Formation of a molten-globule-like state of myoglobin in aqueous hexafluoroisopropanol

The Molecular Mechanism of PSMα3 Aggregation: A New View

The emergence of a novel cross-α fibrillar structure, unlike the commonly observed sequence-independent cross-β one, of a 22-residue bacterial virulent amphipathic α-helical peptide of the phenol soluble modulin (PSM) family, PSMα3, with many deleterious effects on human life, has infused uncertainty to the paradigm of the intrinsically polymorphic, multivariate, multiphasic, and cross-sequence-cross-disease entangled protein aggregation landscape and hence on the identity of the therapeutic target. We, here, deconvolute the factors contributing to the genesis and hence the transition of lower to higher order aggregates of PSMα3 in its natural state and three noncanonical designed variants using conventional and enhanced sampling approach-based atomistic simulations. PSMα3 shows structural polymorphism with nominal α-helicity, substantial β-propensity, and dominant random-coil features, irrespective of the extent of aggregation. Moreover, the individual features of the overall amphipathicity operate alternatively depending on the extent and organization of aggregation; the dominance gradually moves from charged to hydrophobic residues with the progressive generation of higher order aggregates (dimer to oligomer to fibril) and with increasing orderedness of the self-assembled construct (oligomer vs dimer/fibril). Similarly, the contribution of interchain salt bridges decreases with increasing order of aggregation (dimer to oligomer to fibril). However, the intrachain salt bridges consistently display their role in all phases of aggregation. Such phase-independent features also include equivalent roles of electrostatic and van der Waals forces on intrachain interactions, sole contribution of van der Waals forces on interchain cross-talk, and negligible peptide-water relationship. Finally, we propose a conjugate peptide-based aggregation suppressor having a single-point proline mutation.

Insights into Fluctuations of Structure of Proteins: Significance of Intermediary States in Regulating Biological Functions

Proteins are indispensable to cellular communication and metabolism. The structure on which cells and tissues are developed is deciphered from proteins. To perform functions, proteins fold into a three-dimensional structural design, which is specific and fundamentally determined by their characteristic sequence of amino acids. Few of them have structural versatility, allowing them to adapt their shape to the task at hand. The intermediate states appear momentarily, while protein folds from denatured (D) ⇔ native (N), which plays significant roles in cellular functions. Prolific effort needs to be taken in characterizing these intermediate species if detected during the folding process. Protein folds into its native structure through definite pathways, which involve a limited number of transitory intermediates. Intermediates may be essential in protein folding pathways and assembly in some cases, as well as misfolding and aggregation folding pathways. These intermediate states help to understand the machinery of proper folding in proteins. In this review article, we highlight the various intermediate states observed and characterized so far under in vitro conditions. Moreover, the role and significance of intermediates in regulating the biological function of cells are discussed clearly.

First evidence of formation of pre-molten globule state in myoglobin: A macromolecular crowding approach towards protein folding in vivo

Myoglobin is known to show formation of intermediate states under various environmental conditions, in spite of that, this is the first evidence of formation pre-molten globule (PMG) in myoglobin. Polyethylene glycol (PEG) of various molecular sizes shows assorted effects on different proteins. Out of too short and too long PEGs, only PEGs of optimal size interact with proteins leading to change in protein structure that form intermediate state. We are the first one to report the formation of PMG in a protein in the presence of a crowding agent. The PEG-induced intermediate state was characterized by various techniques like absorption, fluorescence, near- and far-UV circular dichroism spectroscopy, ANS binding, and dynamic light scattering measurements to be PMG. Isothermal titration calorimetry and docking studies were further carried out to delineate the mechanism of formation of PMG in myoglobin in physiological conditions. The intermediate formed due to interaction of PEG with myoglobin has physiological implications which are essential to unravel the mystery to solve the massively complicated problems involved in the proper folding of proteins in vivo. Further, outcomes from this study are expected to gain mechanistic insights on the native structure and functions of proteins under in vivo conditions.

Macromolecular crowding induces molten globule state in the native myoglobin at physiological pH

Here, we report the formation of molten globule state of the native myoglobin in crowded environment. We have used Soret absorption spectroscopy and far-UV circular dichroism to monitor changes in tertiary and secondary structures of myoglobin, respectively. Our results reveal that in the presence of ficoll 70, the secondary structure of myoglobin remains unchanged while tertiary structure is lost significantly. 1-anilinonaphthalene-8-sulfonate binding experiments showed that myoglobin in the presence of various concentrations of ficoll 70, has newly exposed hydrophobic surfaces. Dynamic light scattering measurements show that there is almost 1.5 times increase in the hydrodynamic volume of myoglobin in the crowded environment. These structural characteristics of myoglobin in the presence of 300mg/ml ficoll 70 resemble those of molten globule state. Isothermal titration calorimetric (ITC) measurements show that ficoll 70 binds to myoglobin, whereas it shows no interaction with apo form of the protein. ITC results indicate that the reason behind this unique behavior of ficoll 70 towards myoglobin may be interaction of ficoll 70 with the heme group of myoglobin, which was further confirmed by the docking studies. We hypothesize that the soft interactions between heme and ficoll 70 leads to the formation of molten globule in myoglobin.

Solubilizing and Stabilizing Proteins in Anhydrous Ionic Liquids through Formation of Protein-Polymer Surfactant Nanoconstructs

Nonaqueous biocatalysis is rapidly becoming a desirable tool for chemical and fuel synthesis in both the laboratory and industry. Similarly, ionic liquids are increasingly popular anhydrous reaction media for a number of industrial processes. Consequently, the use of enzymes in ionic liquids as efficient, environment-friendly, commercial biocatalysts is highly attractive. However, issues surrounding the poor solubility and low stability of enzymes in truly anhydrous media remain a significant challenge. Here, we demonstrate for the first time that engineering the surface of a protein to yield protein-polymer surfactant nanoconstructs allows for dissolution of dry protein into dry ionic liquids. Using myoglobin as a model protein, we show that this method can deliver protein molecules with near native structure into both hydrophilic and hydrophobic anhydrous ionic liquids. Remarkably, using temperature-dependent synchrotron radiation circular dichroism spectroscopy to measure half-denaturation temperatures, our results show that protein stability increases by 55 °C in the ionic liquid as compared to aqueous solution, pushing the solution thermal denaturation beyond the boiling point of water. Therefore, the work presented herein could provide a platform for the realization of biocatalysis at high temperatures or in anhydrous solvent systems.

Antigen retrieval causes protein unfolding: evidence for a linear epitope model of recovered immunoreactivity

Antigen retrieval (AR), in which formalin-fixed paraffin-embedded tissue sections are briefly heated in buffers at high temperature, often greatly improves immunohistochemical staining. An important unresolved question regarding AR is how formalin treatment affects the conformation of protein epitopes and how heating unmasks these epitopes for subsequent antibody binding. The objective of the current study was to use model proteins to determine the effect of formalin treatment on protein conformation and thermal stability in relation to the mechanism of AR. Sodium dodecyl sulfate polyacrylamide gel electrophoresis was used to identify the presence of protein formaldehyde cross-links, and circular dichroism spectropolarimetry was used to determine the effect of formalin treatment and high-temperature incubation on the secondary and tertiary structure of the model proteins. Results revealed that for some proteins, formalin treatment left the native protein conformation unaltered, whereas for others, formalin denatured tertiary structure, yielding a molten globule protein. In either case, heating to temperatures used in AR methods led to irreversible protein unfolding, which supports a linear epitope model of recovered protein immunoreactivity. Consequently, the core mechanism of AR likely centers on the restoration of normal protein chemical composition coupled with improved accessibility to linear epitopes through protein unfolding.

Photochemical crosslinked electrospun collagen nanofibers: synthesis, characterization and neural stem cell interactions

Currently available crosslinking methods for electrospun collagen nanofibers do not preserve the fibrous architecture over prolonged periods of time. In addition, electrospinning of collagen often involves solvents that lead to extensive protein denaturation. In this study, we demonstrate the advantage of acetic acid over 1,1,1,3,3,3 hexafluoroisopropanol (HFP) in preventing collagen denaturation. A novel photochemical crosslinking method using rose bengal as the photoinitiator is also introduced. Using circular dichorism analyses, we demonstrate the fraction of collagen helical structure to be significantly greater in acetic acid-spun fibers than HFP-spun fibers (28.9 +/- 5.9% vs. 12.5 +/- 2.0%, p < 0.05). By introducing 0.1% (w/v) rose bengal into collagen fibers and subjecting these scaffolds to laser irradiation at a wavelength of 514 nm for 100 sec, biodegradable crosslinked scaffolds were obtained. Scaffold degradation as evaluated by soaking crosslinked collagen scaffolds in PBS at 37 degrees C, indicated a mass loss of 47.7 +/- 7.4% and 68.9 +/- 24.7% at day 7 and day 15, respectively. However, these scaffolds retained fibrous architecture for at least 21 days under physiological conditions. Neural stem cell line, C17.2, cultured on crosslinked collagen scaffolds proliferated after 7 days by forming a confluent layer of cells with extensive cellular projections that were indicative of neurite outgrowth. Taken together, these findings support the potential of acetic acid-electrospun photochemical crosslinked collagen nanofibers for neural tissue engineering.

Solution state structures of human pancreatic amylin and pramlintide

We have employed pramlintide (prAM) as a surrogate for hAM in CD and NMR studies of the conformational preferences of the N-terminal portion of the structure in media which do not provide long-lived monomeric solutions of hAM due to its rapid conversion to preamyloid beta aggregate states. Direct comparison of hAM and prAM could be made under helix-formation-favoring conditions. On the basis of CD and NMR studies: (i) the Cys(2)-Cys(7) loop conformation has a short-span of helix (Ala(5)-Cys(7)); (ii) the extent to which this helix propagates further into the sequence is medium-dependent; a helix from Ala(5) through Ser(20) (with end fraying from His(18) onward) is observed in aqueous fluoroalcohol media; (iii) in 12+ vol.% HFIP, the amyloidogenic region of hAM forms a second helical domain (Phe(23)-Ser(29)); (iv) the two helical regions of hAM do not have any specific geometric relationship as they are connected by a flexible loop that takes different conformations and (v) although the extreme C-terminus is essential for bioactivity, it is found to be extensively randomized with conformer interconversions occurring at a much faster rate than that is observed in the remainder of the peptide sequence. Two NMR-derived structures of the 1-22 sequence fragment of hAM have been derived. The work also serves to illustrate improved methods for the NMR characterization of helices. A detailed quantitative analysis of the NOE intensities observed in aqueous HFIP revealed alternative conformations in the C-terminal portion of the common amylin helix, a region that is known to be involved in the biorecognition phenomena leading to amyloidogenesis. Even though the SNN sequence appears to be a flexible loop, the chemical shifts (and changes induced upon helix structuring) suggest some interactions between the loop and the amyloidogenic segment of hAM that occur on partial helix formation.

Effect of detergents and hexafluoroisopropanol on the conformation of a non-helical and a helical plant protease inhibitor

We have earlier reported the purification of a non-helical proteinase inhibitor from Cajanus cajan and a helical proteinase/amylase inhibitor from Phaseolus aureus. The effect of detergents, viz. sodium dodecyl sulfate (SDS), sodium deoxycholate (DOC) and 3-[(3-cholamidopropy) dimethylammonio]-1-propane sulfonate (CHAPS) and hexafluoroisopropanol on the conformation of these proteinaceous inhibitors was investigated using circular dichroism spectroscopy. The present report focuses on changes in the polypeptide backbone conformation with respect to induction of helical structure. SDS causes minimal changes in the tertiary as well as secondary structure of C. cajan proteinase inhibitor. In the presence of anionic bile salt, deoxycholate, minor changes in the far-UV CD spectrum were accompanied by loss in inhibitory activity while CHAPS did not affect the inhibitor function. As judged from the changes in circular dichroic curves ([Theta](MRW) at 208 and 222 nm), the primarily disorganized polypeptide chain of C. cajan proteinase inhibitor was converted by 3,3,3,3',3',3'-hexafluoro-2-propanol (HFIP) into helical conformation. The P. aureus inhibitor showed increased helicity in the presence of SDS ([Theta](MRW) at 208 nm) as well as sodium deoxycholate and CHAPS ([Theta](MRW) at 222 nm). Fluorescence measurements show slight alterations in the emission intensities. HFIP caused a cooperative increase in alpha-helical secondary structure in the P. aureus inhibitor.

Characterization of a common intermediate of pea lectin in the folding pathway induced by TFE and HFIP

When pea lectin was exposed to a low pH range, it was found that the secondary structure of the lectin resisted conformational changes to a large extent up to pH 2.4 and below this pH, a sharp transition was observed which could be due to the presence of 27 acidic amino acid residues present in the protein. The effects of 1,1,1,3,3,3 hexafluoro-isopropanol (HFIP) and 2,2,2-Trifluoroethanol (TFE) on the conformation of pea lectin at pH 2.4 were studied using circular dichroism and fluorescence spectroscopy. Analysis varying the TFE concentration showed that up to 80% TFE (v/v) protein retained the residual beta-structure accompanied by a loss in tertiary structure. A similar conformation is presumed to exist at 4% HFIP (v/v), with an increase in HFIP concentration structural rearrangements occurred and a transition from beta-structure to alpha-helical structure started from 12% HFIP which completed at 30% HFIP. Our studies show the occurrence of a common intermediate in the folding pathway of pea lectin induced by two different fluoroalcohols, which differ in their mode of action to stabilize the secondary structure of a given protein. While TFE was not found to induce any alpha-helical structure, HFIP caused the transition of pea lectin, which is predominantly a beta-sheet protein, to a structure rich in alpha-helical contacts. Thus, our results also point out the possibility of a non-hierarchical model of protein folding in lectins.

Synchrotron radiation circular dichroism spectroscopy applied to metmyoglobin and a 4-?-helix bundle carboprotein

The novel technique, synchrotron radiation-based circular dichroism (SR-CD), has been applied to the study of metmyoglobin and a carboprotein (carbohydrate-based peptide with protein tertiary structure) with 4-alpha-helix bundle structure, as well as a carbopeptide (carbohydrate-based peptide) with a truncated peptide sequence. The use of synchroton radiation (SR) enabled circular dichroism (CD) measurements in the vacuum ultraviolet (VUV) down to 168 nm in D(2)O and 160 nm in 2,2,2-trifluoroethanol (TFE). The band shape in the CD spectra in the low wavelength region was studied, comparing samples with two types of alpha-helical tertiary structure, namely the globin fold and the 4-alpha-helix bundle motif. No significant differences were found between the CD spectra of the alpha-helical samples (metmyoglobin and carboprotein) in D(2)O solution. The use of 2,2,2-TFE (TFE) as solvent clearly alters the VUV CD but the two samples have very similar CD spectra. The solvent-induced denaturing of metmyoglobin in TFE was observed using absorption and CD spectroscopy of the Soret band, with results indicating heme release. The VUV spectrum of TFE-denatured metmyoglobin exhibits dramatic differences in comparison with previous studies of the native enzyme in aqueous solution. The implications of this observation are discussed.

Characterization of a partially folded intermediate of papain induced by fluorinated alcohols at low pH

A systematic investigation of the effects of aqueous 1,1,1,3,3,3-hexafluoroisopropanol (HFIP) and 2,2,2-trifluoroethanol (TFE) on the structure of acid-unfolded papain (EC. 3.4.22.2) was made using circular dichroism (CD), intrinsic tryptophan fluorescence, and 1-anilino 8-sulfonic acid (ANS) binding. At pH 2, papain exhibits substantial secondary structure as beta-sheet and is relatively less denatured as compared to 6 M guanidine hydrochloride (GdnHCl) but loses the persistent tertiary structure of the native state. Addition of HFIP and TFE caused an induction of alpha-helical structure as evident from the increase in the mean residue ellipticity value at 208 and 222 nm. Induction was 20% more in HFIP than TFE. Interestingly, at 13% (v/v) HFIP and 30% (v/v) TFE a near-UV CD spectrum approaches the native-like spectral features. Tryptophan fluorescence studies indicate the change in the environment of the tryptophan residues on the addition of HFIP and TFE to acid-unfolded papain. Maximum ANS binding occurs at 13% (v/v) HFIP and 30% (v/v) TFE, suggesting a compact "molten globule"-like conformation with enhanced exposure of hydrophobic surface area. Acid-unfolded papain in presence of 13% (v/v) HFIP and 30% (v/v) TFE showed the recovery of enzymatic activity by 54 and 61%, respectively. Thermal stability of these states was assessed by changes in fluorescence emission maximum and absorbance at 292 nm. Temperature-induced unfolding of papain at pH 2 was non-cooperative and the transition curves were biphasic in nature. Temperature-induced unfolding of HFIP and TFE-induced state was weakly cooperative in comparison to cooperative transition of native.

Fluoroalcohol-induced stabilization of the α-helical intermediates of lentil lectin: implication for non-hierarchical lectin folding

An intermediate state of lentil lectin was characterized at pH 1 having low content of secondary as well as tertiary structure. Far- and near-UV CD spectroscopy showed loss of structure when pH was lowered from 7 to 0.8 but the structure loss was less than that of the protein in presence of 6M GndHCl. Intrinsic tryptophan fluorescence studies, ANS binding, and acrylamide quenching experiments supported the existence of the intermediate at low pH. The unfolding process of lentil lectin at pH 1 was also studied by GndHCl denaturation monitored by intrinsic fluorescence spectroscopy. The non-cooperative unfolding at pH 1, in contrast to cooperative unfolding of the native protein further confirmed the presence of loose tertiary structure. The unfolded structure of the lectin at pH 1 was also shown by limited tryptic digestion studies. Further studies were performed on this intermediate state of lentil lectin obtained at low pH in presence of fluoroalcohols 2,2,2-trifluoroethanol (TFE) and 1,1,1,3,3,3-hexafluoroisopropanol (HFIP). Lentil lectin is mainly a beta-sheet protein, and both TFE and HFIP stabilized the acid unfolded structure by inducing alpha-helical contacts. Interestingly, it was observed that induction of the non-native structure resulted in regain of protein activity to some extent. At pH 1, loss in activity was found with both dextran and bromelain while the reported intermediate at the given pH was found to regain activity with bromelain in presence of HFIP and TFE. HFIP induced more structure as compared to TFE and hence a greater regain in activity of about 30% was observed with HFIP as compared to a 15% regain with TFE. Activity with dextran in presence of fluoroalcohols could not be determined as turbidity developed in the corresponding blank preparations. Our results presented here point out the possibility of the formation of a helical structure preceding the formation of the native beta-sheet structure and thus support the non-hierarchical model of protein folding for lentil lectin.

1,1,1,3,3,3-hexafluoroisopropanol induced thermal unfolding and molten globule state of bovine α-lactalbumin: Calorimetric and spectroscopic studies

The thermal denaturation of alpha-lactalbumin was studied at pH 7.0 and 9.0 in aqueous 1,1,1,3,3,3-hexafluoroisopropanol (HFIP) by high-sensitivity differential scanning calorimetry. The conformation of the protein was analyzed by a combination of fluorescence and circular dichroism measurements. The most obvious effect of HFIP was lowering of the transition temperature with an increase in the concentration of the alcohol up to 0.30M, beyond which no calorimetric transition was observed. Up to 0.30M HFIP the calorimetric and van't Hoff enthalpy remained the same, indicating the validity of the two-state approximation for the thermal unfolding of alpha-lactalbumin. The quantitative thermodynamic parameters accompanying the thermal transitions have been evaluated. Spectroscopic observations confirm that alpha-lactalbumin is in the molten globule state in the presence of 0.50M HFIP at pH 7.0 and 0.75M HFIP at pH 9.0. The results also demonstrate that alpha-lactalbumin in the molten globule state undergoes a noncooperative thermal transition to the denatured state. It is observed that two of four tryptophans are exposed to the solvent in the HFIP induced molten globule state of alpha-lactalbumin compared to four in the 8.5M urea induced denatured state of the protein. It is also observed that the HFIP induced molten globule states at the two pH values are different from the acid induced molten globule state (A state) of alpha-lactalbumin.

Alcohol and temperature induced conformational transitions in ervatamin B: sequential unfolding of domains

The structural aspects of ervatamin B have been studied in different types of alcohol. This alcohol did not affect the structure or activity of ervatamin B under neutral conditions. At a low pH (3.0), different kinds of alcohol have different effects. Interestingly, at a certain concentration of non-fluorinated, aliphatic, monohydric alcohol, a conformational switch from the predominantly alpha-helical to beta-sheeted state is observed with a complete loss of tertiary structure and proteolytic activity. This is contrary to the observation that alcohol induces mostly the alpha-helical structure in proteins. The O-state of ervatamin B in 50% methanol at pH 3.0 has enhanced the stability towards GuHCl denaturation and shows a biphasic transition. This suggests the presence of two structural parts with different stabilities that unfold in steps. The thermal unfolding of ervatamin B in the O-state is also biphasic, which confirms the presence of two domains in the enzyme structure that unfold sequentially. The differential stabilization of the structural parts may also be a reflection of the differential stabilization of local conformations in methanol. Thermal unfolding of ervatamin B in the absence of alcohol is cooperative, both at neutral and low pH, and can be fitted to a two state model. However, at pH 2.0 the calorimetric profiles show two peaks, which indicates the presence of two structural domains in the enzyme with different thermal stabilities that are denatured more or less independently. With an increase in pH to 3.0 and 4.0, the shape of the DSC profiles change, and the two peaks converge to a predominant single peak. However, the ratio of van't Hoff enthalpy to calorimetric enthalpy is approximated to 2.0, indicating non-cooperativity in thermal unfolding.

Structural characterization of non-native states of sperm whale myoglobin in aqueous ethanol or 2,2,2-trifluoroethanol media

The effects of aqueous ethanol or 2,2,2-trifluoroethanol media on the structure of sperm whale myoglobin have been investigated by absorption, CD, and NMR spectra. The structural properties of myoglobin such as heme environments, helix contents, protein folding, and interactions between heme and the protein moiety have been sharply manifested in these spectra. The characterization demonstrated that alcohol-induced conformational change of myoglobin depends on the nature of alcohol and its concentration. It was shown for the first time that, upon the alcohol-induced denaturation of myoglobin, heme is released from partially denatured protein of which helix contents is altered by only about 20% relative to that of native state. Myoglobin has shown to unfold and refold reversibly by controlling the alcohol concentration. Novel methods for the preparation of apomyoglobin and in situ reconstitution of apomyoglobin with heme, based on the alcohol-induced denaturation of the protein, were presented.

Identification and characterization of hydrophobic Escherichia coli virulence proteins by liquid chromatography-electrospray ionization mass spectrometry

Virulence of enterotoxicogenic Escherichia coli is mediated by rodlike, rigid, highly hydrophobic proteins designated fimbriae or colonization factors (CFs). More than 20 different colonization factors have been described so far using predominantly immunological and genetic methods. To characterize these hydrophobic proteins by liquid chromatography-mass spectrometry (LC-MS), different methodologies were explored. A novel LC-MS method was developed using hexafluoroisopropanol to maintain the hydrophobic proteins in solution. In addition, these proteins were digested with cyanogen bromide and peptide mapping by LC-MS was established. This technique was particularly useful in identification of closely related CFs. Both LC-MS and peptide mapping methodologies were found to be useful in characterizing highly hydrophobic CFs of E. coli. To search for molecular weights of mature proteins in the National Center for Biotechnology Information (NCBI) database, a new feature was developed and its applicability tested. The identification of a class of pathogenic virulence proteins, either intact or digested, is possible with molecular weight database searching.

Reactivation and refolding of rabbit muscle creatine kinase denatured in 2,2,2-trifluoroethanol solutions

The unfolding and refolding of creatine kinase (ATP:creatine N-phosphotransferase (CK), EC 2.7.3.2) during denaturation and reactivation by trifluoroethanol (TFE) have been studied. Significant aggregation was observed when CK was denatured at TFE concentrations between 10% and 40% (v/v). 50% TFE (v/v) was used to study the denaturation and unfolding of CK. The activity loss of CK was a very quick process, as was the marked conformational changes during denaturation followed by fluorescence emission spectra and far-ultraviolet CD spectra. DTNB modification and size exclusion chromatography were used to find that CK dissociated and was in its monomer state after denaturation with 50% TFE. Reactivation and refolding were observed after 80-fold dilution of the denatured CK into 0.05 M Tris-HCl buffer, pH 8.0. The denatured CK recovered about 38% activity following a two phase course (k(1)=4.82+/-0.41x10(-3) s(-1), k(2)=0.60+/-0.01x10(-3) s(-1)). Intrinsic fluorescence maximum intensity changes showed that the refolding process also followed biphasic kinetics (k(1)=4.34+/-0.27x10(-3) s(-1), k(2)=0.76+/-0.02x10(-3) s(-1)) after dilution into the proper solutions. The far-ultraviolet CD spectra ellipticity changes at 222 nm during the refolding process also showed a two phase course (k(1)=4.50+/-0.07x10(-3) s(-1), k(2)=1.13+/-0.05x10(-3) s(-1)). Our results suggest that TFE can be used as a reversible denaturant like urea and GuHCl. The 50% TFE induced CK denaturation state, which was referred to as the 'TFE state', and the partially refolded CK are compared with the molten globule state. The aggregation caused by TFE during denaturation is also discussed in this paper.

Fluorinated alcohol, the third group of cosolvents that stabilize the molten-globule state relative to a highly denatured state of cytochrome c

The effects of 1,1,1,3,3,3-hexafluoro-isopropanol (HFIP) on the conformation of cytochrome c (cyt c) at pH 1.9 were studied using a combination of spectroscopic and physical methods. Analysis varying the HFIP concentration showed that a compact denatured conformation (M(HF)) accumulates in a low concentration range of HFIP in the middle of structural transition from the highly unstructured acid-denatured state to the highly helical alcohol-denatured state of cyt c. This contrasts clearly with the effect of isopropanol (IP), in which no compact conformation accompanied with the transition. Analysis varying concentrations of HFIP and NaCl concurrently showed that the M(HF) state of cyt c is essentially identical to the salt-induced molten-globule (M(G)) state, and the M(G) state in the presence of salt was also stabilized by a low concentration of HFIP. Furthermore, 2,2,2-trifluoroethanol stabilized M(HF) similarly to HFIP, supporting the proposition that the specific effect observed for HFIP is caused by fluorination of alcohol. The mechanism stabilizing compact conformation by HFIP remains unclear, but is probably distinct from that of salts and polyols, which are also known to stabilize the M(G)-like state.

Formation of a molten-globule-like state of cytochrome c induced by high concentrations of glycerol

The effect of glycerol on the structure of cytochrome c was investigated by circular dichroism, absorbance and EPR spectroscopy. The results obtained show that an increasing concentration of the organic solvent (70-99.2%, v/v) in aqueous-polyalcohol mixtures converts native cytochrome c into a new, low spin form through a fully reversible, two-state transition. The glycerol-stabilized form (that we call here the G state) retains native-like amounts of alpha-helix structure while rigid tertiary structure and native Fe(III)-Met(80) axial bond are lost. Analysis of data suggests a molten globule character of the G state; support to this view is afforded by the striking similarities between the spectroscopic (and, thus, structural) properties of the G state with those of the acidic molten globule of the protein (A state).

Molecular simulation of the effects of alcohols on peptide structure

The effects of alcohols on local protein structure have been simulated using computational approaches and model peptides. Molecular simulations were carried out on a 7-residue peptide created in both an extended conformation and an alpha-helix to explore alcohol-induced changes in peptide structure. It was assumed that alcohols hydrogen bond at peptide carbonyl groups with an optimum geometry and compete with water molecules at these site. Energy minimization of the peptide/alcohol assemblies revealed that alcohols induced a twist in the peptide backbone as a function of (1) the methylene chain length, (2) the hydrogen-bond geometry, (3) halogenation of the molecule, (4) concentration, and (5) the dielectric constant. The rank ordering of the potencies of the alcohols was hexafluoroisopropanol > trifluoroethanol approximately pentanol > butanol > ethanol > methanol. Helix destabilization by cosolvent was measured by examining the hydrogen-bond lengths in peptide structures that resulted from a combination of energy minimization and molecular dynamics simulations. Destabilization was also found to be dependent upon the chemical nature of the alcohol and the hydrogen-bond geometry. The data suggest that alcohols at low concentrations affect protein structure mainly through a combination of hydrogen-bonding and hydrophobic interactions that are influenced by the properties of the solvent.

Trifluoroethanol-induced conformational transitions of proteins: insights gained from the differences between alpha-lactalbumin and ribonuclease A

The trifluoroethanol (TFE)-induced structural changes of two proteins widely used in folding experiments, bovine alpha-lactalbumin, and bovine pancreatic ribonuclease A, have been investigated. The experiments were performed using circular dichroism spectroscopy in the far- and near-UV region to monitor changes in the secondary and tertiary structures, respectively, and dynamic light scattering to measure the hydrodynamic dimensions and the intermolecular interactions of the proteins in different conformational states. Both proteins behave rather differently under the influence of TFE: alpha-lactalbumin exhibits a molten globule state at low TFE concentrations before it reaches the so-called TFE state, whereas ribonuclease A is directly transformed into the TFE state at TFE concentrations above 40% (v/v). The properties of the TFE-induced states are compared with those of equilibrium and kinetic intermediate states known from previous work to rationalize the use of TFE in yielding information about the folding of proteins. Additionally, we report on the properties of TFE/water and TFE/buffer mixtures derived from dynamic light scattering investigations under conditions used in our experiments.

Trifluoroethanol stabilizes the pH 4 folding intermediate of sperm whale apomyoglobin

2,2,2-Trifluoroethanol (TFE) is known to stabilize peptide helices by strengthening hydrogen bonds. On the other hand, TFE destabilizes native proteins, as we confirm here, presumably by weakening the hydrophobic interaction. The stability of the pH 4 folding intermediate of apomyoglobin is known to depend both on the strength of the individual A, G, and H helices and on hydrophobic interactions between helices. We ask which effect of TFE dominates in this case: strengthening helices or weakening hydrophobic interactions between helices? Protein stability is measured by denaturant-induced unfolding curves, and two-state unfolding is tested by monitoring both far-UV CD and tryptophan fluorescence emission. Low concentrations of TFE strongly stabilize the pH 4 folding intermediate. Moreover, low concentrations of TFE compensate for helix-destabilizing mutations in the A and G helices. Consequently, enhancing helix propensity, rather than weakening the hydrophobic interaction, is the dominant effect of TFE on the folding intermediate. This result agrees with earlier mutational evidence that helix propensities are very important in determining the stability of the pH 4 intermediate. Although TFE destabilizes native holomyoglobin, as well as native lysozyme and ribonuclease A, nevertheless, TFE stabilizes native apomyoglobin.