Conformational Dynamics of the Single Lipopolysaccharide O-Antigen in Solution.
The O-antigen is the most variable and highly immunogenic part of the lipopolysaccharide molecule that covers the surface of Gram-negative bacteria and makes up the first line of cellular defense. To provide insight into the details of the O-antigen arrangement on the membrane surface, we simulated its behavior in solution by molecular dynamics. We developed the energetically favorable O-antigen conformation by analyzing free-energy distributions for its disaccharide fragments. Starting from this conformation, we simulated the behavior of the O-antigen chain on long timescales. Depending on the force field and temperature, the single molecule can undergo reversible or irreversible coil-to-globule transitions. The mechanism of these transitions is related either to the rotation of the carbohydrate residues around O-glycosidic bonds or to flips of the pyranose rings. We found that the presence of rhamnose in the O-antigen chain crucially increases its conformational mobility.
Federal Research Clinical Center of Federal Medical & Biological Agency of Russia, Orekhovy boulevard 28, Moscow, 115682, Russia.|Department of Biophysics, Faculty of Biology, M. V. Lomonosov Moscow State University, Leninskie gory 1/24, Moscow, 119992, Russia.|Institut Camille Jordan, University Lyon 1, 43 bd 11 Novembre 1918, Villeurbanne, 69622, France.|INRIA Team Dracula, INRIA Antenne Lyon la Doua, Villeurbanne, 69603, France.
Tatiana
T
Galochkina
Department of Biophysics, Faculty of Biology, M. V. Lomonosov Moscow State University, Leninskie gory 1/24, Moscow, 119992, Russia. dvzlenko@gmail.com.
Dmitry
D
Zlenko
Department of Biophysics, Faculty of Biology, M. V. Lomonosov Moscow State University, Leninskie gory 1/24, Moscow, 119992, Russia.|A. N. Belozersky Institute of Physico-Chemical Biology, M. V. Lomonosov Moscow State University, Moscow, 119992, Russia.
Alexey
A
Nesterenko
Federal Research Clinical Center of Federal Medical & Biological Agency of Russia, Orekhovy boulevard 28, Moscow, 115682, Russia.|Department of Biophysics, Faculty of Biology, M. V. Lomonosov Moscow State University, Leninskie gory 1/24, Moscow, 119992, Russia.
Ilya
I
Kovalenko
Federal Research Clinical Center of Federal Medical & Biological Agency of Russia, Orekhovy boulevard 28, Moscow, 115682, Russia.|Department of Biophysics, Faculty of Biology, M. V. Lomonosov Moscow State University, Leninskie gory 1/24, Moscow, 119992, Russia.
Marina
M
Strakhovskaya
Federal Research Clinical Center of Federal Medical & Biological Agency of Russia, Orekhovy boulevard 28, Moscow, 115682, Russia.
Alexander
A
Averyanov
Department of Biophysics, Faculty of Biology, M. V. Lomonosov Moscow State University, Leninskie gory 1/24, Moscow, 119992, Russia.
Andrey
A
Rubin
D002236:Carbohydrate Conformation; D008070:Lipopolysaccharides / Q000737:chemistry*; D056004:Molecular Dynamics Simulation; D012486:Salmonella typhimurium / Q000737:chemistry; D012996:Solutions; D013499:Surface Properties; D013816:Thermodynamics
D008070:Lipopolysaccharides; D012996:Solutions
antigens; cell recognition; conformation analysis; membranes; molecular dynamics