The Folding Mechanism of Barstar: Evidence for Multiple Pathways and Multiple Intermediates

The mechanism of folding of the small protein barstar in the pre-transition zone at pH 7, 25 degrees C has been characterized using rapid mixing techniques. Earlier studies had established the validity of the three-state U-S reversible arrow U-F reversible arrow N mechanism for folding and unfolding in the presence of guanidine hydrochloride (GdnHCl) at concentrations greater than 2.0 M, where U-S and U-F are the slow-refolding and fast-refolding unfolded forms, respectively, and N is the fully folded form. It is now shown that early intermediates, I-S1 and I-S2 as well as a late native-like intermediate, I-N, are present on the folding pathways of U-S, and an early intermediate I-F1 on the folding pathway of U-F, when bars tar is refolded in concentrations of GdnHCl below 2.0 M. The rates of formation and disappearance of I-N, and the rates of formation of N at three different concentrations of GdnHCl in the pre-transition zone have been measured. The data indicate that in 1.5 M GdnHCl, I-N is not fully populated on the U-S --> I-S1 --> I-N --> N pathway because the rate of its formation is so slow that the U-S reversible arrow U-F reversible arrow N pathway can effectively compete with that pathway. In 1.0 M GdnHCl, the U-S --> I-S1 --> I-N transition is so fast that I-N is fully populated. In 0.6 M GdnHCl, I-N appears not to be fully populated because an alternative folding pathway, U-S --> I-S2 --> N, becomes available for the folding of U-S, in addition to the U-S --> I-S1 --> I-N --> N pathway Measurement of the binding of the hydrophobic dye 1-anilino-8-naphthalenesulphonate (ANS) during folding indicates that ANS binds to two distinct intermediates, I-M1 and I-M2, that form within 2 ms on the U-S --> I-M1 --> I-S1 --> I-N --> N and U-S --> I-M2 --> I-S2 --> N pathways. There is no evidence for the accumulation of intermediates that can bind ANS on the folding pathway of U-F.

Probing the structural changes in the phase transitions of a Bi2MoO6 catalyst: the nature of the intermediate-temperature phase

The nature of the phase transitions of Bi2MoO6 has been investigated by the combined use of X-ray diffraction and Xray absorption spectroscopy. The distorted MoO6 octahedra in the low-temperature form are shown to undergo further distortion in the intermediate-temperature form before transforming to MoO4 tetrahedra in the high-temperature phase. (C) 1995 Academic Press, Inc.

Phase transitions in triammonium hydrogen disulphate: Crystal structure of an intermediate stable phase at-90 degrees C

Triammonium hydrogen disulphate, (NH4)(3)H(SO4)(2), belongs to the family of crystal structures M3H(XO4)(2) (with M = NH4, K, Rb, Cs, and X = S, Se) which display super protonic phases at elevated temperatures, while at room temperature these are relatively poor proton conductors. The crystal structure of triammonium hydrogen disulphate has been determined by X-ray diffraction at -90 degrees C and the variation in the characteristics of the hydrogen bond is discussed in comparison with that of the structures at -110 degrees C and room temperature. It is concluded that the mechanics involving the proton migration in such systems is realised in terms of the variations in the hydrogen bond features with temperature.

An infrared spectroscopic study of the low-spin to intermediate-spin state (1A1–3T1) transition in rare earth cobaltates, LnCoO3 (Ln=La, Pr and Nd)

Low-spin (LS) to intermediate-spin (IS) state transitions in crystals of LnCoO3 (Ln=La, Pr and Nd) have been investigated by variable temperature infrared spectroscopy. The spectra reveal the occurrence of the transition around 120, 220 and 275 K, respectively, in LaCoO3,PrCoO3 and NdCoO3, at which temperatures the intensities of the stretching and the bending modes associated with the LS state decrease, accompanied by an increase in the intensities of the bands due to IS state. The characteristic frequencies of both the spin states decrease with increase in temperature, showing anomalies around the transition.

An infrared spectroscopic study of the low-spin to intermediate-spin state ((1)A(1)-T-3(1)) transition in rare earth cobaltates, LnCoO(3) (Ln = La, Pr and Nd)

Low-spin (LS) to intermediate-spin (IS) state transitions in crystals of LnCoO(3) (Ln = La, Pr and Nd) have been investigated by variable temperature infrared spectroscopy. The spectra reveal the occurrence of the transition around 120, 220 and 275 K, respectively, in LaCoO3,PrCoo(3) and NdCoO3, at which temperatures the intensities of the stretching and the bending modes associated with the LS state decrease, accompanied by an increase in the intensities of the bands due to IS state. The characteristic frequencies of both the spin states decrease with increase in temperature, showing anomalies around the transition. (C) 2001 Published by Elsevier Science B.V.

Efficient statistical modeling for the compression of tree structured intermediate code

We propose a scheme for the compression of tree structured intermediate code consisting of a sequence of trees specified by a regular tree grammar. The scheme is based on arithmetic coding, and the model that works in conjunction with the coder is automatically generated from the syntactical specification of the tree language. Experiments on data sets consisting of intermediate code trees yield compression ratios ranging from 2.5 to 8, for file sizes ranging from 167 bytes to 1 megabyte.

Thermodynamic, kinetic and electrical switching studies on Si(15)Te(85-x)In(x) glasses: Observation of Boolchand intermediate phase

An interesting topic for quite some time is an intermediate phase observed in chalcogenide glasses, which is related to network connectivity and rigidity. This phenomenon is exhibited by Si-Te-In glasses also. It has been addressed here by carrying out detailed thermal investigations by using Alternating Differential Scanning Calorimetry technique. An effort has also been made to determine the stability of these glasses using the data obtained from different thermodynamic quantities and crystallization kinetics of these glasses. Electrical switching behavior by recording I-V characteristics and variation of switching voltages with indium composition have been studied in these glasses for phase change memory applications. (C) 2011 Elsevier Inc. All rights reserved.

Novel ATPase activity of the polyprotein intermediate, Viral Protein genome-linked-Nuclear Inclusion-a protease, of Pepper vein banding potyvirus

Potyviruses temporally regulate their protein function by polyprotein processing. Previous studies have shown that VPg (Viral Protein genome-linked) of Pepper vein banding virus interacts with the NIa-Pro (Nuclear Inclusion-a protease) domain, and modulates the kinetics of the protease. In the present study, we report for the first time that VPg harbors the Walker motifs A and B, and the presence of NIa-Pro, especially in cis (cleavage site (E191A) VPg-Pro mutant), is essential for manifestation of the ATPase activity. Mutation of Lys47 (Walker motif A) and Asp88:Glu89 (Walker motif B) to alanine in E191A VPg-Pro lead to reduced ATPase activity, confirming that this activity was inherent to VPg. We propose that potyviral VPg, established as an intrinsically disordered domain, undergoes plausible structural alterations upon interaction with globular NIa-Pro which induces the ATPase activity. (C) 2012 Elsevier Inc. All rights reserved.

Postcards from oases in the desert: phenomenology of SUSY with intermediate scales

The presence of new matter fields charged under the Standard Model gauge group at intermediate scales below the Grand Unification scale modifies the renormalization group evolution of the gauge couplings. This can in turn significantly change the running of the Minimal Supersymmetric Standard Model parameters, in particular the gaugino and the scalar masses. In the absence of new large Yukawa couplings we can parameterise all the intermediate scale models in terms of only two parameters controlling the size of the unified gauge coupling. As a consequence of the modified running, the low energy spectrum can be strongly affected with interesting phenomenological consequences. In particular, we show that scalar over gaugino mass ratios tend to increase and the regions of the parameter space with neutralino Dark Matter compatible with cosmological observations get drastically modified. Moreover, we discuss some observables that can be used to test the intermediate scale physics at the LHC in a wide class of models.

Manifestation of intermediate phase in mechanical properties: Nano-indentation studies on Ge-Te-Si bulk chalcogenide glasses

Nano-indentation studies have been undertaken on bulk Ge15Te85-xSix glasses (0 <= x <= 9), to estimate hardness, H and elastic modulus, E. It is found that E and H increase initially with the increase in the atomic percent of Si. Further, a plateau is seen in the composition dependence of E and H in the composition range 2 <= x <= 6. It is also seen that the addition of up to 2 at% Si increases the density rho of the glass considerably; however, further additions of Si lead to a near linear reduction in rho, in the range 2 <= x <= 6. Beyond x=6, rho increases again with Si content. The variation of molar volume V-m brings out a more fascinating picture. A plateau is seen in the intermediate phase suggesting that the molecular structure of the glasses is adapting to keep the count of constraints fixed in this particular phase. The observed variations in mechanical properties are associated with the Boolchand's intermediate phase in the present glassy system, in the composition range 2 <= x <= 6, suggested earlier from calorimetric and electrical switching studies. The present results reveal rather directly the existence of the intermediate phase in elastic and plastic properties of chalcogenide glasses. (C) 2012 Elsevier Ltd. All rights reserved.

Asymptotic expansions for the structural wavenumbers of isotropic and orthotropic fluid-filled circular cylindrical shells in the intermediate frequency range

We consider wavenumbers in in vacuo and fluid-filled isotropic and orthotropic shells. Using the Donnell-Mushtari (DM) theory we find compact and elegant asymptotic expansions for the wavenumbers in the intermediate frequency range, i.e., around the ring frequency. This frequency range corresponds to the frequencies where there is a rapid change in the values of bending wavenumbers and is found to exist in isotropic and orthotropic shells (in vacua and fluid-filled) for low circumferential orders n only. The same is first identified using the n=0 mode of an orthotropic shell. Following this, using the expression for the intermediate frequency, asymptotic expansions are found for other cases. Here, in order to get compact expansions we consider slight orthotropy (epsilon << 1) and light fluid loading (mu << 1). Thus, the orthotropy parameter epsilon and the fluid loading parameter mu are used as asymptotic parameters along with the non-dimensional thickness parameter beta. The methodology can be extended to any order of epsilon, only the expansions become unwieldy. The expansions are matched with the numerical solutions of the corresponding dispersion relation. The match is found to be good.

Redox regulation of protein tyrosine phosphatase 1B (PTP1B): Importance of steric and electronic effects on the unusual cyclization of the sulfenic acid intermediate to a sulfenyl amide

The redox regulation of protein tyrosine phosphatase 1B (PTP1B) via the unusual transformation of its sulfenic acid (PTP1B-SOH) to a cyclic sulfenyl amide intermediate is studied by using small molecule chemical models. These studies suggest that the sulfenic acids derived from the H2O2-mediated reactions o-amido thiophenols do not efficiently cyclize to sulfenyl amides and the sulfenic acids produced in situ can be trapped by using methyl iodide. Theoretical calculations suggest that the most stable conformer of such sulfenic acids are stabilized by n(O) -> sigma* (S-OH) orbital interactions, which force the -OH group to adopt a position trans to the S center dot center dot center dot O interaction, leading to an almost linear arrangement of the O center dot center dot center dot S-O moiety and this may be the reason for the slow cyclization of such sulfenic acids to their corresponding sulfenyl amides. On the other hand, additional substituents at the 6-position of o-amido phenylsulfenic acids that can induce steric environment and alter the electronic properties around the sulfenic acid moiety by S center dot center dot center dot N or S center dot center dot center dot O nonbonded interactions destabilize the sulfenic acids by inducing strain in the molecule. This may lead to efficient the cyclization of such sulfenic acids. This model study suggests that the amino acid residues in the close proximity of the sulfenic acid moiety in PTP1B may play an important role in the cyclization of PTP1B-SOH to produce the corresponding sulfenyl amide.

Nucleation of a Stable Solid from Melt in the Presence of Multiple Metastable Intermediate Phases: Wetting, Ostwald's Step Rule, and Vanishing Polymorphs

In many systems, nucleation of a stable solid may occur in the presence of other (often more than one) metastable phases. These may be polymorphic solids or even liquid phases. Sometimes, the metastable phase might have a lower free energy minimum than the liquid but higher than the stable-solid-phase minimum and have characteristics in between the parent liquid and the globally stable solid phase. In such cases, nucleation of the solid phase from the melt may be facilitated by the metastable phase because the latter can ``wet'' the interface between the parent and the daughter phases, even though there may be no signature of the existence of metastable phase in the thermodynamic properties of the parent liquid and the stable solid phase. Straightforward application of classical nucleation theory (CNT) is flawed here as it overestimates the nucleation barrier because surface tension is overestimated (by neglecting the metastable phases of intermediate order) while the thermodynamic free energy gap between daughter and parent phases remains unchanged. In this work, we discuss a density functional theory (DFT)-based statistical mechanical approach to explore and quantify such facilitation. We construct a simple order-parameter-dependent free energy surface that we then use in DFT to calculate (i) the order parameter profile, (ii) the overall nucleation free energy barrier, and (iii) the surface tension between the parent liquid and the metastable solid and also parent liquid and stable solid phases. The theory indeed finds that the nucleation free energy barrier can decrease significantly in the presence of wetting. This approach can provide a microscopic explanation of the Ostwald step rule and the well-known phenomenon of ``disappearing polymorphs'' that depends on temperature and other thermodynamic conditions. Theory reveals a diverse scenario for phase transformation kinetics, some of which may be explored via modem nanoscopic synthetic methods.

Evidence of an intermediate phase in a quaternary Ag bearing telluride glass system using alternating DSC

Alternating Differential Scanning Calorimetric (ADSC) studies on quaternary Ge15Te80-xIn5Agx glasses show the non-reversing enthalpy (Delta H-NR) at T-g to exhibit a broad global minimum in the 8% <= x <= 16% range of Ag, an observation that is taken evidence for existence of an Intermediate Phase (IP) in that range. Glasses at x < 8% are in the flexible phase while those at x > 16% in the stressed-rigid phase. The nature of crystalline phases formed upon crystallization of bulk glasses are elucidated by XRD studies, and reveal presence of Te, GeTe, Ag8GeTe6, AgTe, In2Te3 and In4Te3 phases. These experiments also reveal that the fraction of Ag- bearing phases increases while those of Te- bearing ones decreases with increasing x, suggesting progressive replacement of Te-Te bonds by Ag-Te bonds. (C) 2013 Elsevier Ltd. All rights reserved.