Proteins in Wonderland: The Magical World of Pressure.

Admitting the "Native", "Unfolded" and "Fibril" states as the three basic generic states of proteins in nature, each of which is characterized with its partial molar volume, here we predict that the interconversion among these generic states N, U, F may be performed simply by making a temporal excursion into the so called "the high-pressure regime", created artificially by putting the system under sufficiently high hydrostatic pressure, where we convert N to U and F to U, and then back to "the low-pressure regime" (the "Anfinsen regime"), where we convert U back to N (U→N). Provided that the solution conditions (temperature, pH, etc.) remain largely the same, the idea provides a general method for choosing N, U, or F of a protein, to a great extent at will, assisted by the proper use of the external perturbation pressure. A successful experiment is demonstrated for the case of hen lysozyme, for which the amyloid fibril state F prepared at 1 bar is turned almost fully back into its original native state N at 1 bar by going through the "the high-pressure regime". The outstanding simplicity and effectiveness of pressure in controlling the conformational state of a protein are expected to have a wide variety of applications both in basic and applied bioscience in the future.

Teriparatide Improves Bone and Lipid Metabolism in a Male Rat Model of Type 2 Diabetes Mellitus.

Osteoporosis is a complication of diabetes mellitus (DM). The pathology of diabetic osteoporosis is distinct from postmenopausal osteoporosis, and there are no specific treatment guidelines for diabetic osteoporosis. In the current study, this issue was addressed by evaluating the effect of osteoporosis medications, such as the anabolic agent PTH [teriparatide (TPTD)] and the antiresorptive agents calcitonin [elcatonin (ECT)] and bisphosphonate [risedronate (RIS)], on bone metabolism as well as on glucose and lipid metabolism in spontaneously diabetic Torii (SDT) fatty rats, which are a model of type 2 DM (T2DM). The medicines were injected subcutaneously into 8-week-old male SDT fatty rats three times weekly for 8 weeks. TPTD treatment in SDT fatty rats increased the osteoblast number and function on trabecular bone in vertebrae, and increased the trabecular bone mass, bone mineral density (BMD), and mechanical strength of vertebrae. Additionally, TPTD improved cortical bone structure and increased BMD. RIS decreased the osteoclast number and function, which led to an increase in vertebral bone mineral content and BMD in the femoral diaphysis, and mechanical strength was increased in the vertebrae. ECT showed no clear effects on bone mass or metabolism. Similar to diabetic lesions, all of the drugs had no effects on hyperglycemia, pancreas morphology, or serum insulin and glucagon levels. However, triglyceride levels and lipid droplets in fatty liver were decreased in the TPTD group. These results suggest that TPTD may be useful for treating fatty liver in addition to osteoporosis in T2DM.

Conformational Properties Relevant to the Amyloidogenicity of ß2-Microglobulin Analyzed Using Pressure- and Salt-Dependent Chemical Shift Data.

ß2-Microglobulin (ß2m) is associated with dialysis-related amyloidosis. In vitro experiments have shown that ß2m forms amyloid fibrils at acidic pHs in the presence of moderate concentrations of salt. Previous studies suggested that acid-denatured ß2m has a hydrophobic residual structure, and the exposure of the hydrophobic residues enhances the association with seeds or other ß2m monomers. However, the nature of the residual structure relevant to its amyloidogenicity remains to be investigated. To understand the structural properties of acid-denatured ß2m and the role of salt, we investigated pressure- and salt concentration-dependent conformational changes by nuclear magnetic resonance spectroscopy and other methods. Here, pressure was utilized to characterize the conformers existing in a conformational equilibrium at ambient pressure. The obtained pressure- and salt concentration-dependent chemical shift data were simultaneously subjected to principal component analysis to characterize individual conformational change events. Unexpectedly, the addition of salt induced an expansion of the ß2m molecule, which likely resulted from the exclusion of the N-terminal region from the hydrophobic cluster region. The dissected chemical shift patterns for the salt-induced conformational change and other experimental data indicated that this conformational change caused a rigidification in the intrinsic hydrophobic cluster, leading to the observed amyloidogenicity.

Endogenous calcitonin regulates lipid and glucose metabolism in diet-induced obesity mice.

Calcitonin (CT) plays an important role in calcium homeostasis, and its precursor, proCT, is positively associated with the body mass index in the general human population. However, the physiological role of endogenous CT in the regulation of metabolism remains unclear. Knockout mice with gene-targeted deletion of exon 4 of Calca (CT KO) were generated by targeted modification in embryonic stem cells. Male mice were used in all experiments and were fed a slightly higher fat diet than the standard diet. The CT KO mice did not exhibit any abnormal findings in appearance, but exhibited weight loss from 15 months old, i.e., significantly decreased liver, adipose tissue, and kidney weights, compared with wild-type control mice. Furthermore, CT KO mice exhibited significantly decreased fat contents in the liver, lipid droplets in adipose tissues, serum glucose, and lipid levels, and significantly increased insulin sensitivity and serum adiponectin levels. CT significantly promoted 3T3-L1 adipocyte differentiation and suppressed adiponectin release. These results suggested that CT gene deletion prevents obesity, hyperglycemia, and hyperlipidemia in aged male mice. This is the first definitive evidence that CT may contribute to glucose and lipid metabolism in aged male mice, possibly via decreased adiponectin secretion from adipocytes.

Direct high-pressure NMR observation of dipicolinic acid leaking from bacterial spore: A crucial step for thermal inactivation.

A bacterial spore protects itself with an unusually high concentration (~10% in dry weight of spore) of dipicolinic acid (DPA), the release of which is considered the crucial step for inactivating it under mild pressure and temperature conditions. However, the process of how the spore releases DPA in response to pressure remains obscure. Here we apply 1H high-resolution high-pressure NMR spectroscopy, for the first time, to the spore suspension of Bacillus subtilis natto and monitor directly and in real-time the leaking process of DPA in response to pressure of 200MPa at 20°C. We find that about one third of the total DPA leaks immediately upon applying pressure, but that the rest leaks slowly in hrs upon decreasing the pressure. Once DPA is fully released from the spore, the proteins of the spore become easily denatured at a mild temperature, e.g., 80°C, much below the temperature commonly used to inactivate spores (121°C). The success of the present experiment opens a new avenue for studying bacterial spores and cells at the molecular level in response to pressure, temperature and other perturbations.

Locomotive syndrome is associated with body composition and cardiometabolic disorders in elderly Japanese women.

BACKGROUND: A concept referred to as locomotive syndrome (LS) was proposed by the Japanese Orthopaedic Association in order to help identify middle-aged and older adults who may be at high risk of requiring healthcare services because of problems associated with locomotion. Cardiometabolic disorders, including obesity, hypertension, diabetes, and dyslipidemia, have a high prevalence worldwide. The purpose of this study was to determine the associations between LS and both body composition and cardiometabolic disorders. METHODS: The study participants were 165 healthy adult Japanese women volunteers living in rural areas. LS was defined as a score ≥16 on the 25-question Geriatric Locomotive Function Scale (GLFS-25). Height, body weight, body fat percentage, body mass index (BMI), and bone status were measured. Bone status was evaluated by quantitative ultrasound (i.e., the speed of sound [SOS] of the calcaneus) and was expressed as the percent of Young Adult Mean of the SOS (%YAM). Comorbid conditions of hypertension, hyperlipidemia, and diabetes were assessed using self-report questionnaires. RESULTS: Twenty-nine participants (17.6 %) were classed as having LS. The LS group was older, shorter, and had a higher body fat percentage, a higher BMI, and lower bone status than the non-LS group. Multiple logistic regression analysis showed that participants with a BMI ≥23.5 kg/m2 had a significantly higher risk for LS than those with a BMI <23.5 kg/m2 (odds ratio [OR] = 3.78, p < 0.01). Furthermore, GLFS-25 scores were higher in participants with than those without hypertension, diabetes, or obesity, and significantly increased with the number of present disorders. CONCLUSIONS: These findings suggest that BMI may be a useful screening tool for LS. Furthermore, because hypertension and diabetes were associated with LS, the prevention of these disorders accompanied by weight management may help protect against LS.

Sequential backbone resonance assignments of the E. coli dihydrofolate reductase Gly67Val mutant: folate complex.

Occasionally, a mutation in an exposed loop region causes a significant change in protein function and/or stability. A single mutation Gly67Val of E. coli dihydrofolate reductase (DHFR) in the exposed CD loop is such an example. We have carried out the chemical shift assignments for H(N), N(H), C(α) and C(ß) atoms of the Gly67Val mutant of E. coli DHFR complexed with folate at pH 7.0, 35 °C, and then evaluated the H(N), N(H), C(α) and C(ß) chemical shift changes caused by the mutation. The result indicates that, while the overall secondary structure remains the same, the single mutation Gly67Val causes site-specific conformational changes of the polypeptide backbone restricted around the adenosine-binding subdomain (residues 38-88) and not in the distant catalytic domain.

Functional conformer of c-Myb DNA-binding domain revealed by variable temperature studies.

The conformational fluctuation in the minimum DNA-binding domain of c-Myb, repeats 2 and 3 (R2R3), was studied under closely physiological conditions. A global unfolding transition, involving both the main chain and the side chains, was found to take place at the approximate temperature range 30-70 °C, with a transition temperature of approximately 50 °C. In addition, the observation of simultaneous shift change and broadening of NMR signals in both (1)H one-dimensional and (15)N/(1)H two-dimensional NMR spectra indicated the occurrence of locally fluctuating state at physiological temperature. In the wild-type protein containing a cavity in R2, the local fluctuation of R2 is more prominent than that of R3, whereas it is suppressed in the cavity-filled mutant, V103L. This indicates that the cavity in R2 contributes significantly to the conformational instability and the transition into the locally fluctuating state. For the wild-type R2R3 protein, the more dynamic conformer is estimated to be present to some extent at 37 °C and is likely beneficial for its biological function: DNA-binding. This result is in agreement with the concept of an excited-state conformer that exists in equilibrium with the dominant ground-state conformer and acts as the functional conformer of the protein. From the findings of the present study, it appears that the tandem repeats of two small domains with no disulfide bonds and with a destabilizing cavity function as the evolutionary strategy of the wide-type c-Myb DNA-binding domain to produce an appropriate fraction of the locally fluctuating state at 37 °C, which is more amenable to DNA-binding. Database: Chemical shifts and peak lists have been deposited in the Biological Magnetic Resonance Bank under entries 11584 and 11585.

High-Pressure Fluorescence Spectroscopy.

The combination of fluorescence and pressure perturbation is a widely used technique to study the effect of pressure on a protein system to obtain thermodynamic, structural and kinetic information on proteins. However, we often encounter the situation where the available pressure range up to 400 MPa of most commercial high-pressure fluorescence spectrometers is insufficient for studying highly pressure-stable proteins like inhibitors and allergenic proteins. To overcome the difficulty, we have recently developed a new high-pressure fluorescence system that allows fluorescence measurements up to 700 MPa. Here we describe the basic design of the apparatus and its application to study structural and thermodynamic properties of a couple of highly stable allergenic proteins, hen lysozyme and ovomucoid, using Tryptophan and Tyrosine/Tyrosinate fluorescence, respectively. Finally, we discuss the utility and the limitation of Trp and Tyr fluorescence. We discuss pitfalls of fluorescence technique and importance of simultaneous use of other high-pressure spectroscopy, particularly high-pressure NMR spectroscopy.

Cavity as a source of conformational fluctuation and high-energy state: high-pressure NMR study of a cavity-enlarged mutant of T4 lysozyme.

Although the structure, function, conformational dynamics, and controlled thermodynamics of proteins are manifested by their corresponding amino acid sequences, the natural rules for molecular design and their corresponding interplay remain obscure. In this study, we focused on the role of internal cavities of proteins in conformational dynamics. We investigated the pressure-induced responses from the cavity-enlarged L99A mutant of T4 lysozyme, using high-pressure NMR spectroscopy. The signal intensities of the methyl groups in the (1)H/(13)C heteronuclear single quantum correlation spectra, particularly those around the enlarged cavity, decreased with the increasing pressure, and disappeared at 200 MPa, without the appearance of new resonances, thus indicating the presence of heterogeneous conformations around the cavity within the ground state ensemble. Above 200 MPa, the signal intensities of >20 methyl groups gradually decreased with the increasing pressure, without the appearance of new resonances. Interestingly, these residues closely matched those sensing a large conformational change between the ground- and high-energy states, at atmospheric pressure. (13)C and (1)H NMR line-shape simulations showed that the pressure-induced loss in the peak intensity could be explained by the increase in the high-energy state population. In this high-energy state, the aromatic side chain of F114 gets flipped into the enlarged cavity. The accommodation of the phenylalanine ring into the efficiently packed cavity may decrease the partial molar volume of the high-energy state, relative to the ground state. We suggest that the enlarged cavity is involved in the conformational transition to high-energy states and in the volume fluctuation of the ground state.

Pressure-assisted dissociation and degradation of "proteinase K-resistant" fibrils prepared by seeding with scrapie-infected hamster prion protein.

The crucial step for the fatal neurodegenerative prion diseases involves the conversion of a normal cellular protein, PrP(C), into a fibrous pathogenic form, PrP(Sc), which has an unusual stability against heat and resistance against proteinase K digestion. A successful challenge to reverse the reaction from PrP(Sc) into PrP(C) is considered valuable, as it would give a key to dissolving the complex molecular events into thermodynamic and kinetic analyses and may also provide a means to prevent the formation of PrP(Sc) from PrP(C) eventually in vivo. Here we show that, by applying pressures at kbar range, the "proteinase K-resistant" fibrils (rHaPrP(res)) prepared from hamster prion protein (rHaPrP [23-231]) by seeding with brain homogenate of scrapie-infected hamster, becomes easily digestible. The result is consistent with the notion that rHaPrP(res) fibrils are dissociated into rHaPrP monomers under pressure and that the formation of PrP(Sc) from PrP(C) is thermodynamically controlled. Moreover, the efficient degradation of prion fibrils under pressure provides a novel means of eliminating infectious PrP(Sc) from various systems of pathogenic concern.

3,4-Dihydroxybenzaldehyde Derived from Prunus mume Seed Inhibits Oxidative Stress and Enhances Estradiol Secretion in Human Ovarian Granulosa Tumor Cells.

Granulosa cells form ovarian follicles and play important roles in the growth and maturation of oocytes. The protection of granulosa cells from cellular injury caused by oxidative stress is an effective therapy for female infertility. We here investigated an effective bioactive compound derived from Prunus mume seed extract that protects granulosa cells from hydrogen peroxide (H2O2)-induced apoptosis. We detected the bioactive compound, 3,4-dihydroxybenzaldehyde (3,4-DHBA), via bioactivity-guided isolation and found that it inhibited the H2O2-induced apoptosis of granulosa cells. We also showed that 3,4-DHBA promoted estradiol secretion in granulosa cells and enhanced the mRNA expression levels of steroidogenic factor 1, a promoter of key steroidogenic enzymes. These results suggest that P. mume seed extract may have clinical potential for the prevention and treatment of female infertility.

Tyrosine/tyrosinate fluorescence at 700 MPa: a pressure unfolding study of chicken ovomucoid at pH 12.

The utility of tyrosine/tyrosinate fluorescence for pressure-unfolding studies of Trp-lacking proteins has been explored for the first time, with chicken ovomucoid (OVM) as target. A newly developed fluorescence spectrometer working in the range 0.1-700 MPa is employed for this purpose. At 25 °C at pH 12, all six Tyr residues give tyrosine emission at 306 nm, implying that all five Tyr residues are well buried at pH 12 in the folded OVM, except one giving "half-tyrosinate" emission at 325 nm. Upon increasing pressure, however, a distinct intermediate state, in which domains 1 and 2 are selectively unfolded, appears and increases up to 700 MPa. Extrapolated to 0.1 MPa, this intermediate lies 8.8±2.6 kJ mol(-1) above the native state, characterized with a partial molar volume smaller by -28.9±7.4 ml mol(-1). At 5 °C at 700 MPa, even domain 3 gives a sign of cold denaturation.

A delicate interplay of structure, dynamics, and thermodynamics for function: a high pressure NMR study of outer surface protein A.

Outer surface protein A (OspA) is a crucial protein in the infection of Borrelia burgdorferi causing Lyme disease. We studied conformational fluctuations of OspA with high-pressure (15)N/(1)H two-dimensional NMR along with high-pressure fluorescence spectroscopy. We found evidence within folded, native OspA for rapid local fluctuations of the polypeptide backbone in the nonglobular single layer ß-sheet connecting the N- and C-terminal domains with τ << ms, which may give the two domains certain independence in mobility and thermodynamic stability. Furthermore, we found that folded, native OspA is in equilibrium (τ >> ms) with a minor conformer I, which is almost fully disordered and hydrated for the entire C-terminal part of the polypeptide chain from ß8 to the C-terminus. Conformer I is characterized with ΔG(0) = 32 ± 9 kJ/mol and ΔV(0) = -140 ± 40 mL/mol, populating only ∼0.001% at 40°C at 0.1 MPa, pH 5.9. Because in the folded conformer the receptor binding epitope of OspA is buried in the C-terminal domain, its transition into conformer I under in vivo conditions may be critical for the infection of B. burgdorferi. The formation and stability of the peculiar conformer I are apparently supported by a large packing defect or cavity located in the C-terminal domain.

Extensively hydrated but folded: a novel state of globular proteins stabilized at high pressure and low temperature.

We studied conformational fluctuations of the transcription factor c-Myb R2 subdomain (52 residues with three Trp) at high pressure and low temperature (5°C) using two different spectroscopic methods, Trp fluorescence and (1)H NMR, on its chemically stable mutant C130I (pseudo-wild-type (WT(S))), which has a large internal cavity. As pressure was increased from 3 to 300 MPa, the Trp fluorescence λ(max) of WT(S) shifted from 342 to ∼355 nm, clearly showing that the three Trp rings become fully exposed to the polar environment, which usually is taken to indicate that the protein underwent unfolding. In contrast, as pressure was increased from 3 to 300 MPa, the high-field-shifted (1)H NMR signals characteristic of the folded state showed a still higher-field shift, but no significant changes in their intensity. The last result unequivocally shows that the protein remains largely folded at 300 MPa. The apparent discrepancy between the two predictions would only be solved if one were to postulate the existence of an extensively hydrated but folded state in WT(S). Intriguingly, such a state was not found in a cavity-filling mutant of WT(S), C130I/V103L, suggesting that this state is mediated by cavity hydration. The generality and significance of this state in proteins are discussed.

Pressure-accelerated dissociation of amyloid fibrils in wild-type hen lysozyme.

The dynamics of amyloid fibrils, including their formation and dissociation, could be of vital importance in life. We studied the kinetics of dissociation of the amyloid fibrils from wild-type hen lysozyme at 25°C in vitro as a function of pressure using Trp fluorescence as a probe. Upon 100-fold dilution of 8 mg ml(-1) fibril solution in 80 mM NaCl, pH 2.2, no immediate change occurred in Trp fluorescence, but at pressures of 50-450 MPa the fluorescence intensity decreased rapidly with time (k(obs) = 0.00193 min(-1) at 0.1 MPa, 0.0348 min(-1) at 400 MPa). This phenomenon is attributable to the pressure-accelerated dissociation of amyloid fibrils into monomeric hen lysozyme. From the pressure dependence of the rates, which reaches a plateau at ~450 MPa, we determined the activation volume ΔV(0‡) = -32.9 ± 1.7 ml mol(monomer)(-1) and the activation compressibility Δκ(‡) = -0.0075 ± 0.0006 ml mol(monomer)(-1) bar(-1) for the dissociation reaction. The negative ΔV(0‡) and Δκ(‡) values are consistent with the notion that the amyloid fibril from wild-type hen lysozyme is in a high-volume and high-compressibility state, and the transition state for dissociation is coupled with a partial hydration of the fibril.

Structural plasticity of staphylococcal nuclease probed by perturbation with pressure and pH.

The ionization of internal groups in proteins can trigger conformational change. Despite this being the structural basis of most biological energy transduction, these processes are poorly understood. Small angle X-ray scattering (SAXS) and nuclear magnetic resonance (NMR) spectroscopy experiments at ambient and high hydrostatic pressure were used to examine how the presence and ionization of Lys-66, buried in the hydrophobic core of a stabilized variant of staphylococcal nuclease, affect conformation and dynamics. NMR spectroscopy at atmospheric pressure showed previously that the neutral Lys-66 affects slow conformational fluctuations globally, whereas the effects of the charged form are localized to the region immediately surrounding position 66. Ab initio models from SAXS data suggest that when Lys-66 is charged the protein expands, which is consistent with results from NMR spectroscopy. The application of moderate pressure (<2 kbar) at pH values where Lys-66 is normally neutral at ambient pressure left most of the structure unperturbed but produced significant nonlinear changes in chemical shifts in the helix where Lys-66 is located. Above 2 kbar pressure at these pH values the protein with Lys-66 unfolded cooperatively adopting a relatively compact, albeit random structure according to Kratky analysis of the SAXS data. In contrast, at low pH and high pressure the unfolded state of the variant with Lys-66 is more expanded than that of the reference protein. The combined global and local view of the structural reorganization triggered by ionization of the internal Lys-66 reveals more detectable changes than were previously suggested by NMR spectroscopy at ambient pressure.

The pressure-temperature phase diagram of hen lysozyme at low pH.

The equilibrium unfolding of hen lysozyme at pH 2 was studied as a function of pressure (0.1~700MPa) and temperature (-10°C~50°C) using Trp fluorescence as monitor supplemented by variable pressure 1H NMR spectroscopy (0.1~400MPa). The unfolding profiles monitored by the two methods allowed the two-state equilibrium analysis between the folded (N) and unfolded (U) conformers. The free energy differences ΔG (=GU-GN) were evaluated from changes in the wavelength of maximum fluorescence intensity (λmax) as a function of pressure and temperature. The dependence of ΔG on temperature exhibits concave curvatures against temperature, showing positive heat capacity changes (ΔCp =CpU-CpN= 1.8-1.9 kJ mol-1 deg-1) at all pressures studied (250~400 MPa), while the temperature TS for maximal ΔG increased from about 10°C at 250MPa to about 40°C at 550MPa. The dependence of ΔG on pressure gave negative volume changes (ΔV=VU-VN) upon unfolding at all temperatures studied (-86~-17 mlmol-1 for -10°C~50°C), which increase significantly with increasing temperature, giving a positive expansivity change (Δα~1.07mlmol-1 deg-1). A phase-diagram between N and U (for ΔG=0) is drawn of hen lysozyme at pH 2 on the pressure-temperature plane. Finally, a three-dimensional free energy landscape (ΔG) is presented on the p-T plane.

Pressure acceleration of proteolysis: A general mechanism.

Remarkable acceleration of enzymatic proteolysis by pressure at kbar range is reported with ubiquitin as substrate and α-chymotrypsin as enzyme. The acceleration is interpreted in terms of the shift of conformational equilibrium in ubiquitin from the non-degradable folded conformer to the enzyme-degradable unfolded conformer by pressure because of the lower volume of the latter, while the enzymatic activity of α-chymotrypsin is still largely retained. This mechanism is considered generally applicable to most globular proteins and the method of pressure-accelerated proteolysis will have an enormous potential utility in systems wherever efficient removal of proteins is needed.