Dynamics of the multidomain fibrinolytic protein urokinase from two-dimensional NMR

Christopher Dobson, 1949-2019: Mentor, Friend, Scientist Extraordinaire

It is impossible to do justice in one review article to a researcher of the stature of Christopher Dobson. His career spanned almost five decades, resulting in more than 870 publications and a legacy that will continue to influence the lives of many for decades to come. In this review, I have attempted to capture Chris's major contributions: his early work, dedicated to understanding protein-folding mechanisms; his collaborative work with physicists to understand the process of protein aggregation; and finally, his later career in which he developed strategies to prevent misfolding. However, it is not only this body of work but also the man himself who inspired an entire generation of scientists through his patience, ability to mentor, and innate generosity. These qualities remain a hallmark of the way in which he conducted his research-research that will leave a lasting imprint on science.

Investigating the mechanisms of amylolysis of starch granules by solution-state NMR

Starch is a prominent component of the human diet and is hydrolyzed by α-amylase post-ingestion. Probing the mechanism of this process has proven challenging, due to the intrinsic heterogeneity of individual starch granules. By means of solution-state NMR, we demonstrate that flexible polysaccharide chains protruding from the solvent-exposed surfaces of waxy rice starch granules are highly mobile and that during hydrothermal treatment, when the granules swell, the number of flexible residues on the exposed surfaces increases by a factor of 15. Moreover, we show that these flexible chains are the primary substrates for α-amylase, being cleaved in the initial stages of hydrolysis. These findings allow us to conclude that the quantity of flexible α-glucan chains protruding from the granule surface will greatly influence the rate of energy acquisition from digestion of starch.

Activation of the zymogen to urokinase-type plasminogen activator is associated with increased interdomain flexibility

A key regulatory step for serine proteases of the trypsin clan is activation of the initially secreted zymogens, leading to an increase in activity by orders of magnitude. Zymogen activation occurs by cleavage of a single peptide bond near the N-terminus of the catalytic domain. Besides the catalytic domain, most serine proteases have N-terminal A-chains with independently folded domains. Little is known about how zymogen activation affects the interplay between domains. This question is investigated with urokinase-type plasminogen activator (uPA), which has an epidermal growth factor domain and a kringle domain, connected to the catalytic domain by a 15-residue linker. uPA has been implicated under several pathological conditions, and one possibility for pharmacological control is targeting the conversion of the zymogen pro-uPA to active uPA. Therefore, a small-angle X-ray scattering study of the conformations of pro-uPA and uPA in solution was performed. Structural models for the proteins were derived using available atomic-resolution structures for the various domains. Active uPA was found to be flexible with a random conformation of the amino-terminal fragment domain with respect to the serine protease domain. In contrast, pro-uPA was observed to be rigid, with the amino-terminal fragment domain in a fixed position with respect to the serine protease domain. Analytical ultracentrifugation analysis supported the observed difference between pro-uPA and uPA in overall shape and size seen with small-angle X-ray scattering. Upon association of either of two monoclonal Fab (fragment antigen-binding) fragments that are directed against the catalytic domain of, respectively, pro-uPA and uPA, rigid structures were formed.

Multidimensional triple resonance NMR spectroscopy of isotopically uniformly enriched proteins: a powerful new strategy for structure determination

A procedure is described that affords complete 1H, 13C and 15N resonance assignment in proteins of up to about 25 kDa. The new approach requires uniform isotopic enrichment of the protein with 13C and 15N and correlates resonances of adjacent nuclei using the relatively large and well-resolved one-bond J couplings. Spectral overlap, a common problem in the application of two-dimensional NMR, is removed by increasing the dimensionality of the new methods to three or four, without increasing the number of observed resonances. With complete 1H, 13C and 15N resonance assignments available, the nuclear Overhauser effect (NOE)-based interproton distance constraints can be extracted in a very straightforward manner from four-dimensional NOE spectra.

Evolutionarily conserved functional mechanics across pepsin-like and retroviral aspartic proteases

The biological function of the aspartic protease from HIV-1 has recently been related to the conformational flexibility of its structural scaffold. Here, we use a multistep strategy to investigate whether the same mechanism affects the functionality in the pepsin-like fold. (i) We identify the set of conserved residues by using sequence-alignment techniques. These residues cluster in three distinct regions: near the cleavage-site cavity, in the four beta-sheets cross-linking the two lobes, and in a solvent-exposed region below the long beta-hairpin in the N-terminal lobe. (ii) We elucidate the role played by the conserved residues for the enzymatic functionality of one representative member of the fold family, the human beta-secretase, by means of classical molecular dynamics (MD). The conserved regions exhibit little overall mobility and yet are involved into the most important modes of structural fluctuations. These modes influence the substrate-catalytic aspartates distance through a relative rotation of the N- and C-terminal lobes. (iii) We investigate the effects of this modulation by estimating the reaction free energy at different representative substrate/enzyme conformations. The activation free energy is strongly affected by large-scale protein motions, similarly to what has been observed in the HIV-1 enzyme. (iv) We extend our findings to all other members of the two eukaryotic and retroviral fold families by recurring to a simple, topology-based, energy functional. This analysis reveals a sophisticated mechanism of enzymatic activity modulation common to all aspartic proteases. We suggest that aspartic proteases have been evolutionarily selected to possess similar functional motions despite the observed fold variations.

The kringle stabilizes urokinase binding to the urokinase receptor

The structural basis of the interaction between single-chain urokinase-type plasminogen activator (scuPA) and its receptor (uPAR) is incompletely defined. Several observations indicated the kringle facilitates the binding of uPA to uPAR. A scuPA variant lacking the kringle (Delta K-scuPA) bound to soluble uPAR (suPAR) with the similar "on-rate" but with a faster "off-rate" than wild-type (WT)-scuPA. Binding of Delta K-scuPA, but not WT-scuPA, to suPAR was comparably inhibited by its growth factor domain (GFD) and amino-terminal fragment (ATF). ATF and WT-scuPA, but not GFD, scuPA lacking the GFD (Delta GFD-scuPA), or Delta K-scuPA reconstituted the isolated domains of uPAR. ATF completely inhibited the enzymatic activity of WT-scuPA-suPAR unlike comparable concentrations of GFD. Variants containing mutations that alter the charge, length, or flexibility of linker sequence (residues 43-49) between the GFD and the kringle displayed a lower affinity for uPAR, were unable to reconstitute uPAR domains, and their binding to uPAR was inhibited by GFD in the same manner as Delta K-scuPA. A scuPA variant in which the charged amino acids in the heparin binding site (HBS) in the kringle domain were mutated to alanines behaved like Delta K-scuPA, indicating that that the structure of the kringle as well as its interaction with the GFD govern receptor binding. These data demonstrate an important role for the kringle in stabilizing the binding of scuPA to uPAR.

Maspin inhibits cell migration in the absence of protease inhibitory activity

Maspin is a member of the serpin family of protease inhibitors and is a tumor suppressor gene acting at the level of tumor invasion and metastasis. This in vivo activity correlates with the ability of maspin to inhibit cell migration in vitro. This behavior suggests that maspin inhibits matrix-degrading proteases, such as those of the plasminogen activation system, in a similar manner to the serpin PAI-1. However, there is controversy concerning the protease inhibitory activity of maspin. It is devoid of activity against a wide range of proteases, in common with other non-inhibitory serpins, but has recently been reported to inhibit plasminogen activators associated with cells and other biological surfaces (Sheng, S. J., Truong, B., Fredrickson, D., Wu, R. L., Pardee, A. B., and Sager, R. (1998) Proc. Natl. Acad. Sci. U. S. A. 95, 499-504; McGowen, R., Biliran, H., Jr., Sager, R., and Sheng, S. (2000) Cancer Res. 60, 4771-4778). We have compared the effects of maspin with those of PAI-1 in a range of situations in which plasminogen activation is potentiated, reflecting the biological context of this proteolytic system: urokinase-type plasminogen activator bound to its receptor on the surface of tumor cells, tissue-type plasminogen activator specifically bound to vascular smooth muscle cells, fibrin, and the prion protein. Maspin was found to have no inhibitory effect in any of these situations, in contrast to the efficient inhibition observed with PAI-1, but nevertheless maspin inhibited the migration of both tumor and vascular smooth muscle cells. We conclude that maspin is a non-inhibitory serpin and that protease inhibition does not account for its activity as a tumor suppressor.

Receptor-mediated regulation of plasminogen activator function: plasminogen activation by two directly membrane-anchored forms of urokinase

The generation of the broad specificity serine protease plasmin in the pericellular environment is regulated by binding of the urokinase-type plasminogen activator (uPA) to its specific glycosylphosphatidylinositol (GPI)-anchored cell-surface receptor, uPAR. This interaction potentiates the reciprocal activation of the cell-associated zymogens pro-uPA and plasminogen. To further study the role of uPAR in this mechanism, we have expressed two directly membrane-anchored chimeric forms of uPA, one anchored by a C-terminal GPI-moiety (GPI-uPA), the other with a C-terminal transmembrane peptide (TM-uPA). These were expressed in the monocyte-like cell lines U937 and THP-1, which are excellent models for kinetic and mechanistic studies of cell-surface plasminogen activation. In both cell-lines, GPI-uPA activated cell-associated plasminogen with characteristics both qualitatively and quantitatively indistinguishable from those of uPAR-bound uPA. By contrast, TM-uPA activated cell-associated plasminogen less efficiently. This was due to effects on the K, for plasminogen activation (which was increased up to five-fold) and the efficiency of pro-uPA activation (which was decreased approximately four-fold). These observations suggest that uPAR serves two essential roles in mediating efficient cell-surface plasminogen activation. In addition to confining uPA to the cell-surface, the GPI-anchor plays an important role by increasing accessibility to substrate plasminogen and, thus, enhancing catalysis. However, the data also demonstrate that, in the presence of an alternative mechanism for uPA localization, uPAR is dispensable and, therefore, unlikely to participate in any additional interactions that may be necessary for the efficiency of this proteolytic system. In these experiments zymogen pro-uPA was unexpectedly found to be constitutively activated when expressed in THP-1 cells, suggesting the presence of an alternative plasmin-independent proteolytic activation mechanism in these cells.

Phosphorylation of human pro-urokinase on Ser138/303 impairs its receptor-dependent ability to promote myelomonocytic adherence and motility

Serine phosphorylation of human pro-urokinase (pro-uPA) by A431 human carcinoma cells results in a catalytically active molecule with reduced sensitivity to plasminogen activator inhibitor type 1. We mapped the phosphorylated seryl residues by analyzing the in vivo phosphorylation state of engineered pro-uPA variants carrying a COOH-terminal poly-histidine tag. Stably transfected A431 cells do not incorporate radioactive phosphate into tagged pro-uPA in which the serines 138 and 303 have been replaced with glutamic residues, although endogenous nontagged pro-uPA is 32P-labeled on A and B chains. Moreover, the catalytic-independent ability of the mono- and di-substituted "phosphorylation-like" variants to bind to the GPI-anchored urokinase receptor (uPAR) and promote adherence of differentiating U937, HL-60, and THP-1 myelomonocytic cells was examined. We found that glutamic residues as well as the naturally occurring phosphoserines at positions 138 and 303 abolish proadhesive ability, although they do not interfere with receptor binding. In addition, pro-uPA carrying Glu138/303 lacks the capability to induce a chemotactic response of THP-1 cells. The exclusive presence of Glu138 reduces pro-uPA proadhesive and chemotactic ability by 70-80%, indicating that a phosphoserine residue at the same position plays a major inhibitory role of myeloid cell response to pro-urokinase. The di-substitution does not affect pro-uPA ability to interact with vitronectin or to enhance binding of urea-denatured vitronectin to uPAR. However, unlike wild-type tagged pro-uPA, the di-substituted variant does not induce receptor polarization in pre-adherent U937 cells. Taken together, the data support the possibility that pro-uPA phosphorylation on Ser138/303 can modulate uPAR transducing ability.

Unexpected binding mode of a cyclic sulfamide HIV-1 protease inhibitor

Two cyclic, C2-symmetric HIV-1 protease inhibitors, one sulfamide and one urea derivative, both comprising phenyl ether groups in the P1/P1' positions, were cocrystallized with HIV-1 protease, and the crystal structures were determined to 2.0 A resolution. The structure of the urea 2 showed a conformation similar to that reported for the related urea 3 by Lam et al., while the sulfamide 1 adopted an unanticipated conformation in which the P1' and P2' side chains were transposed.

A novel, picomolar inhibitor of human immunodeficiency virus type 1 protease

The design, synthesis, and molecular modeling studies of a novel series of azacyclic ureas, which are inhibitors of human immunodeficiency virus type 1 (HIV-1) protease that incorporate different ligands for the S1', S2, and S2' substrate-binding sites of HIV-1 protease are described. The synthesis of this series is highly flexible in the sense that the P1', P2, and P2' residues of the inhibitors can be changed independently. Molecular modeling studies on the phenyl ring of the P2 and P2' ligand suggested incorporation of hydrogen-bonding donor/acceptor groups at the 3' and 4-positions of the phenyl ring should increase binding potency. This led to the discovery of compound 7f (A-98881), which possesses high potency in the HIV-1 protease inhibition assay and the in vitro MT-4 cell culture assay (Ki = approximately 5 pM and EC50 = 0.002 microM). This compares well with the symmetrical cyclic urea 1 pioneered at DuPont Merck.

Direct observation of disordered regions in the major histocompatibility complex class II-associated invariant chain

Invariant chain (Ii) is a trimeric membrane protein which binds and stabilizes major histocompatibility complex class II heterodimers in the endoplasmic reticulum and lysosomal compartments of antigen-presenting cells. In concert with an intracellular class II-like molecule, HLA-DM, Ii seems to facilitate loading of conventional class II molecules with peptides before transport of the class II-peptide complex to the cell surface for recognition by T cells. The interaction of Ii with class II molecules is thought to be mediated in large part through a region of 24 amino acids (the class II-associated Ii peptide, CLIP) which binds as a cleaved moiety in the antigenic peptide-binding groove of class II molecules in HLA-DM-deficient cell lines. Here we use nuclear magnetic resonance techniques to demonstrate that a soluble recombinant Ii ectodomain contains significant disordered regions which probably include CLIP.

The crystal structure of the catalytic domain of human urokinase-type plasminogen activator

BACKGROUND

Urokinase-type plasminogen activator (u-PA) promotes fibrinolysis by catalyzing the conversion of plasminogen to the active protease plasmin via the cleavage of a peptide bond. When localized to the external cell surface it contributes to tissue remodelling and cellular migration; inhibition of its activity impedes the spread of cancer. u-PA has three domains: an N-terminal receptor-binding growth factor domain, a central kringle domain and a C-terminal catalytic protease domain. The biological roles of the fibrinolytic enzymes render them therapeutic targets, however, until now no structure of the protease domain has been available. Solution of the structure of the u-PA serine protease was undertaken to provide such data.

RESULTS

The crystal structure of the catalytic domain of recombinant, non-glycosylated human u-PA, complexed with the inhibitor Glu-Gly-Arg chloromethyl ketone (EGRcmk), has been determined at a nominal resolution of 2.5 A and refined to a crystallographic R-factor of 22.4% on all data (20.4% on data > 3 sigma). The enzyme has the expected topology of a trypsin-like serine protease.

CONCLUSIONS

The enzyme has an S1 specificity pocket similar to that of trypsin, a restricted, less accessible, hydrophobic S2 pocket and a solvent-accessible S3 pocket which is capable of accommodating a wide range of residues. The EGRcmk inhibitor binds covalently at the active site to form a tetrahedral hemiketal structure. Although the overall structure is similar to that of homologous serine proteases, at six positions insertions of extra residues in loop regions create unique surface areas. One of these loop regions is highly mobile despite being anchored by the disulphide bridge which is characteristic of a small subset of serine proteases namely tissuetype plasminogen activator, Factor XII and Complement Factor I.

Tissue-type plasminogen activator domain-deletion mutant BM 06.022: modular stability, inhibitor binding, and activation cleavage

Recombinant BM 06.022 (M(r) 39,589) is a domain-deletion mutant of the human tissue-type plasminogen activator (tPA) structured by the kringle 2 and protease modules. Unfolding under various conditions was investigated via 1H-NMR spectroscopy by monitoring the well-resolved high-field methyl resonances at approximately -0.97 ppm (kringle 2) and approximately -0.29 and -0.54 ppm (protease). Reversible acid/base unfolding is manifest under low pH (< 4.8) conditions. It is observed that, relative to the protease, the kringle exhibits higher overall stability at low pH. At pH 4.6, BM 06.022 undergoes two distinct thermal melting transitions, at approximately 334 and approximately 352 K, assigned to an irreversible denaturation of the protease and a reversible unfolding of the kringle 2, respectively. Under the same conditions, the protease reacted with the active site inhibitor 1,5 dansyl-L-glutamylglycyl-L-arginine chloromethyl ketone (EGRck) exhibits a higher (approximately 10 K) thermal stability than the inhibitor-free protease. Upon acidification, the EGRck-modified protease unfolds irreversibly around pH 3.4. As exemplified by BM 06.022, a single-chain protein, as defined by continuity of the polypeptide backbone, can exhibit simultaneous folding reversibility and irreversibility for autonomous segments of the sequence. Conversion of the isolated (single-chain) protease or intact BM 06.022 to their catalytically active two-chain forms via plasminolytic cleavage of the Arg275-Ile276 peptide bond leaves the kringle 2 spectrum unaffected while perturbing the resolved high-field methyl resonances stemming from the protease. The latter also shift when the protease is reacted with EGRck, indicating that these signals are sensitive to events at the binding pocket.(ABSTRACT TRUNCATED AT 250 WORDS)

1H- and 19F-NMR approaches to the study of the structure of proteins larger than 25 kDa

The three-dimensional solution structures of proteins larger than about 25 kDa cannot at present be determined by multi-dimensional nuclear magnetic resonance (NMR) methods. However, for proteins that are larger than 25 kDa, for which X-ray structural information is not available, there are a variety of mostly one-dimensional NMR methods that still represent some of the most informative approaches to obtaining structural answers to questions of biochemical interest. This paper provides recent illustrative examples of 1H- and 19F-NMR experiments that describe ways to focus on proteins by region, by amino acid type, or by individual amino acid. Methods to focus on a particular region of a protein include exploiting domain mobility, using transferred nuclear Overhauser enhancements, the use of difference spectroscopy, the use of paramagnetic species, and domain fragmentation. Particular types of amino acid can be identified using selective deuteration, by incorporation of fluorinated amino acid analogues, by using photochemically induced dynamic nuclear polarization, and from the pH dependence of histidine residues. Individual amino acids can be identified by mutagenesis and, in special circumstances, by chemical shift. Many of the examples given are of plasma proteinases and their protein inhibitors, but other classes of protein are also discussed, including antibodies and DNA-binding proteins.

pH-induced structural changes in human serum apotransferrin. pKa values of histidine residues and N-terminal amino group determined by 1H-NMR spectroscopy

The binding of apotransferrin (80 kDa) to the transferrin receptor is known to be highly pH-dependent. We have investigated pH-induced structural changes in human serum apotransferrin over the pH* (meter reading in D2O solutions) range 2.5-11 using 1H-NMR spectroscopy. The pKa values of 14 (possibly 15) of the 19 His residues in the protein have been determined as well as that of the terminal amino group (Val1, 7.75). About eight His residues deprotonate when the pH* is raised from the endosomal value of about 5.5 to the blood plasma value (7.4). Four His residues have pKa < 6. Sharp discontinuities in the His titration curves were observed below pH 4.3 and at pH 3.5 molten globule states were detected.

1H-NMR spectroscopy of beta B2-crystallin from bovine eye lens. Conformation of the N- and C-terminal extensions

1H-NMR spectroscopic studies of a 46-kDa homodimer, beta B2-crystallin, from bovine eye lens are presented. beta B2-crystallin has terminal extensions extending from globular N- and C-terminal domains that are well resolved in the NMR spectra, whereas, in the main, resonances from the bulk of the protein are not observed. Using two-dimensional NMR methods on beta B2-crystallin, its synthesised terminal extensions and a proteolysed sample of beta B2-crystallin with a portion of its C-terminus removed, it was possible to assign resonances to most of the amino acids in the terminal extensions. One-dimensional experiments at various pH values provided H-2 chemical shifts for the three terminal extension histidines from which their pKa values were measured. It is concluded that the terminal extensions appear to be of little ordered conformation, are accessible to solvent and flex freely from the main body of the protein. The results of the NMR spectroscopic studies of beta B2-crystallin are in excellent agreement with those for the X-ray crystal structure [Bax, B., Lapatto, R., Nalini, V., Driessen, H., Lindley, P. F., Mahadevan, D., Blundell, T. L. & Slingsby, C. (1990) Nature 347, 776-780]. No change in the spectrum of beta B2-crystallin was observed in the presence of calcium, suggesting that the termini are not involved in calcium binding.

Characterization of structural and folding properties of streptokinase by n.m.r. spectroscopy

The structure and physical properties of the fibrinolytic protein streptokinase have been investigated by 1H-n.m.r. spectroscopy. Well-resolved one- and two-dimensional spectra have been obtained for this molecule of molecular mass 47 kDa. Titration of all nine histidine residues has shown that these display a range of pKa values, between 5.6 and 8.2, revealing a variety of environments for these residues in the protein structure. Although at least eight histidine residues can be reversibly modified by diethylpyrocarbonate, only one is sufficiently exposed to be reactive towards photo-excited dye in chemically induced dynamical nuclear polarization spectroscopy experiments. Unfolding studies have been performed by thermal and chemical means. Evidence is presented here for several distinct unfolding transitions suggesting that the protein consists of at least three domains which have independent stability, and that the protein can exist in a number of partially folded states. For one of these, that formed in 2 M guanidine hydrochloride, it has been shown that the N-terminal region of the molecule is extensively unfolded, while other regions of the protein remain in native-like folded states.

Uptake of Al3+ into the N-lobe of human serum transferrin

We have studied the binding of Al3+ to human serum apotransferrin (80 kDa) and recombinant N-lobe human apotransferrin (40 kDa) in 0.1 M-sodium bicarbonate solution at a pH meter reading in 2H2O (pH*) of 8.8 using 1H n.m.r. spectroscopy. The results show that for the intact protein, preferential binding of Al3+ to the N-lobe occurs. Molecular modelling combined with an analysis of ring-current-induced shifts suggest that n.m.r. spectroscopy can be used to probe hinge bending processes which accompany metal uptake in solution.

Proton NMR studies of bovine serum albumin. Assignment of spin systems

A variety of one- and two-dimensional 1H-NMR methods have been applied to the study of defatted 66.5-kDa bovine serum albumin in solution. 1. The majority of the protons gave rise to broad unresolved resonances and spectral enhancement methods for one-dimensional spectra were investigated in detail. A combination of exponential and sine-bell functions was particularly effective. 2. The presence of contaminating glycoproteins in some commercial samples of bovine serum albumin was readily detectable from their N-acetyl resonances at about 2.1 ppm. 3. The release of bound Cys (from mixed disulphide at Cys34) was observed after addition of dithiothreitol. 4. Through the use of two-dimensional shift-correlated spectroscopy, assignments of some 80 spin systems to amino acid type were made. 5. The pKa of the N-terminal Asp was measured as 7.8 (0.1 M phosphate buffer, 310 K). 6. 1H NMR spectra of bovine, human, porcine and rat serum albumins have been compared. Using sequence comparisons, specific assignments have been made for the N-terminal residues of bovine (Asp-Thr-His), human (Asp-Ala-His), porcine (Asp-Thr-Tyr) and rat (Glu-Ala-His) albumins, and for Thr189, Tyr155 and His59/377 of bovine albumin. 7. These NMR data suggest that certain local regions of bovine serum albumin are highly mobile yet structured in solution, and demonstrate that the application of both one- and and two-dimensional NMR methods will allow more detailed investigations of structural transitions in serum albumins induced by, for example, pH, drug and metal binding.

1H-n.m.r. studies of the fibronectin 13 kDa collagen-binding fragment. Evidence for autonomous conserved type I and type II domain folds

A 1H-n.m.r. study of a 117-residue (13 kDa) gelatin-binding fragment of human fibronectin, which contains the sixth (from the N-terminus) type I domain and the first type II domain, was undertaken. The resolution of the 1H-n.m.r. spectrum indicates that the domains are independent and mobile relative to each other. Analysis of two-dimensional 1H-n.m.r. experiments recorded at 500 MHz afforded spin-system identifications for all aromatic and a number of aliphatic residues. Utilizing the fact that phenylalanine residues occur only in the type II portion of this fragment, many spin systems were localized to either the type I or the type II module via analysis of two-dimensional nuclear-Overhauser-effect (NOESY) experiments. This allowed unambiguous assignment of the two tryptophan residues, as they occur singly in each domain. Patterns of NOESY connectivities are found to be consistent with known type I and type II domain structures; this affords a number of tentative sequence-specific assignments. For both domains, evidence of conserved hydrophobic cores and secondary-structure elements is obtained. In addition, 1H-n.m.r.-monitored thermal-melting studies demonstrate conclusively that the domains are independently folded and that the type I domain has high thermal stability relative to the type II domain. This is consistent with the results of calorimetric studies, and also confirms the localization of spin systems determined from the NOESY data.

A 1H NMR probe for mobility in the reactive center loops of serpins: spin-echo studies of native and modified forms of ovalbumin and alpha 1-proteinase inhibitor

It has recently been proposed that the expression of inhibitory activity in serine protease inhibitors (serpins) is a function of the mobility of the extended alpha-helical reactive center loop [Stein, P.E., Leslie, A.G.W., Finch, J.T., Turnell, W.G., McLaughlin, P.J., & Carrell, R.W. (1990) Nature 347, 99-102]. We have employed solution 1H NMR methods, including the Carr-Purcell-Meiboom-Gill (CPMG) and Hahn spin-echo pulse sequences, to try to identify such regions by virtue of their anticipated longer T2 relaxation times in two of the best characterized members of the serpin superfamily, ovalbumin and alpha 1-proteinase inhibitor. The CPMG spectra of native ovalbumin reveal the presence of long-lived resonances from the methyl protons of alanine residues and the CH3 protons of leucine or valine residues as well as the acetyl and ring methine protons of the carbohydrate moieties. Following reaction of ovalbumin with subtilisin Carlsberg to generate plakalbumin [where excision from within the reactive center loop homologue of a hexa- or heptapeptide, with sequence (E)-A-G-V-D-A-A, occurs], its CPMG spectrum retained almost all of the originally present long-lived resonances. Concurrent with the retention of these mobile resonances in plakalbumin is the appearance of two additional resonances consistent with the formation of new C and N termini. On the basis of the proposed mobility of the reactive center loop, it had been expected that removal of the alanine-rich hexapeptide would result in loss of some or all of the long-lived alanine methyl resonances.(ABSTRACT TRUNCATED AT 250 WORDS)

Antigen mobility in the combining site of an anti-peptide antibody

The interaction between a high-affinity antibody, raised against a peptide incorporating the loop region of hen egg lysozyme (residues 57-84), and a peptide antigen corresponding to this sequence, has been probed by proton NMR. The two-dimensional correlated spectroscopy spectrum of the antibody-antigen complex shows sharp, well-resolved resonances from at least half of the bound peptide residues, indicating that the peptide retains considerable mobility when bound to the antibody. The strongly immobilized residues (which include Arg-61, Trp-62, Trp-63, and Ile-78) do not correspond to a contiguous region in the sequence of the peptide. Examination of the crystal structure of the protein shows that these residues, although remote in sequence, are grouped together in the protein structure, forming a hydrophobic projection on the surface of the molecule. The antibody binds hen egg lysozyme with only a 10-fold lower affinity than the peptide antigen. We propose that the peptide could bind to the antibody in a conformation that brings these groups together in a manner related to that found in the native protein, accounting for the high crossreactivity.

Recoverin: a calcium sensitive activator of retinal rod guanylate cyclase

Vertebrate retinal photoreceptors recover from photoexcitation-induced hydrolysis of guanosine 3', 5'-monophosphate (cyclic GMP) by resynthesizing cyclic GMP, which reopens cation channels that have been closed by light. Activation of guanylate cyclase by light-induced depletion of cytosolic calcium is a key event in this recovery process. This cyclase has now been shown to be regulated by a 23-kilodalton calcium binding protein. The protein is present in both rod and cone photoreceptors and was named recoverin because it promotes recovery of the dark state. The amino acid sequence of recoverin exhibits three potential calcium binding sites (EF hands). That recoverin binds calcium was confirmed with calcium-45 and by observing calcium-induced changes in its tryptophan fluorescence. Recoverin activated guanylate cyclase when free calcium was lowered from 450 to 40 nM, an effect that was blocked by an antibody to recoverin. Thus, guanylate cyclase in retinal rods is stimulated during recovery by the calcium-free form of recoverin. A comparison of recoverin with other calcium binding proteins reveals that it may represent, along with the protein visinin, a family of proteins that are regulated by submicromolar calcium concentrations.

Domain interactions in human plasminogen studied by proton NMR

The NMR spectrum of miniplasminogen (V443-plasminogen) under conditions of acidic pH reveals a subset of particularly well-resolved resonances whose chemical shift values are closely similar to those of isolated kringle 5. The temperature dependence of the spectrum indicates that this set of resonances disappears in a single cooperative unfolding transition appropriate for kringle 5, whilst other broader resonances from the protease domain persist to higher temperature. These results provide evidence for significant structural and motional independence of the kringle and protease domains in spite of the short linker between these domains. The NMR spectrum of Glu1-plasminogen is closely similar to that of miniplasminogen under the same conditions. This suggests that the domain independence observed in miniplasminogen is maintained in the intact molecule.

Spin-echo 1H NMR studies of differential mobility in gizzard myosin and its subfragments

The unexpectedly narrow resonances in the 1H NMR spectra of gizzard myosin, heavy meromyosin, and subfragment 1 were examined by spin-echo NMR spectroscopy. These resonances originated predominantly in the myosin heads, or subfragment 1 units. Smooth muscle myosin undergoes a dramatic change in hydrodynamic properties and can exist either as a folded (10S) or as an extended (6S) species. Factors that influence this transition, namely, ionic strength and phosphorylation (or thiophosphorylation), were varied in the NMR experiments. T2 relaxation experiments on dephosphorylated myosin indicated several components of different relaxation times that were not influenced by changes in ionic strength. Our experiments focused on the components with longer relaxation times, i.e., corresponding to nuclei with more mobility, and these were observed selectively in a spin-echo experiment. With dephosphorylated myosin and HMM, increases in ionic strength caused an increased intensity in several of the narrower resonances. The ionic strength dependence of these changes paralleled that for the 10S to 6S transition. With thiophosphorylated myosin and HMM, changes in ionic strength also influenced the intensities of the narrower resonances, and in addition changes in the 1H NMR spectrum due to thiophosphorylation were observed. The narrow resonances seen with myosin and HMM were observed with S1, but the spin-echo spectra of S1 were not influenced either by changes in ionic strength or by phosphorylation. These results suggest that a fraction of the 1H resonances in smooth muscle myosin and its fragments originates from both aliphatic and aromatic residues of increased mobility compared to the mobility expected from hydrodynamic properties of these proteins. In general, the intensities of these residues increase with increasing ionic strength, and this is consistent with an increase in the percentage of mobile residues during the 10S to 6S transition. Segmental flexibility appeared also to be influenced by phosphorylation within the 6S conformation. These changes were not detected in the isolated myosin heads and thus required a higher order of structure, either the subfragment 2 region or the interaction of myosin heads.

Lysosomal degradation of receptor-bound urokinase-type plasminogen activator is enhanced by its inhibitors in human trophoblastic choriocarcinoma cells

We have studied the effect of plasminogen activator inhibitors PAI-1 and PAI-2 on the binding of urokinase-type plasminogen activator (u-PA) to its receptor in the human choriocarcinoma cell line JAR. With 125I-labeled ligands in whole-cell binding assays, both uncomplexed u-PA and u-PA-inhibitor complexes bound to the receptor with a Kd of approximately 100 pM at 4 degrees C. Transferring the cells to 37 degrees C led to degradation to amino acids of up to 50% of the cell-bound u-PA-inhibitor complexes, whereas the degradation of uncomplexed u-PA was 15%; the remaining ligand was recovered in an apparently intact form in the medium or was still cell associated. The degradation could be inhibited by inhibitors of vesicle transport and lysosomal hydrolases. By electron microscopic autoradiography, both 125I-u-PA and 125I-u-PA-inhibitor complexes were located over the cell membrane at 4 degrees C, with the highest density of grains over the membrane at cell-cell interphases, but, after incubation at 37 degrees C, 17 and 27% of the grains for u-PA and u-PA-PAI-1 complexes, respectively, appeared over lysosomal-like bodies. These findings suggest that the u-PA receptor possesses a clearance function for the removal of u-PA after its complex formation with a specific inhibitor. The data suggest a novel mechanism by which receptor-mediated endocytosis is initiated by the binding of a secondary ligand.

Conformational change in the N-terminal domain of the Escherichia coli tryptophan synthase beta 2 subunit induced by its interactions with monoclonal antibodies

A fluorescence energy transfer signal was used to follow conformational changes occurring in two types of protein-protein complexes. The first complex studied was the native-like beta 2 subunit of Escherichia coli tryptophan synthase reconstituted by reassembly of the N- and C-terminal proteolytic domains of the beta chain. The other complexes were formed by the association of the N-terminal fragment (F1) with a monoclonal antibody that recognizes the native dimeric protein; four such complexes, obtained with different antibodies that recognize four distinct antigenic sites on native beta 2, were investigated. It was shown that a structural readjustment, which the isolated F1 domain was unable to undergo alone, was imposed upon F1 by interdomain interactions. Furthermore, with three of the four antibodies studied, the same conformational change in F1 also occurred after formation of the F1-antibody complex. These results demonstrate that, through an "induced fit mechanism", antigen-antibody stereospecific assembly can force the polypeptide chain to adopt a structure more closely resembling the conformation it has in the native protein.

Solubility as a function of protein structure and solvent components

This review deals with ways of stabilizing proteins against aggregation and with methods to determine, predict, and increase solubility. Solvent additives (osmolytes) that stabilize proteins are listed with a description of their effects on proteins and on the solvation properties of water. Special attention is given to areas where solubility limitations pose major problems, as in the preparation of highly concentrated solutions of recombinant proteins for structural determination with NMR and X-ray crystallography, refolding of inclusion body proteins, studies of membrane protein dynamics, and in the formulation of proteins for pharmaceutical use. Structural factors relating to solubility and possibilities for protein engineering are analyzed.

Two-dimensional 1H-NMR studies of horseradish peroxidase C and its interaction with indole-3-propionic acid

The binding of aromatic donor molecules to plant peroxidases has been investigated by examining the complex formed between horseradish peroxidase isoenzyme C and indole-3-propionic acid using two-dimensional 1H-NMR spectroscopy. Despite the relatively high molecular mass and paramagnetism of the protein, this technique can be successfully applied to provide new information on the structure of the complex. A number of relatively well-resolved resonances in certain regions of the one-dimensional spectrum are assigned to amino acid type on the basis of the two-dimensional experiments. Two phenylalanine side chains are found to interact at positions close to the haem group as shown by nuclear Overhauser effect spectroscopy (NOESY). Furthermore, the NOESY spectrum of the complex reveals distinct interactions between these phenylalanine residues and the indole ring of the donor molecule. The binding site is found to comprise of these phenylalanine side chains and also the methyl group of a leucine or valine residue. On the basis of the model structure of horseradish peroxidase isoenzyme C proposed by Welinder and Nørskov-Lauritsen and information from previous studies of the related turnip peroxidases, possible locations for this binding site are discussed. The NMR methods adopted here may be generally applicable to the study of peroxidase--aromatic-donor interactions.

Solution structure of the kringle 4 domain from human plasminogen by 1H nuclear magnetic resonance spectroscopy and distance geometry

Kringle 4 is an autonomous structural and folding domain within the proenzyme plasminogen. Homologous domains are found throughout the blood clotting and fibrinolytic proteins. In this paper, we present the almost complete assignment of the 1H nuclear magnetic resonance (n.m.r.) spectrum of the kringle 4 domain of human plasminogen. A detailed structural analysis has been completed. The sequential pattern of nuclear Overhauser enhancements indicated little regular secondary structure but rather a series of turns and loops connecting beta-strands. A small stretch of antiparallel beta-sheet was identified between the residues 61 to 63 and 71 to 73 and the close proximity of other strands was determined from two-dimensional nuclear Overhauser enhancement spectra. Slowly exchanging amide (NH) resonances were found to be associated with residues of the beta-sheet and neighbouring strands that support the hydrophobic core of the domain. A total of 526 interproton distance constraints and two hydrogen bonds were specified as input to the distance geometry program DISGEO. Tertiary structures were produced that were consistent with the n.m.r. data. The structures were compared with that of our earlier model based on n.m.r. studies and with that of prothrombin fragment 1 determined crystallographically.

Termini of Salmonella flagellin are disordered and become organized upon polymerization into flagellar filament

The terminal regions of Salmonella flagellin are essential for polymerization to form the flagellar filament. It has recently been suggested, on the basis of results from circular dichroism spectroscopy and scanning calorimetry, that these regions are disordered in solution. We report here direct evidence for disorder and mobility in the terminal regions of flagellin using 400 MHz proton nuclear magnetic resonance (n.m.r.) spectroscopy. Comparison of the n.m.r. spectra of monomeric and polymeric flagellin shows that the terminal regions become organized when polymerized to form the filament.

One- and two-dimensional NMR studies of yeast phosphoglycerate kinase

One- and two-dimensional proton NMR studies have been carried out on yeast phosphoglycerate kinase (Mr approximately 45,000) in order to identify amino-acid spin systems and obtain sequence-specific assignments. A number of sequence-specific assignments have been made using a combination of structural information contained in nuclear Overhauser effect spectra and X-ray crystallographic data. The results of substrate binding studies (both 3-phosphoglycerate and Mg.ATP), which indicate mutual reorientation of certain assigned aromatic residues in the inter-domain region of the protein, are discussed.

NMR studies of mobility within protein structure

NMR studies of dynamics within structure have revealed that a quite new approach to protein structure and its relation to function is necessary. This approach requires the consideration in detail of the following: 1. Local movements of groups and small segments to allow fast recognition and fitting. The motion concerns on/off rates as well as binding. The observations affect surface/surface recognition, e.g. of antigen/antibody as well as of substrate and protein. 2. Somewhat larger interdomain or N- and C-terminal segments which allow rearrangement. Cases in point are the movement of segments in blood-clotting proteins or in histones. 3. Relative motion of helices in hinges. These actions are likely in such enzymes as kinases and P-450 cytochromes. 4. Relative motion of helices within domains (relative to other helices or sheets) in mechanical devices (triggers) e.g. in calmodulin. 5. General motion in random proteins. Examples extend from rubber-like proteins (entropy sensors), some glycoproteins, to proteins carrying peptide hormones to be generated only after hydrolysis. 6. Order----disorder transitions locally as in osteocalcin and metallothionine. 7. Swinging arm motions associated with special sequences such as (Ala-Pro)n. 8. Of great interest is the power of NMR to look at proteins which are relatively large, up to 50 kDa proteins, and to isolate certain zones of interest. This needs careful temperature dependent studies and analysis of separated domains [72] as well as the use of a great variety of pulse sequences [15] and of nuclei other than protons. 9. In this article I have illustrated the different possibilities using work in my own group. This is done to lessen the burden of extensive review. I fully realise that the range of examples is now large. I would stress though that the production of the necessary technology was the endeavour of several of us within the Oxford Enzyme Group from 1970 to 1985, i.e. from 270-600 MHz Fourier-transform NMR spectroscopy. 10. While all of these features have been demonstrated by NMR methods there are parallel developments both using X-ray diffraction methods and theoretical approaches. All these procedures are changing the view of protein structure to one which incorporates dynamics all the way from conventional vibronic/rotational coupling to the disordered motions characteristic of random polymers. It is the understanding of dynamics that leads to an appreciation of function.