Pancreatic exocrine insufficiency occurs in most patients following pancreaticoduodenectomy

Background

Pancreatic exocrine insufficiency (PEI) is a well-defined complication of malignant diseases and pancreatic resection; however, study results of PEI are less consistent. Assessment of PEI by estimation of fecal elastase (FE)-1 in stool by enzyme-linked immunosorbent essay (ELISA) is a relatively inexpensive, noninvasive, and simple test. This study assessed exocrine function of pancreas following pancreaticoduodenectomy (PD) by estimating FE-1.

Methods

This prospective hospital-based study involved 30 patients who had undergone PD for malignancy. All 30 patients had an uneventful postoperative period under the unit's enhanced recovery after surgery (ERAS) protocol with no Grade B, C postoperative pancreatic fistula/postpancreatectomy hemorrhage as per the International Study Group of Pancreatic Surgery (ISGPS) definitions. Stool samples were collected postoperatively 3 months after surgery from all patients irrespective of clinical symptoms. The analysis was based on a solid phase ELISA used for the quantitative determination of human elastase 1 in feces. Fecal elastase was considered normal if >200 μg/gm stool, moderately reduced if 100-200 μg/gm stool, and severely reduced if <100 μg/gm stool.

Results

Among 30 patients included, fecal elastase levels were moderately reduced in 10 (33.33%) and severely reduced in 20 (66.67%) patients (P <0.0001). Mean (± standard deviation) of fecal elastase was 87.12 ± 38.76 with median of 74.6 μg/gm stool. There was no significant difference in the fecal elastase levels between men and women (P = 0.057), age (P = 0.48), pancreatic duct diameter (P = 0.609), pancreatic texture (P = 0.286), and presence or absence of clinical symptoms (P = 0.181).

Conclusions

PD was frequently associated with PEI. Unfortunately PEI is an under recognized and under treated long-term sequel of PD. Fecal elastase 1 should be performed routinely in both symptomatic and asymptomatic patients. Pancreatic enzyme replacement therapy should be considered in every patient after PD.

Crumpled structure of the custom hydrophobic lytic peptide cecropin B3

The solution structure of a custom lytic peptide, cecropin B3 (CB3), having two identical hydrophobic segments on both the N- and C-termini, was investigated by two-dimensional NMR spectroscopy. The need to determine the structure of this peptide is rooted in its specific ability to lyse lipid layers that have a high content of anionic lipid. The lytic activities of CB3 on cell membranes including cancer cells and bacteria is found to be less than cecropin B1. The results show that CB3 has four discrete segments forming alpha helical structures. The crumpled structure of CB3 provides evidence for the lysis of the lipid layer being via a pathway that differs from pore formation. The results in this study provide strong clues towards a rational design for a potent antimicrobial and antitumor peptide.

Thermodynamic characterization of the human acidic fibroblast growth factor: evidence for cold denaturation

The thermodynamic parameters characterizing the conformational stability of the human acidic fibroblast growth factor (hFGF-1) have been determined by isothermal urea denaturation and thermal denaturation at fixed concentrations of urea using fluorescence and far-UV CD circular dichroism (CD) spectroscopy. The equilibrium unfolding transitions at pH 7.0 are adequately described by a two-state (native <--> unfolded state) mechanism. The stability of the protein is pH-dependent, and the protein unfolds completely below pH 3.0 (at 25 degrees C). hFGF-1 is shown to undergo a two-state transition only in a narrow pH range (pH 7.0-8.0). Under acidic (pH <6.0) and basic (pH >8.0) conditions, hFGF-1 is found to unfold noncooperatively, involving the accumulation of intermediates. The average temperature of maximum stability is determined to be 295.2 K. The heat capacity change (DeltaC(p)()) for the unfolding of hFGF-1 is estimated to be 2.1 +/- 0.5 kcal.mol(-1).K(-1). Temperature denaturation experiments in the absence and presence of urea show that hFGF-1 has a tendency to undergo cold denaturation. Two-dimensional (1)H-(15)N HSQC spectra of hFGF-1 acquired at subzero temperatures clearly show that hFGF-1 unfolds under low-temperature conditions. The significance of the noncooperative unfolding under acidic conditions and the cold denaturation process observed in hFGF-1 are discussed in detail.

Structural events during the refolding of an all beta-sheet protein

The refolding kinetics of the 140-residue, all beta-sheet, human fibroblast growth factor (hFGF-1) is studied using a variety of biophysical techniques such as stopped-flow fluorescence, stopped-flow circular dichroism, and quenched-flow hydrogen exchange in conjunction with multidimensional NMR spectroscopy. Urea-induced unfolding of hFGF-1 under equilibrium conditions reveals that the protein folds via a two-state (native <--> unfolded) mechanism without the accumulation of stable intermediates. However, measurement of the unfolding and refolding rates in various concentrations of urea shows that the refolding of hFGF-1 proceeds through accumulation of kinetic intermediates. Results of the quenched-flow hydrogen exchange experiments reveal that the hydrogen bonds linking the N- and C-terminal ends are the first to form during the refolding of hFGF-1. The basic beta-trefoil framework is provided by the simultaneous formation of beta-strands I, IV, IX, and X. The other beta-strands comprising the beta-barrel structure of hFGF-1 are formed relatively slowly with time constants ranging from 4 to 13 s.

15N NMR relaxation studies of free and ligand-bound human acidic fibroblast growth factor

15N NMR relaxation data have been used to characterize the backbone dynamics of the human acidic fibroblast growth factor (hFGF-1) in its free and sucrose octasulfate (SOS)-bound states. (15)N longitudinal (R(1)), transverse (R(2)) relaxation rates and (1H)-(15)N steady-state nuclear Overhauser effects were obtained at 500 and 600 MHz (at 25 degrees C) for all resolved backbone amide groups using (1)H- detected two-dimensional NMR experiments. Relaxation data were fit to the extended model free dynamics for each NH group. The overall correlation time (tau(m)) for the free and SOS-bound forms were estimated to be 10.4 +/- 1.07 and 11.1 +/- 1.35 ns, respectively. Titration experiments with SOS reveals that the ligand binds specifically to the C-terminal domain of the protein in a 1:1 ratio. Binding of SOS to hFGF-1 is found to induce a subtle conformational change in the protein. Significant conformational exchange (R(ex)) is observed for several residues in the free form of the protein. However, in the SOS-bound form only three residues exhibit significant R(ex) values, suggesting that the dynamics on the micro- to millisecond time scale in the free form is coupled to the cis-trans-proline isomerization. hFGF-1 is a rigid molecule with an average generalized parameter (S(2)) value of 0.89 +/- 0.03. Upon binding to SOS, there is a marked decrease in the overall flexibility (S(2) = 0.94 +/- 0.02) of the hFGF-1 molecule. However, the segment comprising residues 103-111 shows increased flexibility in the presence of SOS. Significant correlation is found between residues that show high flexibility and the putative receptor binding sites on the protein.

Rapid staining of proteins on polyacrylamide gels and nitrocellulose membranes using a mixture of fluorescent dyes

The present work describes a novel, fluorescence-based method for staining proteins on SDS-PAGE and membrane(s). In this method, proteins are stained using a mixed-dye (sulfo-rhodamine B and 1-anilino-8-naphthalene sulfonic acid (NH(4)(+))) solution. The mixed-dye staining protocol can detect proteins up to a concentration of 15 ng. This method is generally applicable to all proteins and is more sensitive than the conventional Coomassie blue method. The staining method is rapid and efficient. Staining-destaining of proteins using the mixed-dye protocol takes less than half an hour. Another interesting feature of the staining protocol described here is the applicability to the staining of proteins on nitrocellulose membranes.

Identification and characterization of an equilibrium intermediate in the unfolding pathway of an all beta-barrel protein

The guanidinium hydrochloride (GdnHCl)-induced unfolding of an all beta-sheet protein, the human acidic fibroblast growth factor (hFGF-1), is studied using a variety of biophysical techniques including multidimensional NMR spectroscopy. The unfolding of hFGF-1 in GdnHCl is shown to involve the formation of a stable equilibrium intermediate. Size exclusion chromotagraphy using fast protein liquid chromatography shows that the intermediate accumulates maximally at 0.96 m GdnHCl. 1-Anilinonapthalene 8-sulfonate binding, one-dimensional (1)H NMR, and limited proteolytic digestion experiments suggest that the intermediate has characteristics resembling a molten globule state. Chemical shift perturbation and hydrogen-deuterium exchange monitored by (1)H-(15)N heteronuclear single quantum coherence spectra reveal that profound structural changes in the intermediate state (in 0.96 m GdnHCl) occur in the C-terminal, heparin binding region of the protein molecule. Additionally, results of the stopped flow fluorescence experiments suggest that the kinetic refolding of hFGF-1 proceeds through the accumulation of an intermediate at low concentrations of the denaturant. To our knowledge, the present study is the first report wherein an equilibrium intermediate is characterized in detail in an all beta-barrel protein.

Comparison of the structural stability of two homologous toxins isolated from the Taiwan cobra (Naja naja atra) venom

Cardiotoxin analogue III (CTX III) and cobrotoxin (CBTX) isolated from the Taiwan cobra venom (Naja naja atra) are structurally homologous, small molecular weight, all-beta-sheet proteins, cross-linked by four disulfide bonds at identical positions. The conformational stabilities of these toxins are compared based on temperature-dependent chemical shifts and amide proton exchange kinetics using two-dimensional NMR spectroscopy. The structure of CTX III is found to be significantly more stable than that of CBTX. In both the toxins, beta-strand III appears to constitute the stability core. In CTX III, the stability of the triple-stranded beta-sheet domain is observed to be markedly higher than the double-stranded beta-sheet segment. In contrast, in CBTX, both structural domains (double- and triple-stranded beta-sheet domains) appear to contribute equally to the stability of the protein. Estimation of the free energy of exchange (Delta G(ex)) of residues in CBTX and CTX III reveals that the enhanced stability of the structure of CTX III stems from the strong interactions among the beta-strands constituting the triple-stranded beta-sheet domain and also the molecular forces bridging the residues at the N- and C-terminal ends of the molecule.

Elucidation of the solution structure of cardiotoxin analogue V from the Taiwan cobra (Naja naja atra)--identification of structural features important for the lethal action of snake venom cardiotoxins

The aim of the present study is to understand the structural features responsible for the lethal activity of snake venom cardiotoxins. Comparison of the lethal potency of the five cardiotoxin isoforms isolated from the venom of Taiwan cobra (Naja naja atra) reveals that the lethal potency of CTX I and CTX V are about twice of that exhibited by CTX II, CTX III, and CTX IV. In the present study, the solution structure of CTX V has been determined at high resolution using multidimensional proton NMR spectroscopy and dynamical simulated annealing techniques. Comparison of the high resolution solution structures of CTX V with that of CTX IV reveals that the secondary structural elements in both the toxin isoforms consist of a triple and double-stranded antiparallel beta-sheet domains. Critical examination of the three-dimensional structure of CTX V shows that the residues at the tip of Loop III form a distinct "finger-shaped" projection comprising of nonpolar residues. The occurrence of the nonpolar "finger-shaped" projection leads to the formation of a prominent cleft between the residues located at the tip of Loops II and III. Interestingly, the occurrence of a backbone hydrogen bonding (Val27CO to Leu48NH) in CTX IV is found to distort the "finger-shaped" projection and consequently diminish the cleft formation at the tip of Loops II and III. Comparison of the solution structures and lethal potencies of other cardiotoxin isoforms isolated from the Taiwan cobra (Naja naja atra) venom shows that a strong correlation exists between the lethal potency and occurrence of the nonpolar "finger-shaped" projection at the tip of Loop III. Critical analysis of the structures of the various CTX isoforms from the Taiwan cobra suggest that the degree of exposure of the cationic charge (to the solvent) contributed by the invariant lysine residue at position 44 on the convex side of the CTX molecules could be another crucial factor governing their lethal potency.

Proline inhibits aggregation during protein refolding

The in vitro refolding of hen egg-white lysozyme is studied in the presence of various osmolytes. Proline is found to prevent aggregation during protein refolding. However, other osmolytes used in this study fail to exhibit a similar property. Experimental evidence suggests that proline inhibits protein aggregation by binding to folding intermediate(s) and trapping the folding intermediate(s) into enzymatically inactive, "aggregation-insensitive" state(s). However, elimination of proline from the refolded protein mixture results in significant recovery of the bacteriolytic activity. At higher concentrations (>1.5 M), proline is shown to form loose, higher-order molecular aggregate(s). The supramolecular assembly of proline is found to possess an amphipathic character. Formation of higher-order aggregates is believed to be crucial for proline to function as a protein folding aid. In addition to its role in osmoregulation under water stress conditions, the results of this study hint at the possibility of proline behaving as a protein folding chaperone.

Investigation of the structural stability of cardiotoxin analogue III from the Taiwan cobra by hydrogen-deuterium exchange kinetics

The conformational stability of a small ( approximately 7 kDa), all beta-sheet protein, cardiotoxin analogue III (CTX III), from the venom of the Taiwan cobra has been investigated by hydrogen-deuterium (H/D) exchange using two-dimensional NMR spectroscopy. The H/D exchange kinetics of backbone amide protons in CTX III has been monitored at pD 3.6 and 6.6 (at 25 degrees C), for over 5000 h. Examination of H/D exchange kinetics in the protein showed that a number of slowly exchanging residues are in the hydrophobic core of the protein. The average protection factor of the amide protons of residues belonging to the triple-stranded beta-sheet domain is about 20 times greater than that of those in the double-stranded beta-sheet segment. The residues in the C-terminal tail of the molecule, though structureless, have been found to exhibit significant protection against H/D exchange. Comparison of the quenched-flow H/D exchange data on CTX III with those obtained in the present study reveals that the most slowly exchanging portion constitutes the folding core of the protein.

Secondary structure formation is the earliest structural event in the refolding of an all beta-sheet protein

The refolding kinetics of cobrotoxin (CBTX), a small-molecular-weight ( approximately 7 kDa) all beta-sheet protein, has been monitored using a variety of biophysical techniques. The secondary structure formation and hydrophobic collapse occur as distinct events during the refolding of the protein. Complete secondary structure formation occurs prior to the clustering of the hydrophobic residues. The late stage(s) of the refolding pathway of CBTX is characterized by change(s) in the local environment and optical asymmetry of the indole ring of the sole tryptophan residue. The results obtained in the present study, to our knowledge, represent the first unambiguous experimental support for the framework model of protein folding.

Influence of disulfide bonds on the induction of helical conformation in proteins

The effect(s) of TFE (2,2,2-trifluoroethanol) on three different conformational states (native, denatured, and carboxymethylated) of CTX III and RNase A has been examined. Contrary to the general belief, the results of the present study reveal that TFE can induce helical conformation in a protein which has no sequence propensity to form a helix. It is found that the helix induction in TFE is intricately related to the destabilization of the tertiary structural conformation in proteins. More importantly, the disulfide bonds in proteins are found to have significant influence on the TFE-mediated helix induction. The results obtained in this study strongly suggest that information pertaining to the influence of disulfide bonds on helix induction need to be considered to improve the accuracy of secondary structure prediction algorithms.

Structurally homologous toxins isolated from the Taiwan cobra (Naja naja atra) differ significantly in their structural stability

Cardiotoxin and neurotoxin analogues isolated from snake venom sources are highly homologous proteins (>50% homology) with similar three-dimensional structures but exhibit drastically different biological properties. In the present study, we compare the conformational stability of cardiotoxin analogue III (CTX III) and cobrotoxin (CBTX), a neurotoxin analogue, from the Taiwan cobra (Naja naja atra), using circular dichroism spectroscopy and hydrogen-deuterium (H/D) exchange techniques in conjunction with two-dimensional NMR methods. Contrary to expectations, it is found that CTX III and CBTX differ significantly in their structural stabilities. The three-dimensional structure of CBTX is less stable than that of CTX III. The amide protons of residues at the N- and C-terminal ends of the CTX III molecule are strongly protected against H/D exchange, implying that the terminal ends of the molecule are bridged together by significant numbers of hydrogen bonds. However, in CBTX, amide protons at the terminal ends of the molecule do not exhibit an significant protection against H/D exchange. Comparison of the protection factors of the various amide protons in CTX III and CBTX reveals that the extraordinary stability of CTX III stems from the strong network of interactions among the residues at the N- and C-terminal ends and also due to the tight and ordered packing of the nonpolar residues involved in the triple-stranded, anti-parallel, beta-sheet segment of the molecule.

The role of proline in the prevention of aggregation during protein folding in vitro

Proline effectively inhibits protein aggregation during the refolding of bovine carbonic anhydrase. Other osmolytes used such as glycine and ethylene glycol fail to exhibit the 'aggregation-blockade' role shown by proline. Results of viscosity and ANS fluorescence (1-anilino-8-naphthalene sulphonic acid) experiments suggest that proline at high concentrations forms an ordered supramolecular assembly. Based on these results, it is proposed that proline behaves as a protein folding chaperone due to the formation of an ordered, amphipathic supramolecular assembly. To our knowledge, this is the first report wherein proline is proposed as a protein folding aid.

Unfolding and refolding of cardiotoxin III elucidated by reversible conversion of the native and scrambled species

Cardiotoxin analogue III (CTX III) isolated from the venom of the Taiwan Cobra (Naja naja atra) is a small molecular weight, all beta-sheet protein, cross-linked by four disulfide bridges. The unfolding and refolding mechanisms of CTX III have been examined by monitoring the reversible conversion of the native and scrambled species. It is found that, in the presence of a denaturant (urea/guanidinium hydrochloride) and a thiol catalyst, CTX III forms a mixture of scrambled species by shuffling its four native disulfide bonds. Complete unfolding of CTX III can be achieved using either 3.0-4.0 M guanidinium hydrochloride (GdmCl) or 5.0-6.0 M urea. It is observed that GdmCl is thermodynamically more potent but kinetically less efficient than urea in unfolding CTX III. The rate constants of unfolding of CTX III in 8 M urea are significantly greater than that obtained in 5.0 M GdmCl and 8.0 M GdmCl. Interestingly, upon removal of the denaturant, scrambled species of CTX III is found to refold spontaneously through dynamic reshuffling of the non-native disulfides to attain the native disulfide linkages. In addition, CTX III contains highly reactive lysines which are modified by trace amounts of cyanate contaminant which exists invariably even in high-grade urea solutions. The reactive lysines of CTX III are modified by cyanate both in the native and unfolded states of the protein. The modification is nonselective, and the modified product is found to consist of highly heterogeneous species. Surprisingly, these heterogeneous species of modified CTX III are observed to display stability and folding/unfolding properties indistinguishable from those of the native CTX III. The knowledge obtained from the present study, on the conditions to convert the scrambled species, could provide useful clues for a rational design for snake venom cardiotoxins with potential therapeutic applications.

Events in the kinetic folding pathway of a small, all beta-sheet protein

The folding of cardiotoxin analogue III (CTX III), a small (60 amino acids), all beta-sheet protein from the venom of the Taiwan Cobra (Naja naja atra) is here investigated. The folding kinetics is monitored by using a variety of techniques such as NMR, fluorescence, and circular dichroism spectroscopy. The folding of the protein is complete within a time scale of 200 ms. The earliest detectable event in the folding pathway of CTX III is the formation of a hydrophobic cluster, which possess strong affinity to bind to nonpolar dye such as 1-anilino-8-napthalene-sulfonic acid. Quenched-flow deuterium-hydrogen exchange experiments indicate that the segment spanning residues 51-55 along with Lys23, Ile39, Val49, Tyr51 and Val52 could constitute the "hydrophobic cluster." Folding kinetics of CTX III based on the amide-protection data reveals that the triple-stranded, antiparallel beta-sheet segment, which is located in the central core of the molecule, appears to fold faster than the double-stranded beta-sheet segment.

Main-chain dynamics of cardiotoxin II from Taiwan cobra (Naja naja atra) as studied by carbon-13 NMR at natural abundance: delineation of the role of functionally important residues

Cardiotoxin analogue II (CTX II) is an all beta-sheet, small molecular mass (6.8 kDa), basic protein possessing a wide array of biological properties. Nearly complete assignment of the protonated carbon resonances has been achieved by heteronuclear NMR experiments. The study shows that the correlation between the carbon-13 chemical shifts and CTX II structure is good in general, but interesting deviations are also noticed. To characterize the internal dynamics of CTX II, longitudinal, transverse relaxation rates and heteronuclear 13C{1H} NOEs were measured for alpha-carbons at natural abundance by two-dimensional NMR spectroscopy. Relaxation measurements were obtained in a 14.1 T spectrometer for 50 residues, which are evenly spread along the CTX II polypeptide chain. Except for five alpha-carbons, all data were analyzed from a simple two-parameter spectral density function using the model free approach of Lipari and Szabo. The microdynamical parameters (S2, taue, and Rex) were calculated with an overall rotational correlation time (taum) for the protein of 4.8 ns. For most residues, the alpha-carbons exhibit fast (taue < 30 ps) restricted libration motions (S2 = 0.79-0.89). The present study reveals that the functionally important residues located at the tips of the three loops are flexible, and the flexibility of residues in this region could be important in the binding of cardiotoxins to their putative "receptors" which are postulated to be located on the erythrocyte membrane. In addition, the results obtained in the present study support the earlier predictions on the relative role of the lysine residues in the erythrocyte lytic activity of cardiotoxins.

The role of acetic acid in the prevention of salt-induced aggregation of snake venom cardiotoxins

Snake venom cardiotoxins (CTXs) exhibit a strong tendency to aggregate upon desalting and hence it is extremely difficult to prepare salt-free cardiotoxin(s). In the present study, we describe a new method for preparation of salt-free CTX based on dialysis against acetic acid. Based on experimental observation and the three dimensional solution structure of cardiotoxin analogue III from the Taiwan cobra (Naja naja atra), a molecular mechanism for the prevention of aggregation of cardiotoxins by acetic acid is discussed. In our opinion, the results obtained in the present study would pave way for elucidating the structural basis for the broad spectrum of biological activities exhibited by snake venom cardiotoxins.

Snake venom cardiotoxins-structure, dynamics, function and folding

Snake cardiotoxins are highly basic (pI > 10) small molecular weight (approximately 6.5 kDa), all beta-sheet proteins. They exhibit a broad spectrum of interesting biological activities. The secondary structural elements in these toxins include antiparallel double and triple stranded beta-sheets. The three dimensional structures of these toxins reveal an unique asymmetric distribution of the hydrophobic and hydrophilic amino acids. The 3D structures of closely related snake venom toxins such as neurotoxins and cardiotoxin-like basic proteins (CLBP) fail to show similar pattern(s) in the distribution of polar and nonpolar residues. Recently, many novel biological activities have been reported for cardiotoxins. However, to-date, there is no clear structure-function correlation(s) available for snake venom cardiotoxins. The aim of this comprehensive review is to summarize and critically evaluate the progress in research on the structure, dynamics, function and folding aspects of snake venom cardiotoxins.

Acetonitrile-induced conformational transitions in poly-L-lysine

The effect of acetonitrile on the random coil, alpha-helix and beta-sheet conformations induced in poly-L-lysine is studied. It is found that acetonitrile at higher concentrations transforms the backbone of polylysine from a random coil to a helical conformation. Addition of acetonitrile to polylysine (pH 11.5) in the alpha-helix conformation, induces conformational changes in two stages. At concentrations below 60% v/v, acetonitrile stabilizes the helical conformation and at higher concentrations (> 70% v/v), it destabilizes the helix. beta-sheet-->alpha-helix-->random coil conformational transitions are found to occur when polylysine in the heat-induced conformation is titrated with acetonitrile. The possible mechanism(s) of action of acetonitrile in inducing these structural transitions is discussed.

Specificity of helix-induction by 2,2,2-trifluoroethanol in polypeptides

The specificity of helix-induction in polypeptides by 2,2,2-trifluoro ethanol (TFE) is studied using an all beta-sheet protein such as cardiotoxin analogue I (CTX I) from the Taiwan Cobra (Naja naja atra) and a homopolymer such as poly-L-lysine. It is found that alcohols including TFE can 'non-specifically' induce helix at high concentrations both in CTX I and polylysine at neutral pH. However, among the alcohols used, only TFE could transform the heat-induced beta-sheet conformation of polylysine at pH 11.5 into an alpha-helix. The beta-sheet to alpha-helix conversion in polylysine (in the beta-sheet conformation) occurs even at very low concentrations of TFE (< 5% v/v). In addition, experiments on the effect(s) of TFE on the denatured and reduced CTX I (rCTX I) indicate the helix-induction in rCTX I takes place at low TFE concentrations (< 20% v/v). The results of this study hint at the possible influence of disulfide bridges on the induction of helix by TFE.

The mechanism of 2,2,2-trichloroacetic acid-induced protein precipitation

The mechanism of 2,2,2-trichloroacetic acid (TCA)-induced precipitation of proteins is studied. The TCA-induced protein precipitation curves are observed to be U-shaped. It is bound that the protein-precipitate-inducing effects of TCA are due to the three chloro groups in the molecule. Using cardiotoxin III (CTX III) isolated from the Taiwan cobra (Naja naja atra), as a model protein, we attempt to understand the molecular basis for the TCA-induced effects. Employing circular dichroism, proton-deuterium exchange in conjunction with conventional 2D NMR techniques, and 1-anilino naphthalene-8-sulfonate-binding experiments, we demonstrate that CTX III is in a partially structured state similar to the 'A state' in 3% w/v TCA. It is postulated that the formation of this 'sticky' partial structured 'A state' in the TCA-induced unfolding pathway is responsible for the acid-induced protein precipitation.

Solution structure of toxin b, a long neurotoxin from the venom of the king cobra (Ophiophagus hannah)

The solution structure of toxin b, a long neurotoxin (73 amino acids and 5 disulfides) from the venom of Ophiophagus hannah (king cobra), has been determined using 1H NMR and dynamical simulated annealing techniques. The structures were calculated using 485 distance constraints and 52 dihedral angle restraints. The 21 structures that were obtained satisfy the experimental restraints and possess good nonbonded contacts. Analysis of the converged structures revealed that the protein consists of a core region from which three finger-like loops extend outwards. The regular secondary structure in toxin b includes a double and a triple stranded antiparallel beta sheet. Comparison with the solution structures of other long neurotoxins reveals that although the structure of toxin b is similar to those of previously reported long neurotoxins, clear local structural differences are observed in regions proposed to be involved in binding to the acetylcholine receptor. A positively charged cluster is found in the C-terminal tail, in Loop III, and in the tip of Loop II. This cationic cluster could be crucial for the binding of the long neurotoxins to the acetylcholine receptor.

Non-specific helix-induction in charged homopolypeptides by alcohols

The specificity/non-specificity of helix-induction in charged homopolymers such as polylysine and polyglutamic acid, at neutral pH, by various alcohols namely 2,2,2-trifluoroethanol (TFE), methanol, ethanol and 1-propanol is studied. It is found that all the alcohols used, non-specifically induced helical conformation at high concentrations. In addition, the effect(s) of TFE on an all beta-sheet protein, such cardiotoxin analogue I (CTX I) from the Taiwan Cobra (Naja naja atra) is also studied. Evaluation of the helix propensity in the amino-acid sequence of CTX I using helix-coil algorithm, AGADIR, shows a total of 1.15% helical content in the protein. In CTX I, helical conformation is found to be induced at high concentrations of TFE (> or = 70% v/v). Interestingly, upon denaturation and reduction of disulfide bridges in CTX I, helix is found to be induced even at low concentrations of TFE (> or = 20% v/v). The results of this study hints at the possible influence of native tertiary structural interactions and disulfide bridges in the induction of helix by TFE.

Proline is a protein solubilizing solute

The effect of proline on the prevention of trichloroacetic acid (TCA)-induced protein precipitation is studied. It is found that proline at high concentrations (> 4.0 M) completely prevents TCA-induced precipitation of hen egg white lysozyme. Other osmolytes such as ethylene glycol, glycerol and sucrose fail to prevent the TCA-induced precipitation of lysozyme. Viscosity and 1-anilino-8-naphthalene sulphonic acid binding experiments suggest that proline at high concentration forms an ordered supramolecular assembly. Proline is shown to increase the solubility of protein due to formation of such higher order assemblies. A model of the supra-molecular assembly of proline is proposed and a possible in vivo role of the increased levels of proline under water stress is discussed.

Characterization of a partially structured state in an all-beta-sheet protein

Cardiotoxin analogue III (CTX III) is a low-molecular-mass all-beta-sheet protein isolated from the Taiwan cobra (Naja naja atra) venom. A stable partially structured state similar to the "molten globule' state has been identified for CTX III in a 3% (w/v) solution of 2,2,2-trichloroacetic acid at 298 K. This stable state has been structurally characterized using a variety of techniques such as CD, 1-anilinonaphthalene-8-sulphonate fluorescence binding, Fourier transform IR and two-dimensional NMR spectroscopy techniques. Direct assignment of the homonuclear two-dimensional NMR spectra of the protein in 3% trichloroacetic acid showed that drastic structural perturbation had not taken place in the protein and that the 'intermediate' state retained a significant portion of the native secondary-structural interactions. It is found that about 65% of the native beta-sheet structural contacts are maintained in the partially structured state of CTX III in 3% trichloroacetic acid.

Destabilisation of native tertiary structural interactions is linked to helix-induction by 2,2,2-trifluoroethanol in proteins

The effect of 2,2,2-trifluoroethanol (TFE) on the structure of an all beta-sheet protein, cardiotoxin analogue 111 (CTX III) from the Taiwan cobra (Naja naja atra) is studied. It is found that high concentrations (> 80% v/v) of TFE induced a beta-sheet to alpha-helix structural transition. It is found that in denatured and reduced CTX III (rCTX III) helical conformation is induced even upon addition of low concentrations (> 10% v/v) of TFE. Using three other proteins, namely, ribonuclease A (RNase A), lysozyme and alpha-lactalbumin, it is been observed that helix-induction by TFE is intricately linked to drastic destabilization of native tertiary structural interactions in the proteins.

Induction of helical conformation in all beta-sheet proteins by trifluoroethanol

The effect of 2,2,2-Trifluoroethanol (TFE) on the structure of five all beta-sheet proteins, isolated from the venom of the Taiwan cobra (Naja naja atra), is studied. In all the toxins used, it is observed that significant amount of alpha-helix is induced at higher concentrations of TFE. In all these proteins, the induction of helical conformation and disruption of the tertiary structure seem to occur simultaneously. The structural transitions induced by TFE in reduced and denatured protein appear to be different from those observed in the native protein(s). In our opinion, the findings reported herein could have significant implications on research in the area of protein folding.

Thermal denaturation of an all beta-sheet protein--identification of a stable partially structured intermediate at high temperature

The thermal unfolding of an all beta-sheet protein, cardiotoxin analogue III, from the Taiwan Cobra (Naja naja atra) is studied at pH 2.0, 4.0 and 6.0. At pH 4.0, using circular dichroism and 1-anilino naphthalene-8-sulphonic acid (ANS) fluorescence binding studies, a stable partially structured intermediate is detected at 90 degrees C.

Effect of chaotropic denaturant on the binding of 1-anilino-8-naphthalene sulfonic acid to proteins

1-Anilino-8-naphthalene sulfonic acid (ANS), a hydrophobic dye, is widely used to monitor conformational changes occurring in proteins during their folding/unfolding. Using cardiotoxin III (whose conformation remains unperturbed even in 6 M urea) from the Taiwan Cobra (Naja naja atra) venom, it is demonstrated that chaotropic denaturant such as urea directly competes with the interaction between ANS and the protein. The results presented in this report, in our opinion, has significant implication(s) in the area of protein folding, arising out of ANS binding experiments.

2,2,2-Trifluoroethanol induces helical conformation in an all beta-sheet protein

The effect of 2,2,2-trifluoroethanol (TFE) on the structure of an all beta-sheet protein, cardiotoxin analogue II (CTX II), from the Taiwan cobra (Naja naja atra) is studied. Using circular dichroism studies, it is found that higher concentrations of TFE induced a structural transition from beta-sheet to alpha-helix, both in the native state (nCTX II) and in denatured but not disulfide reduced CTX II (dCTX II) samples. The beta-sheet to alpha-helix conversion is shown to be cooperative. However, in denatured and reduced CTX II (rCTX II), a TFE transforms a portion(s) of the protein backbone a random coil to an alpha-helical conformation. Based on the solution structure of CTX II and the physical property of TFE, a possible mechanism for the observed backbone structural transitions induced by TFE is discussed. The results described in this paper question the significance of the structure of the "molten globule" intermediate(s) obtained in organic solvents such as TFE.

Cloning, direct expression, and purification of a snake venom cardiotoxin in Escherichia coli

The cardiotoxin analogue III (CTX III), isolated from the Taiwan cobra (Naja naja atra) venom, is a sixty-amino acid, all beta-sheet protein. We report the direct expression of CTX III from its synthetic gene as inclusion bodies in Escherichia coli. The yield of the expressed protein is about 40 mg/liter of the culture. CTX III trapped as inclusion bodies is dissolved and refolded by the slow refolding technique. The refolded protein is purified by reverse phase high performance liquid chromatography. The purified and refolded CTX III sample is further characterized by SDS-PAGE, circular dichroism, two-dimensional NMR spectroscopy and haemolytic activity. To our knowledge, this is the first report of the direct expression and purification of snake venom cardiotoxins.

Effect of organic acids in the prevention of aggregation on rapid refolding of proteins

The effect of organic acids on the aggregation of protein(s) during rapid refolding is studied. Using egg white lysozyme, it is observed that acetic acid not only prevents aggregation, but also aids the protein to refold back to its native, biologically active state. In contrast, formic acid, propionic acid and butyric acid fail to exhibit this property. Using circular dichroism spectroscopy it has been found that an 'aggregation-insensitive' partially folded intermediate state is induced in 0.35M acetic acid.

Conformational studies of a synthetic cyclic decapeptide fragment of rat transforming growth factor-alpha

The solution conformation of a synthetic cyclic decapeptide [with sequence mimicking the third disulfide loop of rat transforming growth factor-alpha (rTGF-alpha)] in deuterated dimethyl sulfoxide was studied by 2D NMR. The determination of solution structures was based on NOE interproton distances, using a combination of distance geometry and simulated annealing protocols. The convergence of the selected structures was evident from the small atomic pairwise root-mean-square deviation values among them. Good agreement was noted between the experimental and simulated NOESY spectra, thereby reflecting the accuracy of the calculated solution structures. Analysis of the structures indicates that the residues Tyr5 and Arg9 exhibit similar side chain orientation as that in the corresponding disulfide loop of human transforming growth factor-alpha.

Identification of 'molten globule'-like state in all beta-sheet protein

The cardiotoxin analogue III (CTX III), isolated from the Taiwan Cobra venom (Naja naja atra), is a sixty amino acid, all beta-sheet protein. The 2,2,2-trifluoro ethanol (TFE) induced unfolding of CTX III is studied under acidic conditions (pH 2.5). Using circular dichroism, 1-anilino-8-napthalene sulphonic acid binding and NMR experiments, it is shown that stable, partially structured state(s) ['molten globule'-like state] is formed between 50 and 80% TFE concentrations. The protein was found to exist in an unfolded state in 80% TFE containing 2M urea. The TFE induced unfolding process is shown to be completely reversible. In the 'molten globule' state of CTX III in 80% TFE, though portion(s) of the backbone of the protein assume helical conformation, most of the original beta-sheet secondary structural elements in the protein are intact. In our opinion, this is the first report of the identification of a 'molten globule'-like state in the unfolding pathway of an all beta-sheet monomeric protein.

Fluorescent staining for proteins on polyacrylamide gels with 5-dimethylamino-1-naphthalenesulfonyl chloride (dansyl chloride)

A simple and sensitive post electrophoresis fluorescent staining technique for proteins on polyacrylamide gels using 5-dimethylamino-1-naphthalene sulfonyl chloride (dansyl chloride) has been developed. Dansyl chloride staining increases the sensitivity, 0.125 micrograms protein per band can be visualised by this technique. The staining method appears to be applicable to all types of proteins including proteoglycans.

Refolding of RNAse A at high concentrations: identification of non-native species

In this paper, we present an analysis of the soluble species formed on refolding of RNase A at various concentrations, in order to characterize these species with respect to structure and activities. Studies were carried out using reverse-phase high-performance liquid chromatography, circular dichroism, chromatography and ultracentrifugation. At all concentrations of protein used, RNase A refolded to the native form, together with formation of non-native species. These non-native species are either misfolded monomers or aggregates; the percentage of such species increases with increasing concentration of enzyme. Such aggregation appears to be a non-random process governed by intermolecular disulfide crosslinking between monomers. These results reaffirm the principle that the information for folding of the protein is encoded in the amino acid sequence itself.

Trichloroacetic acid-induced unfolding of bovine pancreatic ribonuclease. Existence of molten globule-like state

The exposure of ribonuclease A to trichloroacetic acid was earlier shown to alter the conformation of the protein resulting in reduced enzymatic activity (Sagar, A. J., Subbiah, V., and Pandit, M. W. (1989) Biochim. Biophys. Acta 995, 144-150). We have studied the structure and enzymatic activity of ribonuclease A treated with trichloroacetic acid over a wide range of acid concentrations (0-40%). The far ultraviolet circular dichroism spectra of ribonuclease A, on exposure to acid concentrations less than 10%, indicated an exceptionally high degree of chiral structure. Exposure of ribonuclease A to acid concentrations between 10 and 30% resulted in the formation of a molecule with significant chiral structure (conventionally assigned to residual secondary structure) but reduced tertiary structure (characteristics very similar to those of molten globule). Increased binding of the hydrophobic probe 1-anilinonaphthalene-8-sulfonate to the enzyme treated with 15-30% acid, as compared with the untreated or completely unfolded protein, supported the existence of a state having characteristics of molten globule. Reversed phase high performance liquid chromatography corroborated the data obtained by circular dichroism as well as 1-anilino-naphthalene-8-sulfonate-binding studies. Beyond acid concentrations of 30%, the ribonuclease is completely denatured. The trichloroacetic acid-induced unfolding is shown to be completely reversible.

Origin of multiple bands of proteins on sodium dodecyl sulphate-polyacrylamide gel electrophoresis--intermolecular disulphide cross-linking due to the presence of oxidizing components in the reducing agent

The presence of oxidized products in the reducing agent used in sodium dodecyl sulphate-polyacrylamide gel electrophoresis is shown to yield multiple bands from otherwise homogeneous RNase A. The role of oxidized products in generating multiple bands is elucidated by using varying proportions of oxidized and reduced glutathione in a mixture as a reducing agent.

Multiple bands on the sodium dodecyl sulfate-polyacrylamide gel electrophoresis gels of proteins due to intermolecular disulfide cross-linking

Gel electrophoresis has been used extensively as an analytical technique to check the purity and to determine the molecular weight of proteins. Improved levels of detection of proteins by silver staining of the gels have made the technique more sensitive in detecting heterogeneity. We report here some interesting observations about the anomalous behavior of some proteins in sodium dodecyl sulfate-polyacrylamide gel electrophoresis (SDS-PAGE). This report is concerned with the appearance of multiple bands, after silver staining, on the SDS-PAGE gels of proteins which are shown by HPLC to be homogeneous. We also show the reasons for the appearance of bands that originate from 2-mercaptoethanol itself.

Effect of cationic drugs on suprahelical organization of DNA

Interaction of a minor groove-binding drug Hoechst-33258, and an intercalating drug, proflavin, with the PSI(+) form of DNA, was studied using CD spectroscopy. Both drugs are shown to relax the suprahelical organization of DNA, leading to the formation of a B-like structure, above a certain drug to phosphate ratio. However, unlike proflavin, Hoechst-33258 brings about further structural changes after formation of the B-like structure whereas proflavin does not. A reversal of the CD signal in the 300-450-nm spectral region is also observed with Hoechst-33258, indicating a change in the handedness of the suprahelical organization of DNA. To the best of our knowledge, drug-mediated changes as presented in this paper have not been reported so far.