Relative importance of secondary structure and solvent accessibility to the stability of protein mutants. A case study with amino acid properties and energetics on T4 and human lysozymes

Understanding the factors influencing the stability of protein mutants is an important task in molecular and computational biology. In this work, we have approached this problem by examining the relative importance of secondary structure and solvent accessibility of the mutant residue for understanding/predicting the stability of protein mutants. We have used hydrophobic, electrostatic and hydrogen bond free energy terms and nine unique physicochemical, energetic and conformational properties of amino acids in the present study and these parameters have been related with changes in thermal stability (DeltaTm) of all the single mutants of lysozymes based on single and multiple correlation coefficients. As expected the properties reflecting hydrophobicity and hydrophobic free energy play a major role to distinguish stabilizing and destabilizing mutants. The hydrophobic free energy due to carbon and nitrogen atoms distinguish the stability of coil and strand mutations to the accuracy of 100 and 90%, respectively. In agreement with previous results, the subgroup classification based on secondary structure and the information about its location in the structure yielded good relationship with the experimental DeltaTm. We revealed that the secondary structure information is equally or more important than solvent accessibility for understanding the stability of protein mutants. The comparison of amino acid properties with free-energy terms indicate that the energetic contribution explains the mutant stability better in coil region whereas the amino acid properties do better in strand region. Further, the combination of free energies with amino acid properties increased the correlation significantly. The present study demonstrates the importance of classifying the mutants based on secondary structure to the stability of proteins upon mutations.     

Thermodynamic analysis of lysozyme adsorbed to silica

The structural stability of hen egg white lysozyme in solution and adsorbed to small colloidal silica particles at various surface concentrations was investigated using hydrogen-deuterium (H/D) exchange in combination with mass spectrometry (HDX-MS) and differential scanning calorimetry (DSC). The combination of HDX-MS and DSC allows a full thermodynamic analysis of the lysozyme structure as both the enthalpy and the Gibbs free energy can be derived from the various measurements. Moreover, both HDX-MS and DSC provide information on the relative structural heterogeneity of lysozyme in the adsorbed state compared to that in solution. Results demonstrated that at high surface coverage, the structural stability of lysozyme was only marginally affected by adsorption to silica particles whereas the unfolding enthalpy decreased by more than 10%, meaning that the entropy of lysozyme increased with a similar value upon adsorption. Furthermore, the structural heterogeneity increased considerably. At lower surface concentrations, the structural heterogeneity increased further whereas the enthalpy of unfolding decreased. Further analyses of the HDX-MS experiments clearly indicated that folding/unfolding of lysozyme occurs through a two-domain process. These two domains had a similar amount of structural elements and a difference in stabilization energy of 8 kJ/mol, regardless if lysozyme was in solution or adsorbed to silica.     

Thermal denaturing of mutant lysozyme with both the OPLSAA and the CHARMM force fields

Biomolecular simulations enabled by massively parallel supercomputers such as BlueGene/L promise to bridge the gap between the currently accessible simulation time scale and the experimental time scale for many important protein folding processes. In this study, molecular dynamics simulations were carried out for both the wild-type and the mutant hen lysozyme (TRP62GLY) to study the single mutation effect on lysozyme stability and misfolding. Our thermal denaturing simulations at 400-500 K with both the OPLSAA and the CHARMM force fields show that the mutant structure is indeed much less stable than the wild-type, which is consistent with the recent urea denaturing experiment (Dobson et al. Science 2002, 295, 1719-1722; Nature 2003, 424, 783-788). Detailed results also reveal that the single mutation TRP62GLY first induces the loss of native contacts in the beta-domain region of the lysozyme protein at high temperatures, and then the unfolding process spreads into the alpha-domain region through Helix C. Even though the OPLSAA force field in general shows a more stable protein structure than does the CHARMM force field at high temperatures, the two force fields examined here display qualitatively similar results for the misfolding process, indicating that the thermal denaturing of the single mutation is robust and reproducible with various modern force fields.     

Hydrophobicity Enhances the Formation of Protein-Stabilized Foams

Screening proteins for their potential use in foam applications is very laborious and time consuming. It would be beneficial if the foam properties could be predicted based on their molecular properties, but this is currently not possible. For protein-stabilized emulsions, a model was recently introduced to predict the emulsion properties from the protein molecular properties. Since the fundamental mechanisms for foam and emulsion formation are very similar, it is of interest to determine whether the link to molecular properties defined in that model is also applicable to foams. This study aims to link the exposed hydrophobicity with the foam ability and foam stability, using lysozyme variants with altered hydrophobicity, obtained from controlled heat treatment (77 °C for 0–120 min). To establish this link, the molecular characteristics, interfacial properties, and foam ability and stability (at different concentrations) were analysed. The increasing hydrophobicity resulted in an increased adsorption rate constant, and for concentrations in the protein-poor regime, the increasing hydrophobicity enhanced foam ability (i.e., interfacial area created). At higher relative exposed hydrophobicity (i.e., ~2–5 times higher than native lysozyme), the adsorption rate constant and foam ability became independent of hydrophobicity. The foam stability (i.e., foam collapse) was affected by the initial foam structure. In the protein-rich regime—with nearly identical foam structure—the hydrophobicity did not affect the foam stability. The link between exposed hydrophobicity and foam ability confirms the similarity between protein-stabilized foams and emulsions, and thereby indicates that the model proposed for emulsions can be used to predict foam properties in the future.     

Heat capacities and thermodynamic properties of one manganese-based MOFs

A metal-organic framework [Mn(4,4′-bipy)(1,3-BDC)] _n (MnMOF, 1,3-BDC = 1,3-benzene dicarboxylate, 4,4′-bipy = 4,4′-bipyridine) has been synthesized hydrothermally and characterized by single crystal XRD and FT-IR spectrum. The low-temperature molar heat capacities of MnMOF were measured by temperature-modulated differential scanning calorimetry for the first time. The thermodynamic parameters such as entropy and enthalpy relative to reference temperature 298.15 K were derived based on the above molar heat capacity data. Moreover, the thermal stability and the decomposition mechanism of MnMOF were investigated by thermogravimetry analysis-mass spectrometer. A two-stage mass loss was observed in air flow. MS curves indicated that the gas products of oxidative degradation were H₂O, CO₂, NO, and NO₂.     

Heat capacity corrections to a standard state: a comparison of new and some literature methods for organic liquids and solids

The estimation methods commonly used to correct phase change enthalpies to the standard state are compared where possible to experimental measurements. Heat capacity corrections for liquid-gas equilibria are found to correlate with molecular structure, and we suggest an improved method for estimating these corrections using group methods. A similar improvement for estimating heat capacity corrections for solid-gas equilibria using group methods is also proposed. Heat capacity corrections for liquid-solid equilibria are examined. These corrections were found to be comparable in magnitude to the experimental error associated with heat capacity measurements, so it was not possible to obtain any meaningful correlations.     

Microcalorimetric study of thermal unfolding of lysozyme in water/glycerol mixtures: an analysis by solvent exchange model

Folded protein stabilization or destabilization induced by cosolvent in mixed aqueous solutions has been studied by differential scanning microcalorimetry and related to difference in preferential solvation of native and denatured states. In particular, the thermal denaturation of a model system formed by lysozyme dissolved in water in the presence of the stabilizing cosolvent glycerol has been considered. Transition temperatures and enthalpies, heat capacity, and standard free energy changes have been determined when applying a two-state denaturation model to microcalorimetric data. Thermodynamic parameters show an unexpected, not linear, trend as a function of solvent composition; in particular, the lysozyme thermodynamic stability shows a maximum centered at water molar fraction of about 0.6. Using a thermodynamic hydration model based on the exchange equilibrium between glycerol and water molecules from the protein solvation layer to the bulk, the contribution of protein-solvent interactions to the unfolding free energy and the changes of this contribution with solvent composition have been derived. The preferential solvation data indicate that lysozyme unfolding involves an increase in the solvation surface, with a small reduction of the protein-preferential hydration. Moreover, the derived changes in the excess solvation numbers at denaturation show that only few solvent molecules are responsible for the variation of lysozyme stability in relation to the solvent composition.     

Establishment of Aromatic Pairs at the Surface of Chondroitinase ABC I: the Effect on Activity and Stability

Removal of chondroitin sulfate glycosaminoglycan (GAG) chains with chondroitinase ABC I (chABC I) in CNS injury models promotes both saxon regeneration and plasticity. It has been suggested that direct interaction between an aromatic pair appears to contribute about ??1.3 kcal/mol to the stability of a folded protein, so introducing an aromatic pair by point mutation might increase the enzyme activity and thermal stability as in the case of mesophilic xylanase, although using this approach destabilized T4 lysozyme. In this study, we used site-directed mutagenesis to investigate the effect of new aromatic pairs on activity and stability of chABC I. We replaced Ile295, Ser581, and Gly730 adjacent to pre-existing aromatic residues with Tyr to obtain new aromatic pairs, i.e., Tyr295/His372, Tyr576/Tyr581, and Tyr623/Tyr730. Results showed that K_m values of S581Y and G730Y variants decreased relative to wild-type enzyme while their catalytic efficiency (k_cat/K_m) increased but I295Y variant was inactive. Also, long-term and thermal stability of the active mutants was decreased. Fluorescence and circular dichroism studies showed that these mutations resulted in a more flexible enzyme structures: a finding which was confirmed by thermal and limited proteolytic studies. In conclusion, the activity of chABC I can be improved by introducing appropriate aromatic pairs at the enzyme surface. This approach did not provide any promising results regarding the enzyme stability.     

Thermodynamic properties of methane hydrate in quartz powder

Using the experimental method of precision adiabatic calorimetry, the thermodynamic (equilibrium) properties of methane hydrate in quartz sand with a grain size of 90-100 microm have been studied in the temperature range of 260-290 K and at pressures up to 10 MPa. The equilibrium curves for the water-methane hydrate-gas and ice-methane hydrate-gas transitions, hydration number, latent heat of hydrate decomposition along the equilibrium three-phase curves, and the specific heat capacity of the hydrate have been obtained. It has been experimentally shown that the equilibrium three-phase curves of the methane hydrate in porous media are shifted to the lower temperature and high pressure with respect to the equilibrium curves of the bulk hydrate. In these experiments, we have found that the specific heat capacity of the hydrate, within the accuracy of our measurements, coincides with the heat capacity of ice. The latent heat of the hydrate dissociation for the ice-hydrate-gas transition is equal to 143 +/- 10 J/g, whereas, for the transition from hydrate to water and gas, the latent heat is 415 +/- 15 J/g. The hydration number has been evaluated in the different hydrate conditions and has been found to be equal to n = 6.16 +/- 0.06. In addition, the influence of the water saturation of the porous media and its distribution over the porous space on the measured parameters has been experimentally studied.     

Experimental Considerations for Temperature Modulated DSC at Low Temperature

Temperature modulated DSC (TMDSC) at low temperatures requires attention to the selection of experimental parameters that are within the capability of the instrumentation as well as special care in calibration of heat capacity measurement when high precision is required. Data are presented to facilitate selection of appropriate modulation periods and amplitudes at low temperature when using a mechanical cooling accessory. The standard error of the mean heat capacity measurement for a sapphire standard increased with decreasing temperature, decreasing period, and increasing pan mass. For ice in hermetically sealed pans, the standard error of the mean heat capacity measurement was larger than for sapphire and did not follow a predictable trend with changes in temperature and period of modulation. This was attributed to changes in sample geometry between successive measurements due to melting and resolidification. A simple one-point temperature calibration by TMDSC may be unsuitable for precise measurement of heat capacity because of the random error caused by sample placement and the systematic error caused by cell asymmetry, temperature dependence of the calibration constant, and different sample thermal conductivities. An alternative calibration procedure using standard DSC and either a linear or second order fit of the calibration constant over the temperature range of interest is proposed. This revised version was published online in August 2006 with corrections to the Cover Date.     

Animal inference on human mitochondrial diseases

Several pathological mutations in the human mitochondrial genome have been characterized based on medical, genetic and biochemical evidence. The observation that the structure and core functions of the mitochondrial genome are conserved from animals to man suggests that the analysis of animal variation may be informative to further characterize, and possibly predict, human pathological variants.We studied the distribution of sequence site-wise diversity and structural heterogeneity (based on several scales of hydrophobicity and supercomplex classification of mitochondrial genes) at different taxonomic levels in ∼15,000 human and animal genomes. We found that human pathological mutations tend to lay in regions of low diversity and that states that are pathological in humans appear to be extremely rare in animals, with two noticeable exceptions (T10663C and C14568T). Focusing on hydrophobicity, as possibly the most general site-wise functional parameter of a protein, we deploy the observed range of hydrophobicity in mammals as a proxy for the range of permissible states compatible with an efficient functioning of the mitochondrial machinery. We show that, while non pathological human variants tend to fall within the hypothesized range, pathological mutations generally fall outside this range. We further analyzed this distribution quantitatively to show that the estimated probability of observed states can indeed be used to predict the pathogenicity of a mutation in humans. This study provides a proof of principle that animal data can indeed be informative to predict the pathogenicity of a human mutation alongside, or in the absence of, additional evidence.     

Crowding promotes the switch from hairpin to pseudoknot conformation in human telomerase RNA

Formation of a pseudoknot (PK) in the conserved RNA core domain in the ribonucleoprotein human telomerase is required for function. In vitro experiments show that the PK is in equilibrium with an extended hairpin (HP) structure. We use molecular simulations of a coarse-grained model, which reproduces most of the salient features of the experimental melting profiles of PK and HP, to show that crowding enhances the stability of PK relative to HP in the wild type and in a mutant associated with dyskeratosis congenita. In monodisperse suspensions, small crowding particles increase the stability of compact structures to a greater extent than larger crowders. If the sizes of crowders in a binary mixture are smaller than that of the unfolded RNA, the increase in melting temperature due to the two components is additive. In a ternary mixture of crowders that are larger than the unfolded RNA, which mimics the composition of ribosome, large enzyme complexes and proteins in Escherichia coli , the marginal increase in stability is entirely determined by the smallest component. We predict that crowding can partially restore telomerase activity in mutants with decreased PK stability.     

3C-SiC的结构和热力学性质

利用第一性原理平面波模守恒赝势密度泛函理论研究了3C-SiC的结构, 其零温(0 K)零压下的晶格常数、体弹模量及其对压强的一阶导数、弹性常数的计算结果与实验值和其它理论计算结果相符合. 通过准谐德拜模型, 得到了不同温度不同压强下的热容和德拜温度, 发现热容随着压强增加而减小, 德拜温度随压强增加而增加, 并成功地获得了相对晶格常数、相对体积、体弹模量、热膨胀系数与温度和压强的关系.     

On the estimation of stability parameters from heat-induced conformational transition curves of proteins

A method is suggested to determine valid and authentic values of thermodynamic stability parameters of proteins from their heat-induced conformational transition curves. We show (a) that the estimate of ΔH_m ^van, the enthalpy change on denaturation at T_m, the midpoint of denaturation, is significantly less than ΔH_m ^cal, the value obtained by the calorimetric measurements, if the analysis of the conformational transition curve uses the conventional method which assumes a linear temperature-dependence of the pre- and post-transition baselines; and (b) that there exists an excellent agreement between ΔH_m ^van and ΔH_m ^cal values of proteins, if the analysis of thermal denaturation curves assumes that the temperature-dependence of pre- and post-transition baselines is described by a parabolic function. The latter analysis is supported by our observations that the temperaturedependencies of the absorption and circular dichroism properties of protein groups are indeed nonlinear. It is observed that the estimate of ΔC_p, the constant-pressure heat capacity change is independent of the model used to describe the temperaturedependence of the pre- and post-transition baselines. An important conclusion is that for proteins which exhibit a two-state character, all stability parameters are measured with the same error as that observed with a calorimeter.     

Heat capacities and thermodynamic properties of Ni9(btz)12(DMA)6(NO3)6

The low-temperature molar heat capacity of crystalline Ni₉(btz)₁₂(DMA)₆(NO₃)₆ (1) (btz = benzotriazolate; DMA = N,N′-dimethylacetamide) was measured by temperature-modulated differential scanning calorimetry for the first time. The thermodynamic parameters such as entropy and enthalpy relative to reference temperature 298.15 K were obtained based on the above molar heat capacity data. The compound was synthesized by solvothermal method and characterized by powder X-ray diffraction and FT-IR spectra. Moreover, the thermal stability and the decomposition mechanism of Ni₉(btz)₁₂(DMA)₆(NO₃)₆ were investigated by thermogravimetry (TG) analysis under air atmosphere from 300 to 873 K. The experimental results through TG measurement demonstrate that the compound has a two-stage mass loss in air flow.     

Surface chemistry and in situ spectroscopy of a lysozyme langmuir monolayer

Surface pressure and surface potential-area isotherms were used to characterize a lysozyme Langmuir monolayer. The compression-decompression cycles and stability measurements showed a homogeneous and stable monolayer at the air-water interface. Salt concentration in the subphase and pH of the subphase were parameters controlling the homogeneity and stability of the Langmuir monolayer. In situ UV-vis and fluorescence spectroscopies were used to verify the homogeneity of the lysozyme monolayer and to identify the chromophore residues in the lysozyme. Optimal experimental conditions were determined to prepare a homogeneous and stable lysozyme Langmuir monolayer.     

Influence of thermophysical properties on burning behavior of intumescent fire-retardant materials

Thermophysical properties of intumescent fire-retardant (IFR) materials are important parameters as input data in modeling the combustion process of IFR materials in a fire. In this paper, the influences of several thermophysical properties on burning behavior of IFR materials are simulated based on a combustion model of IFR materials. Thermophysical properties selected here are thermal conductivity of virgin material and char layer, specific heat capacity of virgin material, density of virgin material, surface emissivity of virgin material and char layer, heat of decomposition, heat of combustion, and intumescent temperature. Predicted heat release rates curves for the IFR material at an incident heat flux of 50 kW m^?2 are shown for the varied thermophysical parameters’ values. The results show that these varied parameter values can affect the burning behavior of materials remarkably. A comparison with experimental results demonstrates that the predictions of heat release rates are in reasonably good agreement with the experiment.     

Thermodynamic characterisation of RNAase a in the presence of urea and GuHCl

It is presented a study concerning the influence of guanidinium chloride (GuHCl) and urea on thermal stability of Bovine Pancreatic Ribonuclease A (RNAase A) at differentpH values. As expected, at increasing the denaturant concentration, the protein thermostability decreases. This is shown by a decrease of both the thermodynamic parameters, temperature and heat effect, characterising the denaturation process. In order to analyse the calorimetric curves we adopt a statistical thermodynamic approach. The individual one-dimensional DSC profiles have been expanded into another dimension by varying the GuHCl concentration, so that a heat capacity surface is defined for eachpH. By means of the ICARUS program, developed in our laboratory, we accomplish a two dimensional deconvolution of the experimental data linking the binding equilibrium to the denaturation process. This analysis provides a well founded and complete statistical thermodynamic characterisation of denaturation process of RNAase A in the presence of GuHCl and allows to calculate the thermodynamic parameters associated to the binding of denaturant molecule.     

Importance of individual side chains for the stability of a protein fold: computational alanine scanning of the insulin monomer

A new computational approach is proposed to probe the importance of residue side chains for the stability of a protein fold. Computational mutations to estimate protein stability (CMEPS) is based on the notion that the binding free energy corresponding to the complexation of a given side chain, considered as a "pseudo-ligand" of the wild type protein, reflects the importance of this side chain to the thermodynamic stability of the protein. The contribution of a particular side chain to the folding energy is estimated according to the molecular mechanics-generalized born surface area MM-GBSA approach, using a single molecular dynamics simulation trajectory of the wild type protein. CMEPS is a first principles method which does not contain any adjustable parameter that could be fitted to experimental data. The approach is first validated for Barnase and the B1 domain of protein L, for which a correlation coefficient R = 0.73, between experimental and CMEPS calculated DeltaDeltaG values, is found and then applied to the insulin monomer. In the present application, CMEPS replaces each amino acid by an alanine residue. Therefore, most mutations lead to cavities in the protein. From this the change in stability can be correlated with increased cavity volume. For insulin, this correlation is very similar compared with data previously analyzed for T4 lysozyme from an experiment for buried apolar side chains. There, the increased cavity volume has been related to the hydrophobic effect. However, since CMEPS uses the energetics in terms of electrostatic and van der Waals interactions (and not the hydrophobic effect which is difficult to relate to physical interactions), it is possible to study the effect of mutations of polar and solvent accessible side chains. According to CMEPS, residues Leu A16, Tyr A19, Leu B11, Leu B15, and Arg B22 are most important for the stability of the monomeric insulin fold. This is in agreement with experimental data. As a consequence, mutation of these residues may lead to misfolded and inactive insulin analogues.     

Protein stability prediction: a Poisson-Boltzmann approach

Most proteins are only marginally stable at physiological temperatures. Thus a common defect due to mutation is the loss of protein stability, resulting in loss of their well-defined structures and functions at their functioning temperatures. Quantification of protein stability change upon mutation has attracted a large number of experimental and theoretical studies. In this work, we have extended the Poisson-Boltzmann theory that is originally used for predicting stability changes of charged mutations to predicting stability changes of all mutations. To achieve this, we have proposed a free energy model covering both electrostatic and hydrophobic interactions. A G?-like model for the denatured state that incorporates both nativeness and randomness of the denatured state has been used to calculate the hydrophobic contribution to protein stability. The new model is computationally simple and fast, and performs well for charged and hydrophobic mutations for all four tested proteins. Future directions for extending the method into pH-dependent effect and more accurate prediction for polar mutations are discussed.