Sensitivity of the folding/unfolding transition state ensemble of chymotrypsin inhibitor 2 to changes in temperature and solvent

To better characterize the transition state for folding/unfolding and its sensitivity to environmental changes, we have run multiple molecular dynamics simulations of chymotrypsin inhibitor 2 (CI2) under varying solvent conditions and temperature. The transition state structures agree well with experiment, and are similar under all of the conditions investigated here. Increasing the temperature leads to some movement in the position of the transition state along several reaction coordinates, as measured by changes in properties of the transition state structures. These structural changes are in the direction of a more native-like transition state as denaturation conditions become more severe, as expected for a Hammond effect. These structural changes are not, however, reflected in the global structure as measured by the total number of contacts or the average S-values. These results suggest that the small changes in average Phi-values with temperature seen by experiment may be due to an increase in the sensitivity of the transition state to mutation rather than a change in the average structure of the transition state. A simple analysis of the rates of unfolding indicates that the free energy barrier to unfolding decreases with increasing temperature, but even in our very high temperature simulations there is a small free energy barrier.     

The glassy state and accelerated aging of soybeans

Deteriorative changes in seeds may be expected to reflect changes in physical state as well as in chemical composition. In the present study, measurements of changes in glass transition, lipid phase transition and sugar content were made during accelerated aging of two cultivars of soybeans ( Glycine max Merrill cv. Chippewa 64 and cv. Hodgson 78). The glass transition in axes, as measured by the thermally stimulated depolarization current method, showed gradual decreases in both magnitude and transition temperature during accelerated aging, and eventually, axes of seeds lost their ability to enter the glassy state. Sucrose, raffinose and stachyose contents in seed axes showed little or no change during the aging treatment. Membrane lipids in aged axes retained the liquid crystalline phase during aging. These data suggest that the changes of glass transition during accelerated aging occurred without associated changes in soluble sugar contents or changes in the liquid crystalline state of membrane lipids. The loss of the glass transition during accelerated aging could be a consequence of the annealing effect due to elevated temperature and moisture content. We propose that a loss of the glassy state during accelerated aging leads to an enhanced rate of subsequent deteriorative reactions in seeds and accelerates the loss of viability.     

The Effect of Parameters Change of a Semi-Markov Model on Interval Transition Probabilities

This paper examines the changes in parameters of a Semi-Markov model and its impact on interval transition probabilities. Computational techniques are used to illustrate that the model is sensitive enough to depict changes in the interval transition probabilities if the paramters of the model are modified.     

Temperature- and cyclic nucleotide-induced phase transitions of Histoplasma capsulatum.

The transition from yeast to mycelia of Histoplasma capsulatum could be accomplished by shifting the temperature of incubation from 37 to 25 degrees C. It was accompanied by many changes in cellular metabolism, including changes in respiration, intracellular cyclic adenosine 3',5'-monophosphate (cAMP) levels, and activities of two enzymes specific for the yeast phase, cystine reductase (EC 1.6.4.1) and cysteine oxidase (EC 1.13.11.20). Even at 37 degrees C, the yeast to mycelial transition could be induced by cAMP and agents which raise the intracellular levels of cAMP (theophylline, acetylsalicylic acid, prostaglandin E1, and nerve growth factor). During this morphogenesis the same pattern of changes occurred as in the temperature-induced transition. Therefore, these changes were not simply dependent on a shift in temperature, but rather were part of the process of the phase transition.     

Non-linear rate-equilibrium free energy relationships and Hammond behavior in protein folding

Non-linear rate-equilibrium relationships upon mutation or changes in solvent conditions are frequently observed in protein folding reactions and are usually interpreted in terms of Hammond behavior. Here we first give a general overview over the concept of transition state movements in chemical reactions and discuss its application to protein folding. We then show examples for genuine Hammond behavior and for apparent transition state movements caused by other effects like changes in the rate-limiting step of the folding reaction or ground state effects, i.e. structural changes in either the native state or the unfolded state. These examples show that apparent transition state movements can easily be mistaken for Hammond behavior. We describe experimental tests using self- and cross-interaction parameters to distinguish between structural changes in a single transition state following Hammond behavior and apparent transition state movements caused by other effects.     

The influence of charge on bilayer membranes. Calorimetric investigations of phosphatidic acid bilayers.

The pH-dependence of the phase transition of dimyristoyl phosphatidic acid and dihexadecyl phosphatidic acid has been investigated using differential scanning calorimetry. Varying the pH induces different degrees of ionization of the polar head group. The changes in transition temperature with pH as observed by calorimetry are in good agreement with those obtained by measuring the changes in light scattering, whereas the transition temperatures reported by the fluorescent probe N-phenylnaphthylamine do not always coincide with those determined from calorimetry [1]. The observed maximum of the transition temperature at pH 3.5 corresponds to a minimum in the transition enthalpy vs. pH diagram. At this pH a particular stable bilayer phase is formed. Full protonation of phosphatidic acids leads to suspensions of mycrocrystals. The transition enthalpy approaches the value of the melting enthalpy of crystalline anhydrous phosphatidic acid. The decrease in the transition enthalpy at high pH values is due to a change in the hydrocarbon chain interactions induced by the doubly charged head groups. The cooperativity of the transition varies with the degree of ionization of the head group, being lower for doubly charged phosphatidic acids.     

Effects of pH on the stability of chromatin core particles.

Chromatin core particles near physiological ionic strength undergo a reversible transition induced by changes in pH near neutrality. While sedimentation studies indicate no significant effect on size or shape, changes in tyrosine fluorescence anisotropy and in circular dichroism suggest a somewhat looser structure at high pH. Further support of this suggestion is given by high salt dissociation experiments; at pH 8 core particles begin to show changes at lower salt concentration than at pH 6. The pH transition appears unaffected by the presence of Mg2+ but can be blocked by crosslinking of the histones. A possible relationship is suggested between this transition and increases in intracellular pH which correlate with enhancement in several aspects of cellular activity including DNA replication.     

转型医院医师队伍建设的实践与思考

转型医院涉及到医师队伍的人事变动，如何重组变动的医师团队是关系到医院是否成功转型的关键。文章以原哈尔滨铁路中心医院向哈尔滨医科大学附属第四医院的转型为例，通过比较企业医院向高等医学院校转制型后医师队伍的结构的变化，医院转型前后医师队伍建设的思考与启示，为行业内转型医院优秀医师团队培养与构建提供借鉴。     

The mechanism of helical transition of proteins by organic solvents

This paper describes a theory for the mechanism of three-state transition of proteins which is often observed in aqueous organic cosolvent systems, i.e., from the native, via intermediate to helical forms. The first transition, accompanied by changes in the tertiary and/or secondary structures, was explained by larger bindings of the organic solvent molecules to the intermediate than to the native state; the second transition, resulting in changes mainly in the secondary structure, i.e., helical transition, was explained by less hydration sites for the helical state. Computer simulations of the transition were carried out using plausible values for the number of alcohol and water binding sites of proteins as well as for the equilibrium constant of the transitions in the absence of cosolvent. A reasonable agreement with the experimental transitions was observed. The stronger effect of alcohols with longer alkyl chains was explained by their greater binding to nonpolar groups and their larger exclusion from peptide groups.     

Herpetomonas samuelpessoai: Role of subpellicular microtubules in shape transitions of trypanosomatids

There is a close association between changes in cell volume and shape transition of Herpetomonas samuelpessoai. A rearrangement of the spatial organization of subpellicular microtubules provides the structural basis for the process of shape transition. A model is presented which accounts for the relationship between microtubule arrangement, changes in cell volume, and transition from elongate (promastigote) to the more spherical (para- and opisthomastigote) forms. Its central feature consists of an asymmetrical departure from the regularly helicoidal distribution of the microtubules upon induction of transition. While some microtubules become more linear, others assume a compensatory overspiralized course, allowing for a modification of volume with slight or no change of the cell surface area.     

Metastable behaviour of saturated phosphatidylethanolamines: a densitometric study

The specific volumes of saturated phosphatidylethanolamines having 12-18 carbon atoms per chain and the volume changes resulting from their temperature-induced phase transitions have been investigated using differential scanning densitometry. No dependence on acyl-chain length has been found for the molar volume changes associated with the Lc----L alpha transition, while the L beta----L alpha transition showed delta V-changes that increase with the length of the acyl-chains. The independence of acyl-chain length of the molar volume changes concomitant with the Lc----L alpha transition can be rationalized by the assumption that the volume changes result from the combined effects of hydration and acyl chain melting. An interesting corollary of the present studies is the disappearance of metastability at chain lengths of about 20-22 carbon atoms.     

Interaction of the antimicrobial peptide gramicidin S with dimyristoyl--phosphatidylcholine bilayer membranes: a densitometry and sound velocimetry study

We determined changes in the volume and adiabatic compressibility of large multi- and unilamellar vesicles composed of dimyristoylphosphatidylcholine containing various concentrations of the antimicrobial peptide gramicidin S (GS) by applying densitometry and sound velocimetry. Gramicidin S incorporation was found to progressively decrease the phase transition temperature of DMPC vesicles as well as to decrease the degree of cooperativity of the main phase transition and to increase the volume compressibility of the vesicles. GS probably enhanced thermal fluctuations at the region of main phase transition and provide more freedom of rotational movement for the phospholipid hydrocarbon chains. The ability of GS to increase the membrane compressibility and to decrease the phase transition temperature is evidence for regions of distorted membrane structure around incorporated gramicidin S molecules. At relatively high GS concentration (10 mol%), more significant changes of specific volume and compressibility appear. This might suggest changes in the integrity of the lipid bilayer upon interaction with high concentrations of GS.     

Anomalous change in the specific conductivity in lipoproteins at around physiologic temperatures

Studying the temperature dependence of conductivity sigma of rat and human lipoproteins and apoprotein A-I fractions revealed an anomalous region in the range of temperatures (35-38) +/- 0.5 degree C. The activation energy delta H and temperature coefficient sigma (delta sigma/delta T) on both sides of Tc and the heat of transition (delta H of transition) were calculated. In high-density human lipoproteins and apoA-I, the delta H value was found to be very low. Some mechanisms of interaction of hydrocortizone with high-density lipoproteins and apoA-I were studied by using IR-spectroscopy and conductometry were studied. It was found that the hormone considerably increases the portion of alpha-helices and beta-structures in these proteins (coil<-->alpha-helix and coil<-->beta-structure transitions). In this case, delta H value of the transition increases 13-fold; in addition, the abnormal region in apoA-I shifts 1-2 degrees C downwards. The anomalous changes in conductivity in the range of physiological temperatures in all lipoprotein fractions including apoA-I are probably related to structural phase transitions both in proteins and in phospholipids. Since the delta H value of the transition in human high-density lipoproteins is small, it is assumed that, in phospholipids of these particles, an orientation transition of the A<-->C smectic type takes place, which is assigned to the second-order phase transition. The structural transition in apoA-I can probably also be assigned to the second-order phase transition since the enthalpia of the transition is very small; presumably, this transition is related to changes in symmetry due to changes in the secondary structure (coil<-->beta-tructure transition).     

Lecithin bilayers. Density measurement and molecular interactions.

Density measurement are reported for bilayer dispersions of a series of saturated lecithins. For chain lengths with, respectively, 14, 15, 16, 17, and 18 carbons per chain, the values for the volume changes at the main transition are 0.027, 0.031, 0.037, 0.040 and 0.045 ml/g. The main transition temperature extrapolates with increasing chain length to the melting temperature of polyethylene. Volume changes at the lower transition are an order of magnitude smaller than the main transition. Single phase thermal expansion coefficients are also reported. The combination of X-ray data and density data indicated that the volume changes are predominantly due to the hydrocarbon chains, thus enabling the volume vCH2 of the methylene groups to be computed as a function of temperature. From this and knowledge of intermolecular interactions in hydrocarbon chains, the change in the interchain van der Waals energy, delta UvdW, at the main transition is computed for the lecithins and also for the alkanes and polyethylene at the melting transition. Using the experimental enthalpies of transition and delta UvdW, the energy equation is consistently balanced for all three systems. This yields estimates of the change in the number of gauche rotamers in the lecithins at the main transition. The consistency of these calculations supports the conclusion that the most important molecular energies for the main transition in lecithin bilayers are the hydrocarbon chain interactions and the rotational isomeric energies, and the conclusion that the main phase transition is analogous to the melting transition in the alkanes from the hexagonal phase to the liquid phase, but with some modifications.     

Charge changes in loop 2 affect the thermal unfolding of the myosin motor domain bound to F-actin

The thermal unfolding of Dictyostelium discoideum myosin head fragments with alterations in the actin-binding surface loop 2 was studied by differential scanning calorimetry. Lengthening of loop 2 without concomitant charge changes led to decreases in the transition temperature of not more than 1.8 degrees C. Insertions with multiple positive or negative charges had a stronger destabilizing effect and led to reductions in the thermal transition temperature of up to 3.7 degrees C. In the presence of nucleotide, most mutants displayed similar or higher transition temperatures than M765. Only constructs M765(11/+6) and M765(20/+12) with long positively charged inserts showed transition temperatures that were more than 2 degrees C below the values measured for M765 in the presence of ADP, ADP-V(i), and ADP-BeF(3). Interaction with F-actin in the presence of ADP shifted the thermal transition of M765 by 6 degrees C, from 49.1 to 55.1 degrees C. The actin-induced increase in thermal stability varied between 1.2 and 9.1 degrees C and showed a strong correlation with the mutant constructs' affinity for actin. Our results show that length and charge changes in loop 2 do not significantly affect nucleotide-induced structural changes in the myosin motor domain, but they affect structural changes that occur when the motor domain is strongly bound to actin and affect the coupling between the actin- and nucleotide-binding sites.     

Simulations of the T <--> R conformational transition in aspartate transcarbamylase.

Aspartate transcarbamylase (ATCase) from Escherichia coli is one of the best known allosteric enzymes. In spite of numerous experiments performed by biochemists, no consensus model for the cooperative transition between the tensed (T) and the relaxed (R) forms exists. It is hypothesized, however, that changes in the quaternary structure play a key role in the allosteric properties of oligomeric proteins such as ATCase. Previous normal mode calculations of the two states of ATCase illustrated the type of motions that could be important in initiating the transition. In this work four pathways for the transition were calculated using the targeted molecular dynamics (TMD) method without constraint on the symmetry of the system. The most important quaternary structure changes are the relative rotation and translation of the catalytic trimers and the rotations of the regulatory dimers. The simulations show that these quaternary changes start immediately and finish when about 70% of the transition is completed whereas there are tertiary changes throughout the transition. In agreement with the work of Lipscomb et al., it was found that the relative translation between the catalytic trimers appears to play a central role in allowing the transition to occur. In all the simulations differences are observed in the opening and closing behaviours of the domains in the catalytic and regulatory chains that could provide a structural interpretation for the results of certain site-directed mutagenesis experiments. Overall the motions of the subunits are concerted even though the constraint imposed on the TMD method does not explicitly require that this be so.     

Structural transition in micelles: novel insight into microenvironmental changes in polarity and dynamics

Structural transitions involving shape changes play an important role in cellular physiology. Such transition can be conveniently induced in charged micelles by increasing ionic strength of the medium. Shape changes have recently been shown to result in altered packing and lowering of micellar polarity. As a consequence of reduced polarity, the ionization states of micelle-bound molecules vary in micelles of different shape. The changes in micellar organization and dynamics due to structural transition can be effectively monitored utilizing the red edge excitation shift (REES). These changes are influenced by the position (location) of the probe in the micelle, i.e., the region of the micelle being monitored. Changes in organization and dynamics of probes and peptides upon structural transition are discussed with representative examples. We envisage that the reduction in micellar polarity and tighter packing upon structural transition represent important factors in the incorporation of drugs in micelles (nano-carriers), since micellar polarity plays a crucial role in the incorporation of drugs.     

Exploring the role of large conformational changes in the fidelity of DNA polymerase beta

The relationships between the conformational landscape, nucleotide insertion catalysis and fidelity of DNA polymerase beta are explored by means of computational simulations. The simulations indicate that the transition states for incorporation of right (R) and wrong (W) nucleotides reside in substantially different protein conformations. The protein conformational changes that reproduce the experimentally observed fidelity are significantly larger than the small rearrangements that usually accompany motions from the reactant state to the transition state in common enzymatic reactions. Once substrate binding has occurred, different constraints imposed on the transition states for insertion of R and W nucleotides render it highly unlikely that both transition states can occur in the same closed structure, because the predicted fidelity would then be many orders of magnitude too large. Since the conformational changes reduce the transition state energy of W incorporation drastically they decrease fidelity rather than increase it. Overall, a better agreement with experimental data is attained when the R is incorporated through a transition state in a closed conformation and W is incorporated through a transition state in one or perhaps several partially open conformations. The generation of free energy surfaces for R and W also allow us to analyze proposals about the relationship between induced fit and fidelity.     

Photoselection studies of the P-800 band in the photoreaction center of Rhodospirillum rubrum

Polarization measurements of light-induced absorption changes in photoreaction center prepared from Rhodospirillum rubrum indicate that the 870 nm band is most likely due to a single transition dipole. The 800 nm band appears to be formed by transition dipoles with at least three different orientations. In photoreaction center from strain G9, none of the transition dipoles of the 800 nm band appears to form an angle larger than 70° with the 870 nm transition dipole.