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Query: UNIPROT:P06889 (Mol)
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The crystal structures of the complexes formed between subtilisin Novo and three inhibitors, eglin c, Arg45-eglin c and Lys53-eglin c have been determined using molecular replacement and difference Fourier techniques and refined at 2.4 A, 2.1 A, and 2.4 A resolution, respectively. The mutants Arg45-eglin c and Lys53-eglin c were constructed by site-directed mutagenesis in order to investigate the inhibitory specificity and stability of eglin c. Arg45-eglin became a potent trypsin inhibitor, in contrast to native eglin, which is an elastase inhibitor. This specificity change was rationalized by comparing the structures of Arg45-eglin and basic pancreatic trypsin inhibitor and their interactions with trypsin. The residue Arg53, which participates in a complex network of hydrogen bonds formed between the core and the binding loop of eglin c, was replaced with the shorter basic amino acid lysine in the mutant Lys53-eglin. Two hydrogen bonds with Thr44, located in the binding loop, can no longer be formed but are partially restored by a water molecule bound in the vicinity of Lys53. Eglin c in complexes with both subtilisin Novo and subtilisin Carlsberg was crystallized in two different space groups. Comparison of the complexes showed a rigid body rotation for the eglin c core of 11.5 degrees with respect to the enzyme, probably caused by different intermolecular contacts in both crystal forms.
J Mol Biol 1991 Jan 20
PMID:Refined crystal structures of subtilisin novo in complex with wild-type and two mutant eglins. Comparison with other serine proteinase inhibitor complexes. 199 67

A new and simple method to measure 3JHNH alpha coupling constants of proteins by adding and subtracting traces from corresponding two-dimensional nuclear Overhauser enhanced spectroscopy and two-dimensional correlated spectroscopy cross peaks after scaling is proposed. The optimal scaling for the addition and the subtraction of the two traces is obtained by minimizing an error function. The method was proven to give accurate and precise measurements of coupling constants when tested with a series of simulated spectra. The accuracy of the method was better than 0.1 Hz for all test cases including the limiting case of J = 2.0 Hz and line-width = 11.0 Hz. The accuracy of the method was better than 0.1 Hz for all test cases including The 3JHNH alpha coupling constants were measured in two-dimensional nuclear magnetic resonance spectra of the two proteins barley serine proteinase inhibitor (CI-2) and the bacterial ribonuclease (barnase) of Bacillus amyloliquefaciens. The experimentally measured coupling constants were used to calculate the constants in a Karplus equation to be: 3JHNH alpha = 6.7 cos2(phi-60) -1.3 cos(phi-60) +1.5. These constants are in good accordance with those obtained for basic pancreatic trypsin inhibitor (BPTI). In addition, special emphasis is given to the measurements of positive phi-angles, and to the contribution of molecular dynamics on the apparent coupling constants.
J Mol Biol 1991 Feb 20
PMID:Accurate measurements of coupling constants from two-dimensional nuclear magnetic resonance spectra of proteins and determination of phi-angles. 200 22

The present study confirms that zona pellucidae of rat oocytes became resistant to chymotrypsin digestion (zona hardening) after undergoing in vitro maturation (IVM) in a serum-free medium. However, zona hardening did not occur when empty zonae without oocytes were cultured in the same IVM conditions, suggesting that oocyte-derived factor(s) is responsible for zona hardening in oocytes matured in the serum-free medium. Zona hardening occurred primarily after dictyate oocytes were cultured for 6-8 hours in the IVM medium without serum. Zona hardening could be prevented or alleviated if oocytes were cultured in the IVM medium containing bovine foetal calf serum, a soybean trypsin inhibitor, or beta-mercaptoethanol, and in vitro fertilization rates for such oocytes were normal. Possible mechanisms of the phenomenon of zona hardening in oocytes matured in serum-free conditions are discussed in relation to its possible relevance to the cortical reaction and the physiological block to polyspermy.
Mol Reprod Dev 1991 Mar
PMID:Studies on zona hardening in rat oocytes that are matured in vitro in a serum-free medium. 201 89

Molecular recognition is achieved through the complementarity of molecular surface structures and energetics with, most commonly, associated minor conformational changes. This complementarity can take many forms: charge-charge interaction, hydrogen bonding, van der Waals' interaction, and the size and shape of surfaces. We describe a method that exploits these features to predict the sites of interactions between two cognate molecules given their three-dimensional structures. We have developed a "cube representation" of molecular surface and volume which enables us not only to design a simple algorithm for a six-dimensional search but also to allow implicitly the effects of the conformational changes caused by complex formation. The present molecular docking procedure may be divided into two stages. The first is the selection of a population of complexes by geometric "soft docking", in which surface structures of two interacting molecules are matched with each other, allowing minor conformational changes implicitly, on the basis of complementarity in size and shape, close packing, and the absence of steric hindrance. The second is a screening process to identify a subpopulation with many favorable energetic interactions between the buried surface areas. Once the size of the subpopulation is small, one may further screen to find the correct complex based on other criteria or constraints obtained from biochemical, genetic, and theoretical studies, including visual inspection. We have tested the present method in two ways. First is a control test in which we docked the components of a molecular complex of known crystal structure available in the Protein Data Bank (PDB). Two molecular complexes were used: (1) a ternary complex of dihydrofolate reductase, NADPH and methotrexate (3DFR in PDB) and (2) a binary complex of trypsin and trypsin inhibitor (2PTC in PDB). The components of each complex were taken apart at an arbitrary relative orientation and then docked together again. The results show that the geometric docking alone is sufficient to determine the correct docking solutions in these ideal cases, and that the cube representation of the molecules does not degrade the docking process in the search for the correct solution. The second is the more realistic experiment in which we docked the crystal structures of uncomplexed molecules and then compared the structures of docked complexes with the crystal structures of the corresponding complexes. This is to test the capability of our method in accommodating the effects of the conformational changes in the binding sites of the molecules in docking.(ABSTRACT TRUNCATED AT 400 WORDS)
J Mol Biol 1991 May 05
PMID:"Soft docking": matching of molecular surface cubes. 202 63

The structure of the small squash trypsin inhibitor CMTI-I is refined by directly minimizing the difference between the observed two-dimensional nuclear Overhauser enhancement (NOE) intensities and those calculated by the full relaxation matrix approach. To achieve this, a term proportional to this difference was added to the potential energy function of the molecular dynamics program X-PLOR. Derivatives with respect to atomic co-ordinates are calculated analytically. Spin diffusion effects are thus accounted for fully during the refinement. Initial structures for the refinement were those determined recently by solution nuclear magnetic resonance using the isolated two-spin approximation to derive distance range estimates. The fits to the nuclear magnetic resonance data improve significantly with only small shifts in the refined structures during a few cycles of conjugate gradient minimization. However, larger changes (approximately 1 A) in the conformation occur during simulated annealing, which is accompanied by a further reduction of the difference between experimental and calculated two-dimensional NOE intensities. The refined structures are closer to the X-ray structure of the inhibitor complexed with trypsin than the initial structures. The root-mean-square difference for backbone atoms between the initial structures and the X-ray structure is 0.96 A, and that between the refined structures and the X-ray structure 0.61 A.
J Mol Biol 1991 Jun 05
PMID:Relaxation matrix refinement of the solution structure of squash trypsin inhibitor. 205 85

N-Methyl-N-nitrosourea (MNU)-induced rat mammary adenocarcinomas contain high levels of a novel leupeptin-sensitive serine endopeptidase. Its properties apparently differ from those of other similar endopeptidases reported to be present in various normal and malignant mammalian tissues. The same leupeptinsensitive serine endopeptidase was also detected in normal rat mammary tissues, but at levels approximately 20 times lower than those in MNU-induced mammary tumors. This enzyme, which is a trypsin-like serine endopeptidase, preferentially hydrolyzes various synthetic endopeptidase substrates at the carboxyl side of an arginyl residue. It has an apparent Mr of approximately 160,000 and a Stokes radius of 49 A, as determined by gel filtration. Its isoelectric points range from 4.5 to 4.8, and it has a pH optimum of approximately 7.0. The enzyme is stable from pH 4.0 to 7.0, but is extremely unstable above pH 7.0. Besides leupeptin, its activity is inhibited by antipain, aprotinin, N alpha-p-tosyl-L-lysine chloromethyl ketone and phenylmethylsulfonyl fluoride, but is not inhibited by soybean trypsin inhibitor. Many other potential inhibitors or activators such as 2-mercaptoethanol, p-hydroxymercuribenzoic acid and EDTA have no effect on its activity. The enzyme is adsorbed to p-aminobenzamidine agarose affinity beads at pH 6.5 and elutes at pH 4.0.
Mol Cell Biochem 1990 Apr 18
PMID:A novel leupeptin-sensitive serine endopeptidase present in normal and malignant rat mammary tissues. 216 30

Collagenolytic protease I from the fiddler crab Uca pugilator belongs to the serine proteases of the trypsin family. A graphic molecular model was built using information from sequences and X-ray structures of four homologous proteins which were superimposed to define structurally conserved regions. Protease I sequence was aligned, with sequences of the model proteins, without permitting any deletion or insertion in these regions. Elastase alpha-carbon chain was selected as a template molecule. For the structurally variable regions, fragments of the four homologous proteins which were 'closet' in sequence were selected. Intramolecular steric hindrance, that resulted from the substitution of the residues of the templates by protease I residues, was corrected by adjustment of the side-chain conformational angles. The model was then optimized by energy minimization. The primary specificity pocket in the model of collagenolytic protease I predict a substrate preference for both P1 hydrophobic and positively charged residues which is in agreement with the biochemical observations. As soybean trypsin inhibitor (STI) is known to inhibit collagenolytic protease I, a tentative model of the complex was constructed and possibilities of interaction examined.
J Comput Aided Mol Des 1990 Jun
PMID:Modeling of protease I collagenolytic enzyme from the fiddler crab Uca pugilator. 221 59

Antibodies against two synthetic peptides (aa 299-311 and aa 544-559) selected in different immunogenic domains of the human AR, were induced in rabbits. Antiserum reactivity against the native receptor was investigated by gel permeation chromatography and sucrose density gradient centrifugation using [3H]mibolerone-labeled rat prostate cytosol and [3H]5 alpha-dihydrotestosterone-labeled T-47D cytosol as a source of AR. The absence of cross-reactivity of the antisera with estrogen, progesterone and glucocorticoid receptor was confirmed by density gradient centrifugation of rat uterus cytosol labeled with [3H]E2 or [3H]ORG 2058 and rat liver cytosol labeled with [3H]dexamethasone. After partial proteolytic breakdown of rat prostate AR by endogenous proteases the steroid-labeled receptor was recognized only by the second peptide (aa 544-559) antibody. This proteolytic breakdown could be prevented to a large degree by addition of a high concentration of soybean trypsin inhibitor. The specific AR antibodies provide new tools for the functional analysis of AR, since they interact selectively with specific domains of the receptor.
J Steroid Biochem Mol Biol 1990 Sep
PMID:Antibodies against synthetic peptides recognize the human and rat androgen receptor. 224 51

The interleukin 1 (IL-1) family of proteins has a central role in modulating immune and inflammatory responses. Two major IL-1 proteins, designated alpha (IL-1 alpha) and beta (IL-1 beta), are produced by activated macrophages and other cell types. In an effort to understand the similarities and differences in the physicochemical and functional properties of these two proteins, a program was initiated to determine their structures. Crystals of IL-1 alpha were grown, and the three-dimensional structure at 2.7-A resolution was solved. The technique of multiple-wavelength anomalous dispersion (MAD) with the selenomethionine form of IL-1 alpha was utilized in combination with a single mercury derivative to provide the starting phases. Partial refinement of the IL-1 alpha model has been performed as well. The overall structure is composed of 14 beta-strands and a 3(10) helix. The core of this structure is a capped beta-barrell that possesses 3-fold symmetry and displays a topology similar to that observed for IL-1 beta [Priestle, J. P., et al. (1988) EMBO J. 7, 339-343] and soybean trypsin inhibitor (STI) [McLachlan, A. D. (1979) J. Mol. Biol. 133, 557-563]. In this paper, the overall structure of IL-1 alpha and the nature and fidelity of the internal 3-fold symmetry are discussed. Comparisons with IL-1 beta and STI are made within these contexts.
 ...
PMID:Structure of interleukin 1 alpha at 2.7-A resolution. 234 41

The importance of including different energy contributions in calculations of electrostatic energies in proteins is examined by calculating the intrinsic pKa values of the acidic groups of bovine pancreatic trypsin inhibitor. It appears that such calculations provide a powerful and revealing test; the relevant solvation energies of the ionized acids are of the order of -70 kcal/mol (1 cal = 4.184 J), and microscopic calculations that do not attempt to simulate the complete protein dielectric effect (including the surrounding solvent) can underestimate the solvation energy by as much as 50 kcal/mol. Reproducing correctly, by the same set of parameters, the solvation energies of ionized acids in different sites of a protein cannot be accomplished by including only part of the key energy contributions. The problems associated with macroscopic calculations are also considered and illustrated by the specific case of bovine pancreatic trypsin inhibitor. A promising approach is shown to be provided by a refinement of the previously developed Protein Dipoles Langevin Dipoles model. This model seems to represent consistently the microscopic dielectric of the protein and the surrounding water molecules. The model overcomes the problems associated with the macroscopic models (by treating explicitly the solvent molecules) and avoids the convergence problems associated with all-atom solvent models (by treating the average solvent polarization rather than averaging the actual polarization energy). This paper describes in detail the actual implementation of the model and examines its performance in evaluating intrinsic pKa values. Preliminary microscopic considerations of charge-charge interactions are presented.
J Mol Biol 1985 Sep 20
PMID:Calculations of electrostatic energies in proteins. The energetics of ionized groups in bovine pancreatic trypsin inhibitor. 241 50


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