Circular dichroism spectroscopy of bovine pancreatic trypsin inhibitor and five altered conformational states. Relationship of conformation and the refolding pathway of the trypsin inhibitor

The bonding nature of the chemical interaction between trypsin and chitosan based carriers in immobilization process depend on entrapped method: A review

The review article is dedicated to a comprehensive study of the chemical bond formed during the immobilization of the proteolytic enzyme pancreatic trypsin in chitosan-based polymer matrixes and its derivatives. The main focus of the study is to describe the chemical bond that causes immobilization between chitosan based carriers and trypsin. Because the nature of the chemical bond between the carrier and trypsin is a key factor in determining the area of application of the conjugate. It has been found out that after the chemical nature of functional groups, their degree of ionization, the structure of the chemical cross-linking, the medium pH and ionic strength of chitosan are modified, the mechanism of trypsin immobilization is affected. As a result, the attraction enzyme to the matrix occurs due to polar covalent and hydrogen bonds, as well as electrostatic, hydrophobic, Van der Waals forces. The collected research works on the immobilization of trypsin on chitosan-based carriers have been systematized in the paper and shown schematically in subsystems according to the type of chemical interaction. It has been shown that the immobilization of trypsin on chitosan based matrixes occur more often due to the covalent and hydrogen bonds between the protein and the carrier.

PEG and mPEG-anthracene conjugate with trypsin and trypsin inhibitor: hydrophobic and hydrophilic contacts

The conjugation of trypsin (try) and trypsin inhibitor (tryi) with poly(ethylene glycol) (PEG) and methoxypoly(ethylene glycol) anthracene (mPEG-anthracene) was investigated in aqueous solution, using multiple spectroscopic methods, thermodynamic analysis, and molecular modeling. Thermodynamic parameters ΔS, ΔH, and ΔG showed protein-PEG bindings occur via H-bonding and van der Waals contacts with trypsin inhibitor forming more stable conjugate than trypsin. As polymer size increased more stable PEG-protein conjugate formed, while hydrophobic mPEG-anthracene forms less stable protein complexes. Modeling showed the presence of several H-bonding contacts between polymer and amino acids that stabilize protein-polymer conjugation. Polymer complexation induces more perturbations of trypsin inhibitor structure than trypsin with reduction of protein alpha-helix and major increase in random structures, indicating protein structural destabilization.

Aggregation of trypsin and trypsin inhibitor by Al cation

Al cation may trigger protein structural changes such as aggregation and fibrillation, causing neurodegenerative diseases. We report the effect of Al cation on the solution structures of trypsin (try) and trypsin inhibitor (tryi), using thermodynamic analysis, UV-Visible, Fourier transform infrared (FTIR) spectroscopic methods and atomic force microscopy (AFM). Thermodynamic parameters showed Al-protein bindings occur via H-bonding and van der Waals contacts for trypsin and trypsin inhibitor. AFM showed that Al cations are able to force trypsin into larger or more robust aggregates than trypsin inhibitor, with trypsin 5±1 SE (n=52) proteins per aggregate and for trypsin inhibitor 8.3±0.7 SE (n=118). Thioflavin T test showed no major protein fibrillation in the presence of Al cation. Al complexation induced more alterations of trypsin inhibitor conformation than trypsin.

Two variants of the major serine protease inhibitor from the sea anemone Stichodactyla helianthus, expressed in Pichia pastoris

The major protease inhibitor from the sea anemone Stichodactyla helianthus (ShPI-1) is a non-specific inhibitor that binds trypsin and other trypsin-like enzymes, as well as chymotrypsin, and human neutrophil elastase. We performed site-directed mutagenesis of ShPI-1 to produce two variants (rShPI-1/K13L and rShPI/Y15S) that were expressed in Pichia pastoris, purified, and characterized. After a single purification step, 65 mg and 15 mg of protein per liter of culture supernatant were obtained for rShPI-1/K13L and rShPI/Y15S, respectively. Functional studies demonstrated a 100-fold decreased trypsin inhibitory activity as result of the K13L substitution at the reactive (P1) site. This protein variant has a novel tight-binding inhibitor activity of pancreatic elastase and increased activity toward neutrophil elastase in comparison to rShPI-1A. In contrast, the substitution Y15S at P2' site did not affect the Ki value against trypsin, but did reduce activity 10-fold against chymotrypsin and neutrophil elastase. Our results provide two new ShPI-1 variants with modified inhibitory activities, one of them with increased biomedical potential. This study also offers new insight into the functional impact of the P1 and P2' sites on ShPI-1 specificity.

Conjugation of biogenic and synthetic polyamines with trypsin and trypsin inhibitor

Polyamine–protein conjugates can be used as delivery tools to transport antitumor polyamine analogues.

Effective protocol for the investigation of physicochemical and conformational stability and aggregation kinetics measurements of therapeutic IgG2 monoclonal antibody

Characterisation of monoclonal antibodies (mAbs) represents an ongoing challenge due to their diverse 3-dimensional structures that can affect their stability, immunogenicity and/or toxicity. Although circular dichroism (CD) spectroscopy provides rapid determinations of protein secondary structure in solutions, there is a pressing need for an improvement in current practices in applying the technique for batch QC. There is a lack of experimental evidence in the literature which is concerned with improving the current practices. This work is based on an effective protocol for the study of IgG2a stability in solution using the simultaneous measurements of absorbance, turbidity and CD. A novel approach has been developed for the study of the effects of pH and additives with minimum protein shock that may cause premature aggregation and deceptive results. A computer programme has been designed for the rapid and simultaneous analysis of aggregation during UV and CD measurements, also, highlighting instrumental variations. Temperature stability determination, elucidation of unfolding pathways and aggregation kinetics were estimated with accuracy. This experimental approach provides important information about mAbs physicochemical and conformational stability, helps distinguish between unfolded, refolded, aggregated, and flocculated states and is an excellent tool in the development of therapeutic antibodies.

Increased aggregation propensity of IgG2 subclass over IgG1: role of conformational changes and covalent character in isolated aggregates

Aggregation of human therapeutic antibodies represents a significant hurdle to product development. In a test across multiple antibodies, it was observed that IgG1 antibodies aggregated less, on average, than IgG2 antibodies under physiological pH and mildly elevated temperature. This phenomenon was also observed for IgG1 and IgG2 subclasses of anti-streptavidin, which shared 95% sequence identity but varied in interchain disulfide connectivity. To investigate the structural and covalent changes associated with greater aggregation in IgG2 subclasses, soluble aggregates from the two forms of anti-streptavidin were isolated and characterized. Sedimentation velocity analytical ultracentrifugation (SV-AUC) measurements confirmed that the aggregates were present in solution, and revealed that the IgG1 aggregate was composed of a predominant species, whereas the IgG2 aggregate was heterogeneous. Tertiary structural changes accompanied antibody aggregation as evidenced by greater ANS (8-Anilino-1-naphthalene sulfonic acid) binding to the aggregates over monomer, and differences in disulfide character and tryptophan environments between monomer, oligomer and aggregate species, as observed by near-UV circular dichroism (CD). Differences between subclasses were observed in the secondary structural changes that accompanied aggregation, particularly in the intermolecular β-sheet and turn structures between the monomer and aggregate species. Free thiol determination showed ∼2.4-fold lower quantity of free cysteines in the IgG1 subclass, consistent with the 2.4-fold reduction in aggregation of the IgG1 form when compared with IgG2 under these conditions. These observations suggested an important role for disulfide bond formation, as well as secondary and tertiary structural transitions, during antibody aggregation. Such degradations may be minimized using appropriate formulation conditions.

Atypical Kunitz-type serine proteinase inhibitors produced by the ruminant placenta

Recently, an unusual family of genes was identified with expression confined to the trophoblast of ruminant ungulate species. The members of this family (the trophoblast Kunitz domain proteins, or TKDPs) are characterized by the presence of one or more similar, approximately 80-residue repeat sequences placed ahead of a Kunitz serine proteinase-inhibitor domain. To examine the specificity of the Kunitz moiety, the Kunitz domains of selected TKDPs and a control Kunitz protein, bovine pancreatic trypsin inhibitor (BPTI), were produced as glutathione S-transferase fusions, and their abilities to inhibit six serine proteinases were examined. Circular dichroism spectroscopy confirmed that the Kunitz fold was intact. Three of the TKDPs had unusual residues at their P1 "warhead" (ovine TKDP-1, Asn; bovine TKDP-3, Thr; and bovine TKDP-5, Ile) and exhibited no measurable inhibitory activity toward any of the proteinases. Three (ovine TKDP-3, bovine TKDP-3, and bovine TKDP-4) lacked the conserved cysteines at residues 14 and 38 that form one of the highly conserved disulfide bonds that are structurally important in all known mammalian Kunitz proteins. Ovine TKDP-3 and bovine TKDP-4 had P1 lysines and inhibited trypsin and plasmin with K(i) values only approximately 10-fold higher than that of BPTI. Bovine TKDP-2 had a P1 lysine and the three conserved disulfides, but it possessed an unusual residue (Asp) at P2. It exhibited no inhibitory activity. These data suggest that the function of the TKDP, like certain Kunitz proteins found in snake venoms, may not be in proteinase inhibition.

Structural characterisation of the human alpha-lactalbumin molten globule at high temperature

Molten globules are partially folded forms of proteins thought to be general intermediates in protein folding. The 15N-1H HSQC NMR spectrum of the human alpha-lactalbumin (alpha-LA) molten globule at pH 2 and 20 degrees C is characterised by broad lines which make direct study by NMR methods difficult; this broadening arises from conformational fluctuations throughout the protein on a millisecond to microsecond timescale. Here, we find that an increase in temperature to 50 degrees C leads to a dramatic sharpening of peaks in the 15N-1H HSQC spectrum of human alpha-LA at pH 2. Far-UV CD and ANS fluorescence experiments demonstrate that under these conditions human alpha-LA maintains a high degree of helical secondary structure and the exposed hydrophobic surfaces that are characteristic of a molten globule. Analysis of the H(alpha), H(N) and 15N chemical shifts of the human alpha-LA molten globule at 50 degrees C leads to the identification of regions of native-like helix in the alpha-domain and of non-native helical propensity in the beta-domain. The latter may be responsible for the observed overshoot in ellipticity at 222 nm in kinetic refolding experiments.

Protein folding in the post-genomic era

Protein folding is a topic of fundamental interest since it concerns the mechanisms by which the genetic message is translated into the three-dimensional and functional structure of proteins. In these post-genomic times, the knowledge of the fundamental principles are required in the exploitation of the information contained in the increasing number of sequenced genomes. Protein folding also has practical applications in the understanding of different pathologies and the development of novel therapeutics to prevent diseases associated with protein misfolding and aggregation. Significant advances have been made ranging from the Anfinsen postulate to the "new view" which describes the folding process in terms of an energy landscape. These new insights arise from both theoretical and experimental studies. The problem of folding in the cellular environment is briefly discussed. The modern view of misfolding and aggregation processes that are involved in several pathologies such as prion and Alzheimer diseases. Several approaches of structure prediction, which is a very active field of research, are described.

Enhancement of chymotrypsin-inhibitor/substrate interactions by 3 M NaCl

A series of 16 bovine pancreatic trypsin inhibitor variants mutated at the P(1) position of the binding loop and seven tetrapeptide p-nitroanilide (pNa) substrates of the general formula: suc-Ala-Ala-Pro-Aaa-pNa (where Aaa denotes either: Phe, Arg, Lys, Leu, Met, Nva, Nle) were used to investigate the influence of high salt concentration on the activity of bovine chymotrypsin. The increase of the association constant (K(a)) and the specificity index (k(cat)/K(m)) in the presence of 3 M NaCl highly depends on the chemical nature of the residue at the P(1) position. The highest increase was observed for inhibitors/substrates containing the basic side chains at this site. Surprisingly, for the remaining 13 residues the observed salt effect is not correlated with any side chain properties. In particular, there is a lack of correlation between the accessible non-polar surface area and the magnitude of the salt effect. It suggests that salt-induced increase of the K(a) and k(cat)/K(m) values is not caused by the enhancement of the hydrophobic interactions in chymotrypsin-inhibitor/substrate complex. Moreover, the increase of the K(a) and k(cat)/K(m) values occurs only in the presence of Na(+) ions, while K(+) and Li(+) ions do not change the activity of chymotrypsin. Additionally, the activities of two other proteinases: bovine trypsin and Streptomyces griseus proteinase B were tested in the presence of 3 M NaCl using their specific substrates. The activity of both enzymes was almost not affected by the presence of high NaCl concentration.

Substitutions at the P(1) position in BPTI strongly affect the association energy with serine proteinases

The role of the S(1) subsite in trypsin, chymotrypsin and plasmin has been examined by measuring the association with seven different mutants of bovine pancreatic trypsin inhibitor (BPTI); the mutants contain Gly, Ala, Ser, Val, Leu, Arg, and Trp at the P(1) position of the reactive site. The effects of substitutions at the P(1) position on the association constants are very large, comprising seven orders of magnitude for trypsin and plasmin, and over five orders for chymotrypsin. All mutants showed a decrease of the association constant to the three proteinases in the same order: Ala>Gly>Ser>Arg>Val>Leu>Trp. Calorimetric and circular dichroism methods showed that none of the P1 substitutions, except the P1-Val mutant, lead to destabilisation of the binding loop conformation. The X-ray structure of the complex formed between bovine beta-trypsin and P(1)-Leu BPTI showed that the P(1)-Leu sterically conflicts with the side-chain of P(3)-Ile, which thereby is forced to rotate approximately 90 degrees. Ile18 (P(3)) in its new orientation, in turn interacts with the Tyr39 side-chain of trypsin. Introduction of a large side-chain at the P1' position apparently leads to a cascade of small alterations of the trypsin-BPTI interface that seem to destabilise the complex by it adopting a less optimized packing and by tilting the BPTI molecule up to 15 degrees compared to the native trypsin-BPTI complex.

Early events in the disulfide-coupled folding of BPTI

Recent studies of the refolding of reduced bovine pancreatic trypsin inhibitor (BPTI) have shown that a previously unidentified intermediate with a single disulfide is formed much more rapidly than any other one-disulfide species. This intermediate contains a disulfide that is present in the native protein (between Cys14 and 38), but it is thermodynamically less stable than the other two intermediates with single native disulfides. To characterize the role of the [14-38] intermediate and the factors that favor its formation, detailed kinetic and mutational analyses of the early disulfide-formation steps were carried out. The results of these studies indicate that the formation of [14-38] from the fully reduced protein is favored by both local electrostatic effects, which enhance the reactivities of the Cys14 and 38 thiols, and conformational tendencies that are diminished by the addition of urea and are enhanced at lower temperatures. At 25 degrees C and pH 7.3, approximately 35% of the reduced molecules were found to initially form the 14-38 disulfide, but the majority of these molecules then undergo intramolecular rearrangements to generate non-native disulfides, and subsequently the more stable intermediates with native disulfides. Amino acid replacements, other than those involving Cys residues, were generally found to have only small effects on either the rate of forming [14-38] or its thermodynamic stability, even though many of the same substitutions greatly destabilized the native protein and other disulfide-bonded intermediates. In addition, those replacements that did decrease the steady-state concentration of [14-38] did not adversely affect further folding and disulfide formation. These results suggest that the weak and transient interactions that are often detected in unfolded proteins and early folding intermediates may, in some cases, not persist or promote subsequent folding steps.

Interscaffolding additivity: binding of P1 variants of bovine pancreatic trypsin inhibitor to four serine proteases

Different families of protein inhibitors of serine proteases share similar conformation of the enzyme-binding loop, while their scaffoldings are completely different. In the enzyme-inhibitor complex, the P1position of the loop makes numerous contacts within the S1pocket and significantly influences the energy of the interaction. Here, we determine the association energies (DeltaGavalues) for the interaction of coded P1variants of bovine pancreatic trypsin inhibitor (BPTI) with bovine beta-trypsin (BT), anionic salmon trypsin (AST), bovine alpha-chymotrypsin (BCHYM), and human neutrophil elastase (HNE). The respective DeltaGaranges are 15, 13, 9, and 8 kcal mol-1(1 cal=4.18 J). Next, through interscaffolding additivity cycles, we compare our set of DeltaGavalues determined for BCHYM and HNE with similar data sets available in the literature for three other inhibitor families. The analysis of the cycles shows that 27 to 83 % of cycles fulfil the criteria of additvity. In one particular case (comparison of associations of P1variants of BPTI and OMTKY3 with BCHYM) there is a structural basis for strongly non-additive behaviour. We argue that the interscaffolding additvity depends on sequential and conformational similarities of sites where the mutation(s) are introduced and on the particular substitution. In the second interscaffolding analysis, we compare binding of the same P1mutants to BT and AST. The high correlation coefficient shows that both trypsins recognize with comparable strength the non-cognate side-chains. However, the cognate Arg and Lys side-chains are recognized significantly more strongly by AST.

Stability of the residual structure in unfolded BPTI in different conditions of temperature and solvent composition measured by disulphide kinetics and double mutant cycle analysis

The folding funnel model proposes a clear description of the protein folding process. To test this model, additional data on the structures populated in different stages of folding and their influence on further folding are required. Here, we use the double mutant strategy and disulphide formation kinetics measurements to study the impact on folding of the residual structure in unfolded bovine pancreatic trypsin inhibitor (BPTI). We show how five amino acid residues stabilise a folding initiation site, possibly a beta-hairpin, and influence the shape of the upper region of the folding funnel in BPTI in different conditions of temperature and solvent composition. Our data provide experimental evidence for the mechanism by which a fast search for a proper chain topology is made possible early in the folding of proteins. The results apply to proteins in general, not necessarily just to disulphide bonded proteins, since cysteine residues are used here merely as reporter groups.

Determinants of backbone dynamics in native BPTI: cooperative influence of the 14-38 disulfide and the Tyr35 side-chain

15Nitrogen relaxation experiments were used to characterize the backbone dynamics of two modified forms of bovine pancreatic trypsin inhibitor (BPTI). In one form, the disulfide between Cys14 and Cys38 in the wild-type protein was selectively reduced and methylated to generate an analog of the final intermediate in the disulfide-coupled folding pathway. The second form was generated by similarly modifying a mutant protein in which Tyr35 was replaced with Gly (Y35G). For both selectively reduced proteins, the overall conformation of native BPTI was retained, and the relaxation data for these proteins were compared with those obtained previously with the native wild-type and Y35G proteins. Removing the disulfide from either protein had only small effects on the observed longitudinal relaxation rates (R1) or heteronuclear cross relaxation rates (nuclear Overhauser effect), suggesting that the 14-38 disulfide has little influence on the fast (ps to ns) backbone dynamics of either protein. In the wild-type protein, the pattern of residues undergoing slower (micros to ms) internal motions, reflected in unusually large transverse relaxation rates (R2), was also largely unaffected by the removal of this disulfide. It thus appears that the large R2 rates previously observed in native wild-type protein are not a direct consequence of isomerization of the 14-38 disulfide. In contrast with the wild-type protein, reducing the disulfide in Y35G BPTI significantly decreased the number of backbone amides displaying large R2 rates. In addition, the frequencies of the backbone motions in the modified protein, estimated from R2 values measured at multiple refocusing delays, appear to span a wider range than those seen in native Y35G BPTI. Together, these observations suggest that the slow internal motions in Y35G BPTI are more independent in the absence of the 14-38 disulfide and that formation of this bond may lead to a substantial loss of conformational entropy. These effects may account for the previous observation that the Y35G substitution greatly destabilizes the disulfide. The results also demonstrate that the disulfide and the buried side-chain influence the dynamics of the folded protein in a highly cooperative fashion, with the effects of removing either being much greater in the absence of the other.

Specificity of human cathepsin G

A series of tetrapeptide p-nitroanilide substrates of the general formula: suc-Ala-Ala-Pro-Aaa-p-nitroanilide was used to map the S1 binding pocket of human cathepsin G. Based on the kcat/Km parameter, the following order of preference was found: Lys=Phe>Arg=Leu>Met>Nle=Nva>Ala>Asp. Thus, the enzyme exhibits clear dual and equal trypsin- and chymotrypsin-like specificities. Particularly deleterious were beta-branched side chains of Ile and Val. The P1 substrate preferences found for cathepsin G are distinctly different from many other serine proteinases, including fiddler crab collagenase and chymotrypsin. The kcat/Km values obtained for P1 Lys, Phe, Arg and Leu substrates correlate well with those determined for analogous P1 mutants of basic pancreatic trypsin inhibitor (BPTI) obtained through recombinant techniques. To characterise the subsite specificity of the enzyme, a series of Cucurbita maxima trypsin inhibitor I (CMTI I) mutants were used comprising P2-P3' and P12' positions. All the mutants obtained were inhibitors of cathepsin G with association constants in the range: 105-109 M-1. Some of the mutations destabilised complex formation. In particular, Met8-->Arg substitution at P3', which increased association constant for chymotrypsin 46-fold, led to a 7-fold decrease of binding with cathepsin G. In addition, mutation of Ile6 at position P1' either to Val or Asp was deleterious for cathepsin G. In two cases (Ala18-->Gly (P12') and Pro4-->Thr (P2)), about a 10-fold increase in association constants was observed.

Simulations of the structural and dynamical properties of denatured proteins: the "molten coil" state of bovine pancreatic trypsin inhibitor

The dynamic nature of denatured, unfolded proteins makes it difficult to characterize their structures experimentally. To complement experiment and to obtain more detailed information about the structure and dynamic behavior of the denatured state, we have performed eleven 2.5 ns molecular dynamics simulations of reduced bovine pancreatic trypsin inhibitor (BPTI) at high temperature in water and a control simulation at 298 K, for a total of 30 ns of simulation time. In a neutral pH environment (acidic residues ionized), the unfolded protein structures were compact with an average radius of gyration 9% greater than the native state. The compact conformations resulted from the transient formation of non-native hydrophobic clusters, turns and salt bridges. However, when the acidic residues were protonated, the protein periodically expanded to a radius of gyration of 18 to 20 A. The early steps in unfolding were similar in the different simulations until passing through the major transition state of unfolding. Afterwards, unfolding proceeded through one of two general pathways with respect to secondary structure: loss of the C-terminal helix followed by loss of beta-structure or the opposite. To determine whether the protein preferentially sampled particular conformational substates in the denatured state, pairwise Calpha root-mean-square deviations were measured between all structures, but similar structures were found between only two trajectories. Yet, similar composite properties (secondary structure content, side-chain and water contacts, solvent accessible surface area, etc.) were observed for the structures that unfolded through different pathways. Somewhat surprisingly, the unfolded structures are in agreement with both past experiments suggesting that reduced BPTI is a random coil and more recent experiments providing evidence for non-random structure, demonstrating how ensembles of fluctuating structures can give rise to experimental observables that are seemingly at odds.

Structure of single-disulfide variants of bovine pancreatic trypsin inhibitor (BPTI) as probed by their binding to bovine beta-trypsin

Native bovine pancreatic trypsin inhibitor (BPTI) contains three disulfide bonds: Cys5-Cys55, Cys14-Cys38 and Cys30-Cys51. Correct cysteine pairing, native structure, and full anti-proteinase activity can be restored in the process of oxidative refolding of reduced BPTI. Oxidative refolding starts with the formation of single disulfide intermediates. All 15 single-disulfide variants of BPTI (three native and 12 non-native combinations) have been expressed in Escherichia coli. In each variant the remaining four cysteine residues were replaced by alanine. Four of these variants are shown here to inhibit bovine beta-trypsin: three of them contain native and one non-native (Cys5-Cys51) disulfide. All but one (Cys5-Cys55) variant are slowly digested by the enzyme, therefore measurements were performed at pH 4.0, at which trypsin activity is low. Binding constants of these four single disulfide variants were at least two orders of magnitude lower than for native BPTI. Remarkably, in some of the variants the binding constants were found to be higher for the reduced rather than for the oxidized form of the variant. Also for the fully reduced native BPTI, determined here, the binding constant is of considerable value. Two sets of control experiments demonstrated that the binding of reduced native BPTI to trypsin is specific. In the first, mutation of Lys15 (P1 position) in the binding loop abolished binding of the reduced forms to trypsin. In the second, the binding of reduced native BPTI to anhydrotrypsin yielded the expected UV difference spectra. In general, the results obtained indicate that the inhibitor activity can be induced even in the reduced protein. This activity is not a local effect, such as the nature of residues surrounding the binding loop, but rather is induced by residual structure in the unfolded protein. This structure has been shown to consist of a set of hydrophobic residues and the data presented here indicate that reduced cysteine residues provide further stabilization of such a hydrophobic cluster. On the other hand, improper pairing of the cysteine residues in non-native single disulfide variants destabilizes the enzyme-inhibitor complex by inducing deformations of the binding loop region.

Identification of cooperative folding units in a set of native proteins

Cooperative unfolding penalties are calculated by statistically evaluating an ensemble of denatured states derived from native structures. The ensemble of denatured states is determined by dividing the native protein into short contiguous segments and defining all possible combinations of native, i.e., interacting, and non-native, i.e., non-interacting, segments. We use a novel knowledge-based scoring function, derived from a set of non-homologous proteins in the Protein Data Bank, to describe the interactions among residues. This procedure is used for the structural identification of cooperative folding cores for four globular proteins: bovine pancreatic trypsin inhibitor, horse heart cytochrome c, French bean plastocyanin, and staphylococcal nuclease. The theoretical folding units are shown to correspond to regions that exhibit enhanced stability against denaturation as determined from experimental hydrogen exchange protection factors. Using a sequence similarity score for related sequences, we show that, in addition to residues necessary for enzymatic function, those amino acids comprising structurally important folding cores are also preferentially conserved during evolution. This implies that the identified folding cores may be part of an array of fundamental structural folding units.

Probing protein folding and stability using disulfide bonds

Disulfide bonds are required to stabilize the folded conformations of many proteins. The rates and equilibria of processes involved in disulfide bond formation and breakage can be manipulated experimentally and can be used to obtain important information about protein folding and stability. A number of experimental procedures for studying these processes, and approaches to interpreting the resulting data, are described here.

Spectroscopic characterization of tick anticoagulant peptide

Tick anticoagulant peptide (TAP) is a disulfide rich potent inhibitor of factor Xa. Although this peptide is of potential clinical utility, very little is known about its higher order structure. Therefore, the secondary structure of recombinant TAP (rTAP) has been examined by circular dichroism (CD) and Fourier transform infrared (FTIR) spectroscopy. Both techniques suggest that rTAP is rich in beta-sheet structure. Disulfide bonds play a significant role in the folding and structural stability of rTAP. This is apparent from the resistance of rTAP to fluorescence-detected unfolding by guanidinium chloride (Gdn-HCl), unless disulfides are first reduced. The protein's tryptophan and tyrosine residues exhibit greater solvent exposure upon reduction of the cystines as indicated by fluorescence spectra and second derivative UV spectroscopy. A considerable amount of beta-structure appears to be retained after reduction of disulfides, although the CD spectrum manifests an increased amount of disordered structure in the reduced peptide. While rTAP does not bind the hydrophobic fluorescence probe 2-p-toludinylnaphthalene-6-sulfonate (TNS) at neutral or acidic pH, the reduced peptide binds TNS at pH 2.0 but not at pH 7.0. The secondary structure of the reduced peptide at pH 2 is, however, similar to that at pH 7 as judged by CD spectroscopy. The reduced form of rTAP at acidic pH thus resembles a molten globule-like state.

Partially folded, molten globule and molten coil states of bovine pancreatic trypsin inhibitor

Three denatured states of bovine pancreatic trypsin inhibitor have been characterized, using two chemically synthesized analogues designed for study of folding intermediates. One analogue, [14-38]Abu, retains only the 14-38 disulphide. At pH 4.5-6 and 1-7 degrees C, [14-38]Abu is a highly ordered beta-sheet molten globule; it has the circular dichroism (CD), ANS-binding and folding kinetics of a molten globule; is partially folded by NMR analysis; and undergoes cooperative thermal denaturation. At low temperature [14-38]Abu also forms an acid state at pH 1.5, as well as a denatured state at pH 2.5. A second BPTI analogue with all three disulphide bridges eliminated, [R]Abu, lacks detectable secondary and tertiary structure but has stable hydrophobic surfaces and is collapsed. We term this species a 'molten coil'.

Native disulfide bonds greatly accelerate secondary structure formation in the folding of lysozyme

To assess the respective roles of local and long-range interactions during protein folding, the influence of the native disulfide bonds on the early formation of secondary structure was investigated using continuous-flow circular dichroism. Within the first 4 ms of folding, lysozyme with intact disulfide bonds already had a far-UV CD spectrum reflecting large amounts of secondary structure. Conversely, reduced lysozyme remained essentially unfolded at this early folding time. Thus, native disulfide bonds not only stabilize the cfinal conformation of lysozyme but also provide, in early folding intermediates, the necessary stabilization that favors the formation of secondary structure.

Small effects of amino acid replacements on the reduced and unfolded state of pancreatic trypsin inhibitor

The effects of amino acid replacements on the hydrodynamic volume of reduced and unfolded bovine pancreatic trypsin inhibitor (BPTI) have been examined by gel electrophoresis. The electrophoretic mobilities of the reduced forms of 46 BPTI variants were compared at room temperature in the absence of denaturants. The single substitutions examined include many different types of replacements at sites throughout the polypeptide, and, collectively, alter 22 of the 58 residues of the wild-type protein. The only substitutions found to alter the electrophoretic mobility of the reduced protein by more than approximately 3% are those that change the net charge of the protein. For nine mutants, the rates of disulfide formation in the reduced protein were also examined and found to be very similar to that of the wild-type protein. These results suggest that any structure that may be present in the reduced protein is either relatively insensitive to amino acid replacements or does not greatly influence the averaged properties of the polypeptide chain.

The compact state of reduced bovine pancreatic trypsin inhibitor is not the compact molten globule

Reduced bovine pancreatic trypsin inhibitor (BPTI) has been shown to be in a compact state [(1988) Biochemistry 27, 8889-8893]. This leads to the proposal that this compact state may be a compact molten globule folding intermediate. Optical rotatory dispersion in the visible region failed to show the presence of pronounced secondary structures in the reduced BPTI and no binding of 8-anilino-1-naphthalenesulphonic acid to reduced BPTI could be detected. Yet, no cooperative thermal transition was detected by tyrosine fluorescence. These experiments show that reduced BPTI is not in the compact molten globule state.

The partially folded conformation of the Cys-30 Cys-51 intermediate in the disulfide folding pathway of bovine pancreatic trypsin inhibitor

The best-characterized protein folding pathway is that of bovine pancreatic trypsin inhibitor, which folds from the reduced form through a series of disulfide bond intermediates. The crucial one-disulfide intermediate of bovine pancreatic trypsin inhibitor with the disulfide bond between Cys-30 and Cys-51 is shown here to have a partially folded conformation in which the major elements of secondary structure interact via a core of apolar side chains, which resembles part of the native conformation. The stability of this structure can account for the predominance of this one-disulfide intermediate during folding. Much of the remaining one-third of the polypeptide chain, in particular the N-terminal 14 residues, is largely disordered; this accounts for the ability of this intermediate to form readily any of the three possible second disulfide bonds involving Cys-5, -14, and -38. The partially folded conformation of this intermediate provides direct evidence for the importance of native-like interactions between elements of secondary structure in directing protein folding, which is assumed in many studies.

Disulfide bond-coupled folding of bovine pancreatic trypsin inhibitor derivatives missing one or two disulfide bonds

The disulfide bond-coupled folding and unfolding mechanism (at pH 8.7, 25 degrees C in the presence of oxidized and reduced dithiothreitol) was determined for a bovine pancreatic trypsin inhibitor mutant in which cysteines 30 and 51 were replaced with alanines so that only two disulfides, between cysteines 14 and 38 and cysteines 5 and 55, remain. Similar studies were made on a chemically-modified derivative of the mutant retaining only the 5-55 disulfide. The preferred unfolding mechanism for the Ala30/Ala51 mutant begins with reduction of the 14-38 disulfide. An intramolecular rearrangement via thiol-disulfide exchange, involving the 5-55 disulfide and cysteines 14 and/or 38, then occurs. At least five of six possible one-disulfide bond species accumulate during unfolding. Finally, the disulfide of one or more of the one-disulfide bond intermediates (excluding that with the 5-55 disulfide) is reduced giving unfolded protein. The folding mechanism seems to be the reverse of the unfolding mechanism; the observed folding and unfolding reactions are consistent with a single kinetic scheme. The rate constant for the rate-limiting intramolecular folding step--rearrangements of other one-disulfide bond species to the 5-55 disulfide intermediate--seems to depend primarily on the number of amino acids separating cysteines 5 and 55 in the unfolded chain. The energetics and kinetics of the mutant's folding mechanism are compared to those of wild-type protein [Creighton, T. E., & Goldenberg, D. P. (1984) J. Mol. Biol. 179, 497] and a mutant missing the 14-38 disulfide [Goldenberg, D. P. (1988) Biochemistry 27, 2481]. The most striking effects are destabilization of the native structure and a large increase in the rate of unfolding.

The legumin precursor from white lupin seed. Identity of the subunits, assembly and proteolysis

The precursors of the legumin-like storage protein from developing white lupin seeds (35 days after flowering) are trimers composed of protomers of M(r) 72,000 or 67,000. Some subunits of these oligomers contain processed precursor polypeptides, namely alpha polypeptides of either 52,000 or 44,000 linked through disulphide bonds to a beta polypeptide of 21,000, typical of the mature legumin. The prolegumin is glycosylated. Legumin oligomers purified from the same seeds are both trimers and hexamers; some of their subunits are still made of precursor polypeptides. The hexamer contains less precursor polypeptide than the trimer. A low level or absence of precursor appears to be a condition of hexamer assembly. The heterogenous prolegumin and legumin oligomers represent intermediates in the processing of the prolegumin to mature legumin. Hydrophobic-interaction chromatography on TSK-phenyl-5PW and titration with the hydrophobic probe 8-anilino-1-naphthalenesulphonate indicate that the legumin is less hydrophobic than the prolegumin. This is attributed to structural rearrangements at processing of the propolypeptide, made evident by the behaviour in CD and by the second-derivative ultraviolet spectra of the two proteins. The total protein extract of developing cotyledons at 40 days after flowering contains endopeptidases, similar to those existing in the resting seeds, which cause a limited cascade degradation of the prolegumin and legumin.

Analysis of the circular dichroism spectrum of proteins using the convex constraint algorithm: a practical guide

Due to the time scale of circular dichroism (CD) measurements, it is theoretically possible to deconvolute such a spectrum if the pure CD spectra differ significantly from one another. In the last decade several methods have been published aiming at obtaining the conformational weights, or percentages (which are the coefficients for a linear combination) of the so-called typical secondary structural elements making up the three-dimensional structure of proteins. Two methods that can be used to determine the secondary structures of proteins are described here. The first method, called LINCOMB, is a simple algorithm based on a least-squares fit with a set of reference spectra representing the known secondary structures and yielding an estimation of weights attributed to alpha-helix, beta-pleated sheet (mainly antiparallel), beta-turns, unordered form, and aromatic/disulfide (or nonpeptide) contributions of the protein being analyzed. This method requires a "template" or reference curve set, which was obtained from the second method. The second method, "convex constraint analysis," is a general deconvolution method for a CD spectra set of any variety of conformational type. The algorithm, based on a set of three constraints, is able to deconvolute a set of CD curves to its common "pure"-component curves and conformational weights. To analyze a single CD spectrum with this method, the spectrum is appended to the data set used as a reference data set. As a way to determine the reliability of the algorithm and provide a guideline to its usage, some applications are presented.

Kinetic roles and conformational properties of the non-native two-disulphide intermediates in the refolding of bovine pancreatic trypsin inhibitor

The most productive folding pathway of reduced bovine pancreatic trypsin inhibitor (BPTI) proceeds through the disulphide intermediates (30-51), (30-51, 5-14), and (30-51, 5-38); these are important kinetic intermediates in folding, even though the latter pair contain non-native disulphide bonds. Analogues of these intermediates have been prepared by protein engineering methods and their conformational properties examined by circular dichroism and 1H-nuclear magnetic resonance. The (30-51), (30-51, 5-14) and (30-51, 5-38) analogues exhibit comparable degrees of stable structure, which cannot include those portions of the polypeptide chain involving Cys5, Cys14 and Cys38. These properties are consistent with the roles of (30-51, 5-14) and (30-51, 5-38) in the folding pathway of BPTI, which demand that they exhibit a considerable degree of conformational flexibility in part of the molecule.

(14-38, 30-51) double-disulphide intermediate in folding of bovine pancreatic trypsin inhibitor: a two-dimensional 1H nuclear magnetic resonance study

An analogue of the BPTI folding intermediate that contains only the disulphide bonds between Cys14 and Cys38 and between Cys30 and Cys51 has been prepared in Escherichia coli by protein engineering methods. The other two Cys residues of native BPTI (at positions 5 and 55) have been replaced by Ser. Essentially complete proton resonance assignments of the analogue were obtained by employing two-dimensional 1H nuclear magnetic resonance techniques. The intermediate has a more extended conformation in the N-terminal (residues 1 to 7) region and there are other differences in the C-terminal (residues 55 to 58) region. The remainder of the protein is substantially identical to native BPTI. The conformational properties of the analogue can explain several aspects of the kinetic role that the normal (14-38, 30-51) intermediate plays in the folding of BPTI.

Two-dimensional 1H nuclear magnetic resonance study of the (5-55) single-disulphide folding intermediate of bovine pancreatic trypsin inhibitor

An analogue of the bovine pancreatic trypsin inhibitor (BPTI) folding intermediate that contains only the disulphide bond between Cys5 and Cys55 has been prepared in Escherichia coli by protein engineering methods, with the other four Cys residues replaced by Ser. Two-dimensional 1H nuclear magnetic resonance studies of the analogue have resulted in essentially complete resonance assignments of the folded form of the protein. The folded protein has a compact conformation that is structurally very similar to that of native BPTI, although there are subtle differences and the folded conformation is not very stable. Approximately half of the protein molecules are unfolded at 3 degrees C, and this proportion increases at higher temperatures. The folded and unfolded conformations are in slow exchange. The conformational properties of the analogue can explain many aspects of the kinetic role that the normal (5-55) intermediate plays in the folding of BPTI.

The 5-55 single-disulphide intermediate in folding of bovine pancreatic trypsin inhibitor

An analogue of the BPT1 folding intermediate that contains only the disulphide bond between Cys-5 and Cys-55 has been prepared by mutation of the other four Cys residues to Ser. On the basis of its circular dichroism and 1H-nuclear magnetic resonance spectra and its electrophoretic mobility, this intermediate is shown to be at least partially folded at low temperatures. This probably accounts for several of the unique properties of this intermediate observed during folding.

Protein folding

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Theoretical study of the contribution of aromatic side chains to the circular dichroism of basic bovine pancreatic trypsin inhibitor

Circular dichroism (CD) spectroscopy is frequently employed to determine the secondary structure composition of a protein. However, this assumes that the far-UV region of the spectrum, which is used for these analyses, is due only to contributions from the polypeptide backbone. Basic bovine pancreatic trypsin inhibitor (BPTI) possesses an unusual far-UV CD spectrum, which has made such an analysis difficult. One possible reason for the discrepancy is that other chromophores, such as the aromatic side chains (four tyrosines, four phenylalanines), might be responsible. The CD spectrum of BPTI was calculated by employing a variation of the matrix method. Including only the peptide backbone gave poor agreement between theory and experiment. This was shown to be independent of the quality of the calculation performed. Subsequent inclusion of tyrosine contributions did little to improve the fit. However, further inclusion of the phenylalanine chromophores provided a good fit between the calculated and experimental far-UV spectrum. The important contributions arise from the cluster of aromatic amino acids formed by two tyrosines (Tyr21 and Tyr23) and three phenylalanines (Phe22, Phe4, and Phe45). Consideration of both types of side chains and the entire peptide backbone is essential to produce an accurate description of the CD curve. Overall, these results indicate that contributions from aromatic amino acids can significantly perturb the far-UV CD spectrum of a protein, making secondary structure analysis difficult. This is particularly true in systems like BPTI, with low amounts of alpha-helical structure and clusters of aromatic amino acids.

Contribution of disulfide bonds to stability of the folding intermediate of alpha-lactalbumin

The secondary structure formed in disulfide reduced alpha-lactalbumin is investigated by CD spectrum and is compared with that of the folding intermediate of the disulfide intact protein. The peptide backbone structure of the reduced protein depends strongly on salt concentration in contrast to that of the intermediate. It is close to a random coil in the absence of salt, but it is almost the same as that of the intermediate at a high concentration of salt. The secondary structures of both the proteins undergo broad unfolding transitions when temperature is raised or when urea is added. The secondary structure of the reduced protein is less stable against both heat and urea. These results show that the disulfide bonds are not a determinant of the secondary structure formed at an early stage of folding, and they stabilize the secondary structure of the folding intermediate.

Conformational forces affecting the folding pathways of dendrotoxins I and K from black mamba venom

The conformations of the major intermediates trapped during the folding of dendrotoxins I and K from venom of black mamba snakes, have been investigated by circular-dichroism spectroscopy. Local alterations to the native, folded conformations are observed in toxins I and K and in a protein of similar sequence, bovine pancreatic trypsin inhibitor. The inability of intermediates (30-51, 14-38) to complete refolding by forming directly the 5-55 disulphide bond is explained. The following observations on the role of secondary structure in the folding of the three proteins are of interest. 1. It is not necessary for the three proteins to acquire elements of secondary structure at the same stage of folding in order to attain similar three-dimensional conformations. 2. The stability of the final folded state is not directly correlated to an early appearance of secondary structure. 3. The degree of secondary structure already present in intermediates (30-51) seems to determine the pathway of refolding preferred by the corresponding protein.

Underlying assumptions in the estimation of secondary structure content in proteins by circular dichroism spectroscopy--a critical review

Recombinant DNA technology has made possible the large-scale production of proteins for pharmaceutical applications. As a result, there has been a renaissance in methodology which can provide information on the structural stability and character of these materials. Circular dichroism (CD) spectroscopy, with its sensitivity to the secondary structure adopted by the polypeptide chain, is a powerful tool in this regard. Quantitative analysis of the CD spectra of proteins is now wide-spread, aided by the availability of such algorithms on commercial instrumentation. However, there are basic assumptions made when conducting these calculations, many of which have not been addressed or summarized. Some of these assumptions are independent of the selection of basis spectra and the algorithm employed. These assumptions are listed and the available data concerning their validity is presented and discussed.

Metal-ion binding and the molecular conformational properties of alpha lactalbumin

Mammary galactosyltransferase and alpha lactalbumin are the two protein components of lactose synthase which catalyze the transfer of galactose from UDP-gal to glucose in the presence of divalent cations. Recent studies suggest that alpha lactalbumin may have a broader function in modifying cell surface carbohydrates in cell-cell interactions and cell differentiation. Since the discovery that alpha lactalbumin, like galactosyltransferase, is a metalloprotein, there has been a great deal of interest in the metal-binding properties of this protein and how these relate to the metal-ion requirements of the lactose synthase reaction. The recent availability of an X-ray crystal structure of alpha lactalbumin has provided further impetus for establishing the molecular determinants of its biological activity. This review is directed toward critically examining and integrating our present knowledge of the properties of this protein, particularly the relationship between metal-ion binding and conformational state, and how these might relate to its biological function.

On the relevance of non-random polypeptide conformations for protein folding

The possibility that any non-random conformation in reduced bovine pancreatic trypsin inhibitor (BPTI) and ribonuclease A might be significant for folding has been considered, using the experimental data available on forming the first disulphide bond in each. It is a thermodynamic necessity that whatever conformation stabilises a particular disulphide bond be stabilised to the same extent by the presence of the disulphide. The stabilising effects of disulphides are known approximately, so the stability of any non-random conformation found in a one-disulphide intermediate can be estimated in the absence of the disulphide bond. The non-random conformation in the BPTI intermediates is sufficiently labile to indicate that it would be expected to be present in no more than 5% of the reduced BPTI molecules. There is much less non-random conformation apparent in ribonuclease A. Whatever conformations are represented in the bulk of these two reduced proteins cannot favour disulphide formation and further productive folding.