title: A novel Arg H52/Tyr H33 conservative motif in antibodies: A correlation between sequence of antibodies and antigen binding.
abstract: Antibodies are the family of proteins, which are responsible for antigen recognition. The computational modeling of interaction between an antigen and an antibody is very important when crystallographic structure is unavailable. In this research, we have discovered the correlation between the amino acid sequence of antibody and its specific binding characteristics on the example of the novel conservative binding motif, which consists of four residues: Arg H52, Tyr H33, Thr H59, and Glu H61. These residues are specifically oriented in the binding site and interact with each other in a specific manner. The residues of the binding motif are involved in interaction strictly with negatively charged groups of antigens, and form a binding complex. Mechanism of interaction and characteristics of the complex were also discovered. The results of this research can be used to increase the accuracy of computational antibody-antigen interaction modeling and for post-modeling quality control of the modeled structures.
authors.affiliation: * Kolmogorov Advanced Educational Scientific Center, Lomonosov Moscow State University, Kremenchugskaya st., 11, Moscow, 121357, Russia.
authors.forename: Artem
authors.initials: A
authors.lastname: Petrov
authors.affiliation: † Faculty of Bioengineering and Bioinformatics, Lomonosov Moscow State University, LenGory, 1, b.73, Moscow, 119991, Russia.
authors.forename: Vladimir
authors.initials: V
authors.lastname: Arzhanik
authors.affiliation: ‡ Department of Chemistry, Lomonosov Moscow State University, LenGory, 1, b.3, Moscow, 119991, Russia.
authors.forename: Gennady
authors.initials: G
authors.lastname: Makarov
authors.affiliation: * Kolmogorov Advanced Educational Scientific Center, Lomonosov Moscow State University, Kremenchugskaya st., 11, Moscow, 121357, Russia.
authors.forename: Oleg
authors.initials: O
authors.lastname: Koliasnikov
mesh_terms: D020816:Amino Acid Motifs; D000595:Amino Acid Sequence; D000596:Amino Acids / Q000032:analysis; D000906:Antibodies / Q000737:chemistry* / Q000235:genetics / Q000378:metabolism*; D000941:Antigens / Q000737:chemistry / Q000378:metabolism*; D001120:Arginine / Q000737:chemistry; D001665:Binding Sites; D017124:Conserved Sequence; D056004:Molecular Dynamics Simulation; D014443:Tyrosine / Q000737:chemistry
chemical_list: D000596:Amino Acids; D000906:Antibodies; D000941:Antigens; D014443:Tyrosine; D001120:Arginine
keywords: CDR H2; antibody–antigen binding complex; conservative motif