The three-dimensional structure of the Fab fragment of a monoclonal antibody (LNKB-2) to human interleukin-2 (IL-2) complexed with a synthetic antigenic nonapeptide, Ac-Lys-Pro-Leu-Glu-Glu-Val-Leu-AsnLeu-OMe, has been determined at 3.0 Å resolution. In the structure, four out of the six hypervariable loops of the Fab (complementarity determining regions [CDRs] L1, H1, H2, and H3) are involved in peptide association through hydrogen bonding, salt bridge formation, and hydrophobic interactions. The Tyr residues in the Fab antigen binding site play a major role in antigen-antibody recognition. The structures of the complexed and uncomplexed Fab were compared. In the antigen binding site the CDR-L1 loop of the antibody shows the largest structural changes upon peptide binding. The peptide adopts a mostly ␣-helical conformation similar to that in the epitope fragment 64-72 of the IL-2 antigen. The side chains of residues Leu 66, Val 69, and Leu 70, which are shielded internally in the IL-2 structure, are involved in interactions with the Fab in the complex studied. This indicates that antibody-antigen complexation involves a significant rearrangement of the epitope-containing region of the IL-2 with retention of the ␣-helical character of the epitope fragment.Keywords: Monoclonal antibody; Fab-antigen binding fragment; interleukin-2 antigen; antibody-antigen interaction; three-dimensional structure; X-ray analysis Monoclonal antibodies are used widely in biomedical research because of their stereochemical complementarity to specific antigens. Determination of the structural basis of antibody-antigen specificity is important to understanding the mechanism of immune recognition and the rational design of pharmacological agents, synthetic vaccines, and antibodies with novel selectivities. Some aspects of the recognition process remain unclear. The determination of the X-ray crystal structures of a number of unliganded antibodies, isolated antigens, and their complexes has advanced understanding of the nature of antibody-protein-antigen interactions (see selected references:
DNA authentication of wines is a process of verifying their authenticity by genetic identification of the main plant component. The sample preparation of experimental and commercial wines was carried out by precipitation of wine debris by centrifugation with preliminary exposure with precipitators and co-precipitators, including developed macro- and micro- volume methods applicable to white or red wines, using polyvinylpyrrolidone as a co-precipitator. Addition of 2-mercaptoethanol and proteinase K to the lysing solution made it possible to adapt the technology for DNA extraction from the precipitated wine debris. The additionally tested technique of DNA extraction from wine debris by dimethyl sulfoxide (DMSO) lysis had fewer stages and, consequently, a lower risk of contamination. The results of further testing of one of the designed primer pairs (UFGT-F1 and UFGT-R1) in conjunction with the tested methods of wine material sample preparation and nucleic acid extraction, showed the advantage in the given set of oligonucleotides over previously used ones in terms of sensitivity, specificity and reproducibility. The developing strategy for genetic identification of grape varieties and DNA authentication of wines produced from them based on direct sequencing of polymerase chain reaction (PCR) products is implemented by interpreting the detected polymorphic positions of variable Vitis vinifera L. UFGT gene locus with distribution and split into 13 UFGT gene-associated groups.
Direct x-ray analysis has been used to determine the crystal structure of [D-Hyi2, L-Hyi4]meso-valinomycin (cyclo[-D-Val-D-Hyi-L-Val-L-Hyi-(D-Val-L-Hyi-L-Val-D-+ ++Hyi)2-], C60H102N6O18), which crystallized from acetone with two solvent molecules. The crystals are trigonal, space group P32, number of molecules per unit cell Z = 3, cell parameters a = b = 15.2085 (8) A, c = 29.3250 (9) A, gamma = 120 degrees. The standard (R) and weighted (Rw) reliability factors after refinement of the atomic coordinates for C, N, and O atoms in the anisotropic thermal motion approximation, allowing for isotropic H atom contributions, were 0.070 and 0.082, respectively. The molecule adopts a distorted bracelet structure which is stabilized by six N-H ... O = C 4----1 type intramolecular hydrogen bonds. The side chains predominantly occupy external pseudoaxial positions relative to the cylindrical axis of the molecule. In contrast to meso-valinomycin, only four of the six Val carbonyl oxygen atoms are directed inwards to form a coordination centre for the molecule, and the carbonyl oxygen atoms of residues D-Val1 and L-Val3 are twisted outward and point away from the centre of the molecule. Although the analogue has a partially formed ion-binding center, it is inaccessible because the hydrophobic isopropyl groups of the D-Hyi2 and L-Hyi4 residues screen the molecular cavity on both sides.
scite is a Brooklyn-based organization that helps researchers better discover and understand research articles through Smart Citations–citations that display the context of the citation and describe whether the article provides supporting or contrasting evidence. scite is used by students and researchers from around the world and is funded in part by the National Science Foundation and the National Institute on Drug Abuse of the National Institutes of Health.