TY - JOUR

T1 - Structural insight into the role of mutual polymorphism and conservatism in the contact zone of the NFR5–K1 heterodimer with the nod factor

AU - Igolkina, A. A.

AU - Porozov, Yu B.

AU - Chizhevskaya, E. P.

AU - Andronov, E. E.

PY - 2018/4/11

Y1 - 2018/4/11

N2 - Sandwich-like docking configurations of the heterodimeric complex of NFR5 and K1 Vicia sativa receptor-like kinases together with the putative ligand, Nod factor (NF) of Rhizobium leguminosarum bv. viciae, were modeled and two of the most probable configurations were assessed through the analysis of the mutual polymorphisms and conservatism. We carried out this analysis based on the hypothesis that in a contact zone of two docked components (proteins or ligands) the population polymorphism or conservatism is mutual, i.e., the variation in one component has a reflected variation in the other component. The population material of 30 wild-growing V. sativa (leaf pieces) was collected from a large field (uncultivated for the past 25-years) and pooled; form this pool, 100 randomly selected cloned fragments of NFR5 gene and 100 of K1 gene were sequenced by the Sanger method. Congruence between population trees of NFR5 and K1 haplotypes allowed us to select two respective haplotypes, build their 3D structures, and perform protein–protein docking. In a separate simulation, the protein-ligand docking between NFR5 and NF was carried out. We merged the results of the two docking experiments and extracted NFR5–NF–K1 complexes, in which NF was located within the cavity between two receptors. Molecular dynamics simulations indicated two out of six complexes as stable. Regions of mutual polymorphism in the contact zone of one complex overlapped with known NF structural variations produced by R. leguminosarum bv. viciae. A total of 74% of the contact zone of another complex contained mutually polymorphic and conservative areas. Common traits of the obtained two stable structures allowed us to hypothesize the functional role of three-domain structure of plant LysM-RLKs in their heteromers.

AB - Sandwich-like docking configurations of the heterodimeric complex of NFR5 and K1 Vicia sativa receptor-like kinases together with the putative ligand, Nod factor (NF) of Rhizobium leguminosarum bv. viciae, were modeled and two of the most probable configurations were assessed through the analysis of the mutual polymorphisms and conservatism. We carried out this analysis based on the hypothesis that in a contact zone of two docked components (proteins or ligands) the population polymorphism or conservatism is mutual, i.e., the variation in one component has a reflected variation in the other component. The population material of 30 wild-growing V. sativa (leaf pieces) was collected from a large field (uncultivated for the past 25-years) and pooled; form this pool, 100 randomly selected cloned fragments of NFR5 gene and 100 of K1 gene were sequenced by the Sanger method. Congruence between population trees of NFR5 and K1 haplotypes allowed us to select two respective haplotypes, build their 3D structures, and perform protein–protein docking. In a separate simulation, the protein-ligand docking between NFR5 and NF was carried out. We merged the results of the two docking experiments and extracted NFR5–NF–K1 complexes, in which NF was located within the cavity between two receptors. Molecular dynamics simulations indicated two out of six complexes as stable. Regions of mutual polymorphism in the contact zone of one complex overlapped with known NF structural variations produced by R. leguminosarum bv. viciae. A total of 74% of the contact zone of another complex contained mutually polymorphic and conservative areas. Common traits of the obtained two stable structures allowed us to hypothesize the functional role of three-domain structure of plant LysM-RLKs in their heteromers.

KW - Heterodimeric receptor

KW - K1

KW - Mutual polymorphism

KW - NFR5

KW - Nod factor

KW - Population polymorphism

KW - Sliding cylinder

KW - LEGUME

KW - PROTEIN

KW - RECOGNITION

KW - heterodimeric receptor

KW - MOLECULAR EVOLUTION

KW - LYSM DOMAINS

KW - sliding cylinder

KW - mutual polymorphism

KW - PERCEPTION

KW - GENE

KW - MEDICAGO-TRUNCATULA

KW - LIPOCHITIN-OLIGOSACCHARIDE

KW - RECEPTOR-LIKE KINASES

KW - population polymorphism

UR - http://www.scopus.com/inward/record.url?scp=85045478235&partnerID=8YFLogxK

UR - http://journal.frontiersin.org/article/10.3389/fpls.2018.00344/full

UR - http://www.mendeley.com/research/structural-insight-role-mutual-polymorphism-conservatism-contact-zone-nfr5k1-heterodimer-nod-factor

U2 - 10.3389/fpls.2018.00344

DO - 10.3389/fpls.2018.00344

M3 - Article

AN - SCOPUS:85045478235

VL - 9

JO - Frontiers in Plant Science

JF - Frontiers in Plant Science

SN - 1664-462X

M1 - 344

ER -