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Unformatted text preview: The immune system
Biophysical Chemistry 1, Fall 2010 B-cells and T-cells Catalytic antibodies Reading assignment: Chap. 14 A Textbook of Structural Biology B-cell or humoral immunity uses a protein G fold Constant domain
C C F G C'' Variable domain
C C C' F G E D B A D N E B A N FIGURE 14.1 The immunoglobulin (Ig) fold. Many proteins in the immune system have this fold, as well as proteins involved in cell adhesion and the nervous system. Left: ribbon representations of the fold of a constant domain and a variable domain (PDB: 1AQK, heavy chain). Right: a simplified representation of the sandwich that constitutes the Ig fold. The constant domain has a four-stranded and a three-stranded antiparallel sheet, but in the variable domain there are two extra strands C' and C'' (darker blue). The red connections between some strands in the variable domain are the complementary-determining regions, CDR1, CDR2 and CDR3, consecutively along the polypeptide chain. These regions form the antigen-binding surface. IgG's have a characteristic Y-shape The Immune Syste N
N N N Fab Fab C C papain C C Fc 2 The IgG molecule is built of four multidomain chains, two heavy (blue ight chains (red domains). The heavy chains are composed of four domains ns have two domains. The light blue and red domains are the variable doma en binding occurs. The darker domains are the constant domains. The hea d to each other and the light chains are each linked to one of the heavy chain s (yellow). If IgG is treated by a proteolytic enzyme such as papain, the hea "fragment crystalline"). When it was first produced, it crystallized spontaneously in the dialysis tube! The two identical fragments are called Fabs (fragment antigen-binding). The antigen IgG's can be rather flexible (purple) binds between the two variable domains of each Fab fragment. FIGURE 14.3 A detailed structure of IgG in two orientations. The heavy chain consists of the VH, CH1, CH2, and CH3 domains and the light chain of the VL and the CL domains. The Fab units are seen above and have very flexible links to the Fc unit below. The chains are connected by disulfide bonds. All cysteines that form disulfide bonds are shown and the ones that connect the chains are indicated by arrows. The Fc unit has carbohydrate modifications at the CH2 domain, drawn as ball-and-stick models (PDB: 1IGT). Examples of fab's binding to protein antigens The Immune System in green. Genetic selection processes are key
Gene elements for the light chain V1 V2 Vn-1 Vn J1 J2 J3 J4 J5 Recombination V3 V4 J2 J3 J4 C C Transcription V4 J2 J3 J4 C Splicing V4 J2 C Translation B-cell or humoral immunity The Immune System 443 GURE 14.6 The structure of major histocompatibility complex (MHC) proteins of class I (left) Basic ideas of catalysis (again) Catalytic antibodies
Chem. Rev. 1997, 97, 1281-1301
1281 Binding Energy and Catalysis: The Implications for Transition-State Analogs and Catalytic Antibodies
Mary M. Mader and Paul A. Bartlett* Binding Energy and Catalysis
Contents Department of Chemistry, Grinnell College, Grinnell, Iowa 50112-0806, and Department of Chemistry, University of California, Berkeley, California 94720-1460 Received November 21, 1996 (Revised Manuscript Received February 19, 1997) Figure 1. Thermodynamic box illustrating relationship between ground-state and transition-state binding for an enzyme with a single substrate. pending on the concentration of substrate, I. Introduction II. Transition-State Theory and Catalysis III. Protein-Ligand Interactions: Forces Available for Binding and Catalysis IV. Transition-State Analog Inhibitors: Qualitative and Quantitative Analysis V. Transition-State Analogs and Catalytic Antibodies A. Kinetic Issues B. Structural Issues 1. Shortcomings in Hapten Design 2. Fidelity of the Replica 3. Antibody Diversity C. Thermodynamic Issues D. Limitations from the Immune Process Itself 1. Binding Energy Available 2. Time Scale of Antibody Generation E. Intervention 1281 1281 1284 1285 1289 1290 1292 1292 1294 1296 1296 1297 1297 1297 1297 similar for enzymes and antibodies, both the mechanism and the goal of the selection processes by which these proteins are tailored differ significantly. II. Transition-State Theory and Catalysis
Explanations for the extraordinary power of enzymes to accelerate chemical reactions have been sought ever since this behavior was observed. Modern explanations of the catalytic process date from Haldane's classic treatise on enzymatic activity,1 through comments made by Pauling in the 1940s,2,3 and have culminated in the currently accepted view that catalysis of a reaction rests on the enzyme's ability to stabilize the transition-state structure of the substrate relative to that of the ground state.4-7 Catalysis of a transformation often involves alternative reaction pathways from that of the noncatalyzed 11,12 transformation, usually taking advantage of an as- F no Testing also be step case that there isstate stabilization idea the the in the enzyme-catalyzedchange in ratelimiting transition transformation among the various substrates. The most extensive applications of this approach have involved the peptidases, because it is for these enzymes that regular variation in substrate structure is most permissible, especially at substrate sites that do not significantly affect the rate of the noncatalyzed reaction. Correlations between inhibitor Ki and substrate Km/kcat have been demonstrated for the Chemical Reviews, peptide inhibitors of 1287 phosphorus-containing 1997, Vol. 97, No. 5thermolysin,23,65 carboxypeptidase A,66 and pepsin.44 The correlations observed for the thermolysin inhibitors already described, the phosphonamidates 1nn, the phosphinates 1cn, the phosphonates 1on, and the esters 1no, demonstrate many of the points made above. Thermolysin catalyzes the direct addition of a water molecule to the peptide bond, generating a high energy, tetrahedral intermediate 2 (Figure 3). In geometry and in some electronic aspects,50 the tetrahedral PO2- moiety mimics this geminal diol. Each series among these inhibitors shows a slope close to one in the graph of log Ki against log Km/kcat for the related peptide substrates (Figure 3). Within a given series, the structural variations are at the P2 residue and should not affect kun significantly, which is an important consideration. It is important to recognize the meaning of the slope of the line through these data points. It does not represent a measure of how well the inhibitor approximates the transition state; as indicated by eq 16, that metric, d, along with kun, only contributes to the intercept of line. Since the logarithm of an equilibrium constant is directly proportional to the free energy of binding, a slope of 1 in the correlation of eq 16 means that a structural alteration leading to a given incremental change in the binding energy of the transition state produces the same effect in the inhibitors, which is a reasonably intuitive definition of transition-state analogy. This approach can only gauge the degree to which the varied part of the inhibitor structure mimics the corresponding region of the transition state, and it dkun. For this analysis to be valid, of course, it must Figure 3. Comparison of Ki values for phosphonate inhibitors of thermolysin with Km/kcat values for the corresponding substrates.23,65 The diagonal lines correspond to slopes of 1. the same manner that they do in the transition state. Except for the geometry of the phosphorus moiety, which presumably allows the P2 residues to adopt the transition-state orientation, these results do not nature of the other oxyanion in the phosphonate is Proto-typical transition-state analogues comings; for example, the unprotonated, anionic the reverse of the proton-donating, partially cationic water molecule in the transition state (7 vs 8). The oxabicyclic diacid 9 that inhibits the chorismate mutases46 is much more compact than the expanded transition state 10 and does not emulate its charge separation.110 Clearly, we cannot expect even a faithful complement of an imperfect template to compete with an enzyme optimized to bind the true transition state. case the anio entrance of t backbone NH For each antib vicinity of the tetrahedral ha the neutral, p transition sta tional groups mechanism is residues that though its pre must be fair catalyzed reac intermediate w by water or h was raised fro as 17E8, the n heavy chain) antibody retai sured as kcat/K One of the o body combinin enzymes is the exposed to th moieties of the of the antibody catalytic mach T-cell immunity relies on peptide presentations
444 A Textbook of Structural Biology FIGURE 14.7 The binding of peptides to MHC class I (left) and class II (right) molecules. The peptide-binding site is a groove with a base of eight strands and two helices surrounding the peptide. The peptide is shown as a ball-and-stick figure. In MHC class I, some residues block the ends of the groove, while the ends of the groove are open in MHC class II. peptide-binding site is groove Peptides bind toaMHCwitha adefinedfigure. In MHC class some residues block in base of eight strands and two I, helices surrounding the peptide. The peptide is shown as ball-and-stick ways the ends of the groove, while the ends of the groove are open in MHC class II. FIGURE 14.8 The structures of the peptides bound to MHC class I (above) and class II (below). The sheets of MHC have been aligned but are not shown. They are located below the peptides. The class I peptides are shown in different colors for different lengths: 8 (yellow), 9 (red) and 13 residues (green). The binding groove is closed at the ends in class I; therefore, peptides of lengths longer than eight residues will bulge. (Reprinted with permission from Rudolph MG et al. (2006) How TCRs bind MHCs, peptides and coreceptors. Annu Rev Immunol 24: 419466. Copyright Annual Reviews.) There are also non-classical MHC molecules which bind glycolipids and lipopep- TCRs interact with antigenic peptides bound to MHCs, the TCRs bind T-cell immunity involvesglycoproteins or non-classical MHC molecules. As in a complex of many proteins directly to pathogen-derived T-cell T-cell TCR Peptide MHC Class I TCR Peptide MHC Class II Antigen-producing cell Antigen-producing cell FIGURE 14.9 The interactions between MHC molecules and T-cell receptors. Left: orthogonal significant. The relative orientation of the receptor and the MHC complex could be important for T-cell T-cell immunity, againsignaling, but there is no full understanding of how this is transmitted into the cell. T-cell T-cell TCR Peptide MHC Class I CD4 CD8 Antigen-producing cell TCR Peptide MHC Class II Antigen-producing cell FIGURE 14.10 The interaction between the D1 domain of CD4 (cyan) and the MHC class II of chains, T-cell eight and CD3 traversing the consist of side-by-side interacting Ig folds immunityeach heterodimers membrane. The extracellular domains of the CD3 T-cell CD3 CD3 TCR FIGURE 14.11 Left: a schematic illustration of the interactions between TCRs and CD3s in the T cells. The CD3 and CD3 are heterodimers that interact with TCR. Their location in the membrane defines their interactions and the intracellular signals transmitted. Right: the extracellular domains of the CD3- / dimer associate with an approximate twofold axis that is vertical in this view. The / dimer is formed in the same way. The N-termini leads to the transmembrane region (PDB: 1XIW). ...
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