Crystal structure of an anti-interleukin-2 monoclonal antibody Fab complexed with an antigenic nonapeptide.

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-Asn-Leu-OMe, has been determined at 3.0 A 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 alpha-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 alpha-helical character of the epitope fragment.

[A new crystal form of the Fab fragment of a monoclonal antibody to human interleukin-2: the three-dimensional structure at 2.7 A resolution]. / Prostranstvennaia struktura Fab-fragmenta monoklonal'nogo antitela k interleikinu-2 cheloveka v novoi kristallicheskoi forme pri razreshenii 2.7 A.

The three-dimensional structure of the antigen-binding fragment of a monoclonal antibody to human interleukin-2 in a new crystal form (space group P2(1)2(1)2(1); unit cell parameters: a = 42.82, b = 90.68, and c = 139.82 A) was determined by the X-ray molecular replacement method at the resolution of 2.7 A. The protein folding and the stereochemistry of its antigen-binding site were comparatively analyzed. The English version of the paper: Russian Journal of Bioorganic Chemistry, 2004, vol. 30, no. 5; see also http: // www.maik.ru.

[Crystalline and molecular structure of the K+-complex of meso-valinomycin, cyclo(-(D-Val-L-Hyi-L-Val-D-Hyi)3-).KAuCl4]. / Kristallicheskaia i molekuliarnaia struktura K+-kompleksa mezo-valinomitisna, cyclo(-(D-Val-L-Hyi-L-D-Hyi)3-).KAuCl4.

Crystal structure of the complex of meso-valinomycin with KAuCl4 (C60H102N6O18KAuCl4) was determined using direct X-ray diffraction analysis. The conformational state of the complex is similar to that determined earlier for free meso-valinomycin. Characteristic of it is the centrosymmetric bracelet shape stabilized by six intramolecular NH...OC hydrogen bonds of 4 --> 1 type. The K+ ion is located in an inner negatively charged octahedral cavity formed by six carbonyl oxygen atoms of ester groups. The observed differences in conformational angles of the complex and free are caused by readjustment of the geometry of the ion-binding cavity to the size of the ion bound during complexation.

[Crystallization and molecular structure of cyclic dodecadepsipeptide cyclo]D-Val-D-Hyi-Val-Hyi-(D-Val-Hyi-Val-D-Hyi)2-].2C3H60]. / Kristallicheskaia i molekuliarnaia struktura tsiklicheskogo dodekadepsipeptida cyclo[D-Val-D-Hyi-(D-Val-Hyi-Val-D-Hyi)2-].2C3H6O.

The crystal structure of a synthetic analogue of meso-valinomycin, crystallized with two acetone molecules, has been solved by X-ray direct methods. The trigonal crystals belong to the P32 space group, with the number of molecules in the unit cell z = 3, and cell dimensions a = b = 15,2085 A, c = 29,3250 A, alpha = beta = 90 degrees, gamma = 120 degrees. The standard (R) and weighted (Rw) factors after the structure refinement of atoms C, N, O in anisotropic thermal motion approximation and with the contribution from H atoms taken into account are 0,070 and 0,082, respectively. The molecule adopts an asymmetric conformations stabilized by six amide intramolecular hydrogen bonds NH ... OC of the 4----4 type; one of those is strong and the other are weakened in different extent. The side chains occupy the external pseudoaxial positions towards the cyclic frame of the molecule, whereas six free ester carbonyl groups have different orientations. In contrast to meso-valinomycin, the analogue under study has no specific binding site for metal ions. The isopropyl side chains of D-Hyi(2) and Hyi(4) residues effectively shield, from both sides, the access to the inner molecular cavity.

[Structure of macrocyclic K+, Rb+-complexon of meso-valinomycin monohydrate, cyclo[-(D-Val-Hyi-Val-D-Hyi)3-].H2O, in a crystalline complex with dioxane by x-ray structural data]. / Struktura makrotsiklicheskogo K+, Rb+-kompleksona mezo-valinomitsina- monogidrata, cyclo]-(D-Val-Hyi-Val-D-Hyi)3-].H2O, v kristallicheskom komplekse s dioksanom po dannym rentgenostrukturnogo analiza.

The crystal structure of a valinomycin analogue, cyclo[-(D-Val-Hyi-Val-D-Hyi)3-]x(C60H102N6O18) crystallized with dioxane and water molecules, has been solved by X-ray direct methods. The conformation found is analogous to one established for free meso-valinomycin crystallized from other organic solvents. It is characterized by a centrosymmetric bracelet form, stabilized by six intramolecular 4----1 type hydrogen bonds between amide N-H and C = O groups. One water molecule is fixed asymmetrically by hydrogen bonds in the internal negatively charged cavity of the complexon. The meso-valinomycin molecule "bracelets" in the crystal form stacks alternatively with dioxane molecules.

[Spatial structure of a Fab-fragment of a monoclonal antibody to human interleukin-2 in two crystalline forms at a resolution of 2.2 and 2.9 angstroms]. / Prostranstvennaia struktura Fab-fragmenta monoklonal'nogo antitela k interleikinu-2 cheloveka v dvukh kristallicheskikh formakh pri razreshenii 2.2 i 2.9 A.

The three-dimensional structure of the antigen-binding fragment of a monoclonal antibody to human interleukin-2 was determined in two crystal forms by the X-ray method of molecular replacement at 2.2 and 2.9 A resolutions. The spatial structure of the protein and the stereochemistry of its antigen-binding site were analyzed.

[Isolation, crystallization, and preliminary x-ray study of a Fab fragment of monoclonal antibody against human interleukin-2 and its complex with antigenic peptide]. / Poluchenie, kristallizatsiia i predvaritel'nye rentgenostrukturnye issledovaniia Fab-fragmenta monoklonal'nogo antitela k interleikinu-2 cheloveka i ego kompleksa s antigennym peptidom.

Antigen-binding fragments (Fab) of mouse monoclonal antibodies to human interleukin-2 were obtained in preparative quantities by a modified procedure. These Fab-fragments were shown to be homogeneous according to the isoelectric focusing method. Various monocrystals of these free Fab-fragments and their complexes with the antigenic peptide corresponding to the 59-72 sequence of interleukin-2 were obtained. These were shown to be suitable for X-ray and were preliminarily studied by X-ray.

Crystal and molecular structure of the centrosymmetric meso-valinomycin analogue--cyclo (D-Val-D-Hyi-D-Val-L-Hyi-L-Val-D-Hyi-L-Val-L-Hyi-L-Val-D-Hyi-D-Val-L-Hy i) (C60H102N6O18).

The crystal structure of cyclo (D-Val-D-Hyi-D-Val-L-Hyi-L-Val-D-Hyi-L-Val-L-Hyi -L-Val-D-Hyi-D-Val-L-Hyi).2H2O has been solved by x-ray direct methods. The crystals (grown from a mixture of octane/CH2Cl2) are an orthorhombic, centrosymmetric space group Pbca, cell parameters a = 11.458 (2), b = 25.613 (3), c = 23.691 (3) A, Z = 4; therefore the molecule lies on a center of inversion in the cell. The atomic coordinates for the C, N, and O atoms were refined in the anisotropic thermal motion approximation (allowing for H-atom contribution to Fcal) to a standard R-factor value of 0.081. In contrast to meso-valinomycin, the analogue under study does not adopt an octahedral cage bracelet conformation. It has an unusual centrosymmetric elongated form with two type II terminal beta-bends formed by N-H ... C=O 4-->1 type intramolecular H bonds. Two symmetry-related water molecules reside in the elongated molecular cavity of the centrosymmetric depsipeptide ring.