
Biological system are in water

F=E-TS

  • Hydrophopic hydration:
  • energetically favorable
  • Entropically unfavorable
common protein force fields
Common protein force fields
  • TIP3P
  • SPC
  • SPC/E
  • TIP4P
  • TIP5P
  • CHARMM
  • AMBER
  • OPLS
  • GROMOS

Parameterization:

an initio + bulk properties + energetical properties

hydration free energy
Hydration free energy

Fhydr =-kTln(c1/c2)

Water

Fhydr – hydration free energy

Air

Fhydr – free energy of coupling one solute molecule into the rest of solution

“computational alchemistry methods”

amino acid r h analogs
Amino acid R-H-analogs

Conformational simplicity is important

hydration free energies r h analogs
Hydration free energies (R-H-analogs)

FF: OPLS-AA + SPC.

R=0.997

Overest. 0-4 kJ/mol

hydration at interface
Hydration at interface

Water

Air

Hydrophobicity scale

Fads =-kTln(ca/c2)

Solvent accessible surface of a protein

Fads – adsorption free energy

water air interface
Water-air interface

C1

C2

C(z)

W(z)=-kTln(C(z)) – free energy profile (PMF)

Fhydr=-kTln(C2/C1) – hydration free energy

Solute concentration

water interface system1
Water-interface system

surface potential drop is −0.59 V

adsorption energies
Adsorption energies

-Gibbs excess

experimental comparison
Experimental comparison

Bull & Breese (1974) - adsorption energy scale for amino acids side chains

Correlation is R=0.65

Fhydr~Fbb+FR

Fads≠Fbb+FR

summary
Summary
  • ) We developed a rigorous methodology of estimating adsorption free energies at liquid/gas interface
  • ) We statistically described the hydration process of small molecules as water/vapor interface
  • ) Adsorption energies can be used for quality assessment and tuning of molecular forcefields

A.K. Shaytan, V.A. Ivanov, K.V. Shaitan , A.R. Khokhlov "Free energy profiles of amino acid side chain analogs near water-vapor interface obtained via MD simulations", // Journal of Computational Chemistry, 2010, 31(1), pp 204-216, DOI:10.1002/jcc.21267