Structure of the complex formed by bovine trypsin and bovine pancreatic trypsin inhibitor. II. Crystallographic refinement at 1.9 A resolution

A computer-generated three-dimensional model of the B chain of bovine alpha-thrombin

A computer graphic molecular display system has been used to construct a three-dimensional model of the B chain of bovine thrombin. The model is derived from the bovine alpha-chymotrypsin structure as determined by X-ray crystallographic studies. The amino acid sequence of bovine thrombin has been substituted for that of alpha-chymotrypsin, preserving the beta-barrel structure and maximizing homology of the amino acid sequence of the two proteins. With the exception of an area in the vicinity of the specificity binding pocket, most of the changes observed in thrombin occur on the surface of the molecule. The most notable changes observed in the model are the increases on the surface of positively charged (arginine and lysine) and negatively charged (glutamate and aspartate) residues. A glutamate replaces methionine 192 near the entrance to the specificity binding pocket. The nature of this site was further altered by the substitution of an aspartate for serine 189 and an alanine for serine 190. The structure of the resulting specificity binding pocket is consistent with that of serine proteases, which have trypsin-like substrate specificity. The computer graphics molecular display system has been used to insert models of synthetic thrombin inhibitors into the active site of the thrombin B chain model. With the model, it has been possible to correlate the interaction of thrombin with the observed binding constants of two inhibitors of trypsin-like serine proteases, p-amidinophenylmethylsulfonylfluoride (Ki = 1.27 x 10(-6) M) and m-[m-(trifluoromethyl)phenoxypropoxy]benzamidine (KD = 2.9 x 10(-6) M).

Real-time color graphics in studies of molecular interactions

Studies of the structures and interactions of large biological molecules require both coordinate data and three-dimensional visualization. Orthodox molecular models often bear a tenuous relationship to the coordinate data. In contrast, computer graphics requires that the display directly and accurately represent the data, and storage of modified configurations and recovery of original structures are simple. Software has been developed that allows real-time display of color line and surface displays of several interacting molecules, while quantitatively monitoring the stereochemistry.

Soybean trypsin inhibitor (Kunitz) is doubleheaded. Kinetics of the interaction of alpha-chymotrypsin with each side

Further evidence is presented for the formation of a ternary complex between alpha-chymotrypsin (EC 3.4.21.1) and soybean trypsin inhibitor as well as between alpha-chymotrypsin and a performed complex of soybean trypsin and inhibitor (EC 3.4.21.1). This is well in agreement with our earlier sedimentation equilibrium studies. We report on different elution patterns of the ternary forms as compared to the inhibitor trypsin complex and the individual components in gel filtration studies. We also demonstrate the decrease of a given chymotryptic activity on a substrate if the solution is mixed with another one containing the preformed stoichiometric inhibitor-trypsin complex. A fourth piece of evidence for the formation of a chymotrypsin-inhibitor-trypsin complex is the appearance of a difference spectrum in absorbance, when chymotrypsin is mixed with the inhibitor-trypsin complex. Inhibition studies with purified inhibitor show that one molecule of inhibitor binds two molecules of alpha-chymotrypsin, with dissociation constants K1 about 1 microM and K2 about 300 nM at pH 8. The site with weaker affinity for chymotrypsin is specifically blocked by stoichiometric amounts of trypsin. Purification of commercially available preparations of soybean trypsin inhibitor (Kunitz) ("inhibitor") to apparent homogeneity using sodium dodecyl sulfate (SDS)-polyacrylamide gel electrophoresis, and first-order association kinetics with beta-trypsin, is achieved by a combination of gel filtration and ion-exchange chromatography. The kinetics of the interaction of chymotrypsin with inhibitor or with inhibitor-trypsin complex were measured in a stopped-flow photometer by following the displacement of proflavine from the active site of chymotrypsin. A complete reaction scheme is presented with all rates and equilibrium constants as well as their pH-dependence.

A novel chiral microenvironmental probe at the active site of trypsin. Extrinsic cotton effects of acyl-trypsin possessing an enantiomeric pair of chromophores

p-Amidinophenyl esters of an enantiomeric pair of N-(2,4-dinitrophenyl)alanine (N2Ph-Ala) were both efficiently hydrolyzed by trypsin. The acylation and deacylation rate constants for the D-isomer are 1/2.5 of those for the L-isomer. Slow rates of deacylation of the two substrates made it possible to prepare the pair of enantiomeric acyl-trypsins. Circular dichroic (CD) spectra of the purified acyl-trypsins revealed that the two extrinsic chromophores are somewhat differently oriented in the chiral environment of the active site, although both chromophores could couple intermolecularly with similar intrinsic chromophores near the active site. When p-amidinophenol was added, not only was the deacylation rate of N2Ph-DAla-trypsin noticeably increased, but also the transient CD spectrum of the enzyme derivative changed markedly in comparison with that of the L-derivative. The observations indicate that the two enantiomeric acyl groups at the active site are situated in different microenvironments.

Model for haptoglobin heavy chain based upon structural homology

A model has been constructed for haptoglobin heavy chain by using the known sequence homology to the mammalian serine proteases. The three-dimensional structures for three serine proteases, chymotrypsin, trypsin, and elastase, were compared and the structural features that are conserved in all three were extracted. The haptoglobin heavy chain sequence was aligned to the sequences of the three serine proteases by maximizing sequence homology in the regions of conserved structure. The resulting alignment shows that haptoglobin heavy chain must be very closely homologous to these proteases in structure as well as in sequence. Coordinates were derived for the heavy chain by using the homologous structures. The problems associated with these coordinates are outlined and methods for solving them are indicated. The features of the haptoglobin heavy chain structure are described. Implications of the structure for the very strong interaction between this subunit and hemoglobin are discussed.

Empirical torsional potential functions from protein structure data. Phi- and psi-potentials for non-glycyl amino acid residues

The torsional potential functions Vt(phi) and Vt(psi) around single bonds N--C alpha and C alpha--C, which can be used in conformational studies of oligopeptides, polypeptides and proteins, have been derived, using crystal structure data of 22 globular proteins, fitting the observed distribution in the (phi, psi)-plane with the value of Vtot(phi, psi), using the Boltzmann distribution. The averaged torsional potential functions, obtained from various amino acid residues in L-configuration, are Vt(phi) = 1.0 cos (phi + 60 degrees); Vt(psi) = 0.5 cos (psi + 60 degrees) - 1.0 cos (2 psi + 30 degrees) - 0.5 cos (3 psi + 30 degrees). The dipeptide energy maps Vtot(phi, psi) obtained using these functions, instead of the normally accepted torsional functions, were found to explain various observations, such as the absence of the left-handed alpha helix and the C7 conformation, and the relatively high density of points near the line psi = 0 degrees. These functions derived from observational data on protein structures, will, it is hoped, explain various previously unexplained facts in polypeptide conformation.

[Activation, activity and inhibition of bovine trypsin]

Trypsin is a prototype of a large group of enzymes belonging to serine proteinases. The X-ray crystal-structure analyses of its proenzyme trypsinogen, of the active trypsin and of their complexes formed with the pancreatic trypsin inhibitor (PTI) have considerably enhanced our understanding of the mechanisms of activitation, action and inhibition. The trypsinogen is an incompletely folded molecule. Its substrate-binding site becomes only completely fixed upon the enzymatic cleavage of an N-terminal peptide. The contact regions of trypsin and PTI are almost complementary. The complex formed is a (stable) intermediate in the normal tryptic substrate-cleavage reaction.

Crystal structure analysis of the tetragonal crystal form are preliminary molecular model of pig-heart citrate synthase

The crystal structure of pig heart citrate synthase was analyzed at 0.35-nm resolution. Chain tracing was possible and an initial molecular model constructed. The dimensions of the dimer molecule (located on a crystallographic diad) are 7.5 x 6.0 x 9.0 nm. The chain folding is characterized by the predominance of helices and the absence of sheet structure. The electron density accounts for 355 residues per monomer, so that about 80 residues must be disordered in the crystal. The disordered segment in probably N-terminal. The ordered part consists of two closely associated domains, a large domain with 300 residues and a C-terminal domain of 55 residues consisting of 3(anti)parallel helices. The large domain is built from 12 helical segments, some of which are buried in the interior of the molecule. Inhibitor binding studies with citrate and CoA revealed citrate binding sites but showed no electron density for CoA. It is suggested that CoA binds to the disordered, flexible N-terminal domain. Experiments of limited proteolysis with trypsin showed that under conditions a segment of Mr 9000 is cleaved off selectively. The remaining 35 000-Mr part is dimeric.

Individual assignments of the methyl resonances in the 1H nuclear magnetic resonance spectrum of the basic pancreatic trypsin inhibitor

In earlier work the resonances of the 20 methyl groups in the basic pancreatic trypsin inhibitor (BPTI) had been identified in the 360-MHz 1H nuclear magnetic resonance (NMR) spectra and most of the methyl lines had from spin-decoupling experiments been assigned to the different types of amino acid residues. The assignments to the different amino acid types were now completed by studies of the saturation transfer between the denatured and the globular forms of the inhibitor and by spin-decoupling experiments in nuclear Overhauser enhancement (NOE) difference spectra. These distinguished between the methyl resonances of Ala and Thr. Furthermore, for most of the methyl resonances, individual assignments to specific residues in the amino acid sequence were obtained from measurements of intramolecular proton-proton NOE's, use of lanthanide NMR shift and relaxation probes, and comparative studies of various chemically modified forms of BPTI. These data provide the basis for individual assignments of the methyl 13C NMR lines in BPTI and for detailed investigations of the relations between the spatial structure of the protein and the chemical shifts of the methyl groups. The methyl groups in BPTI are of particular interest since they are located almost exclusively on the surface of the protein and thus represent potential natural NMR probes for studies of the protein-protein interactions in the complexes formed between BPTI and a variety of proteases.

Kinetics of the interaction of alpha-chymotrypsin with trypsin kallikrein inhibitor (Kunitz) in which the reactive-site peptide bond Lys-15--Ala-16 is split

Modified trypsin kallikrein inhibitor (I*), with the reactive-site peptide bond Lys-15--Ala-16 split, reacts with alpha-chymotrypsin (E) via an intermediate X to the stable tetrahedral complex C:E + I in equilibrium X leads to C. Formation X constitutes a fast pre-equilibrium (equilibrium constant Kx = 7 X 10(-5) M, association rate constant kx = 4 X 10(3)M-1s-1) to the slow reaction X leads to C (rate constant kc = 2 X 10(-3) s-1), all values at pH 7.5. No intermediate X is observed when alpha-chymotrypsin reacts with I*-OMe in which the carboxyl group of Lys-15 is esterified by methanol. This observation as well as the different pH dependence of the overall association rate constants in the case of I* and I*-OMe indicate tha formation of X precedes formation of the acyl enzyme in the catalytic pathway. The data are compared to the similar results obtained with beta-trypsin and I* or I*-OMe.

The role of geometry and elastic strains in dynamic states of proteins

A theory is developed, where a linear macromolecule with geometrically constrained ends, elastically strained, exchanging energy with the solvent molecules through random collisions may provide a mechanism for the following specific functions in proteins: a) Induction of transient, oriented strains in substrates during transition between conformations. b) External variation of the rigidity and geometry of the active site. More generally, a macromolecule in solution possessing appropriate geometrical and elastic properties constitutes a machine, whose possible operations have common features with biological function such as passive transport, enzymatic catalysis and active transport. The theory suggests a quantitative law by which new information about the dynamical state of the protein molecule can be elucidated from the Arrhenius plot. It predicts a relationship between the rate of catalysis and the local viscosity of the solution.