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PubMed2005

Thermodynamic stability of RNA structures formed by CNG trinucleotide repeats. Implication for prediction of RNA structure.

Trinucleotide repeat expansion diseases (TREDs) are correlated with elongation of CNG DNA and RNA repeats to pathological level. This paper shows, for the first time, complete data concerning thermodynamic stabilities of RNA with CNG trinucleotide repeats. Our studies include the stability of oligoribonucleotides composed of two to seven of CAG, CCG, CGG, and CUG repeats. The thermodynamic parameters of helix propagation correlated with the presence of multiple N-N mismatches within CNG RNA duplexes were also determined. Moreover, the total stability of CNG RNA hairpins, as well as the contribution of trinucleotide repeats placed only in the stem or loop regions, was evaluated. The improved thermodynamic parameters allow to predict much more accurately the thermodynamic stabilities and structures of CNG RNAs.

Models, Molecular↗

PubMed2006

Measurement of thermodynamic parameters for hydrophobic mismatch 2: intermembrane transfer of a transmembrane helix.

Hydrophobic matching between proteins and lipids is essential for the thermodynamic stability of integral membrane proteins. However, there is no direct thermodynamic information available about the intermembrane transfer of proteins between membranes with different hydrophobic thicknesses, which is crucial for understanding hydrophobic mismatch. This article reports the complete set of thermodynamic parameters (DeltaG, DeltaH, DeltaS, and DeltaC(p)) for the intermembrane transfer of the inert hydrophobic model transmembrane helix NBD-(AALALAA)(3)-NH(2) (NBD: 7-nitro-2-1,3-benzoxadiazol-4-yl), which is exchangeable between vesicles, from 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine (POPC) to dimonounsaturated-phosphocholine lipid bilayers with different hydrophobic thicknesses (C14-C22) at 37-58 degrees C. The transfer free energies were calculated from equilibrium values of the extent of helix transfer from donor to acceptor lipid vesicles, as monitored by a decrease in fluorescence resonance energy transfer from the NBD group to a lipid-labeled Rhodamine in the donor upon transfer to the quencher-free acceptor. Under hydrophobic mismatch conditions up to approximately 7 A, the helix partitioning became unfavorable up to +7 kJ mol(-)(1), hampered by an increase in entropic (up to +20 kJ mol(-)(1)) and enthalpic (up to +66 kJ mol(-)(1)) terms in thinner and thicker membranes, respectively. Together with the results that H/D exchange at the membrane interface was accelerated in thinner membranes the obtained thermodynamic parameters were reasonably explained assuming that hydrophobic mismatch induces aqueous exposure or membrane burial of the helix termini, resulting in excess energies originating from the hydration of terminal hydrophobic residues or the unfavorable Born energy of terminal partial charges of the helix macrodipole.

Dimerization↗

PubMed1997

Thermodynamic analysis of the interaction between a bactericidal antibody and a PorA epitope of Neisseria meningitidis.

An antibody-peptide model system was used to study the binding characteristics between a bactericidal antibody (MN12H2) and the P1. 16 epitope of class 1 outer membrane protein PorA of Neisseria meningitidis by means of a thermodynamic approach. A series of four linear peptides and three "head-to-tail" cyclic peptides (with ring sizes of 9, 15 and 17 amino acids) were synthesized and evaluated as ligands. The peptides contain a fluorescein label and the core determinant amino acid sequence TKDTNNN (residues 180-186) of the PorA P1.16 epitope of meningococcal strain H44/76. Thermodynamic data of the binding of the peptide homologs of the epitope by MN12H2 were assessed by measuring affinity constants (Ka) over a temperature range of 4-55 degrees C, using fluorescence spectroscopy. Curvilinear plots of ln Ka versus T (K) revealed strong temperature dependencies of enthalpy (DeltaH) and entropy (DeltaS). The Gibbs free energy change (DeltaG) was only weakly temperature dependent. The large negative enthalpy value indicated the importance of polar interactions in the binding of both linear and cyclic peptides by MN12H2. Sturtevant's analysis of the thermodynamic parameters showed large unfavorable vibrational contributions to the binding for all linear peptides [Sturtevant, J. M. (1977) Proc. Natl. Acad. Sci.U.S.A. 74, 2236-2240]. The large hydrophobic contribution compensating these vibrational modes was partially attributed to aspecific interaction of the fluorescein label with the antibody. Binding of MN12H2 to conformationally restricted epitope sequences was characterized by a dramatic reduction in the size of unfavorable vibrational components of the thermodynamic parameters. Substitution of individual charged amino acids of the P1.16 epitope sequence revealed that aspartate-182 was essential for the binding. The pH profile observed for the MN12H2-peptide complexes with a midpoint pH of approximately 8.5 suggests a positively charged histidine from the antibody binding site to be involved in a charge interaction with Asp-182. These findings are consistent with the results from the crystal structure of the Fab fragment of MN12H2 in complex with a linear fluorescein-conjugated peptide homolog of the P1.16 epitope [van den Elsen et al. (1997) Proteins (in press)], thereby identifying the basis of an increased incidence of endemic disease in England and Wales since 1981 caused by a mutant meningococcal strain.

Animals↗

PubMed1998

Thermodynamic consequences of an abasic lesion in duplex DNA are strongly dependent on base sequence.

The abasic site in DNA may arise spontaneously, as a result of nucleotide base damage, or as an intermediate in glycosylase-mediated DNA-repair pathways. It is the most common damage found in DNA. We have examined the consequences of this lesion and its sequence context on DNA duplex structure, as well as the thermal and thermodynamic stability of the duplex, including the energetic origins of that stability. To this end, we incorporated a tetrahydrofuran abasic site analogue into a family of 13-mer DNA duplexes, wherein the base opposite the lesion (A, C, G, or T) and the base pairs neighboring the lesion (C.G or G.C) were systematically varied and characterized by a combination of spectroscopic and calorimetric techniques. The resulting data allowed us to reach the following conclusions: (i) the presence of the lesion in all sequence contexts studied does not alter the global B-form conformation characteristic of the parent undamaged duplex; (ii) the presence of the lesion induces a significant enthalpic destabilization of the duplex, with the magnitude of this effect being dependent on the sequence context; (iii) the thermodynamic impact of the lesion is dominated by the identity of the neighboring base pairs, with the cross strand partner base exerting only a secondary thermodynamic effect on duplex properties. In the aggregate, our data reveal that even in the absence of lesion-induced alterations in global structure, the abasic lesion can significantly alter the thermodynamic properties of the host duplex, with the magnitude of this impact being strongly dependent on sequence context.

Base Composition↗

PubMed1999

Thermodynamics of the alkaline transition of cytochrome c.

The apparent equilibrium constant (Kapp) of the alkaline transition (AT) of beef heart cytochrome c, obtained from pH titrations of the current intensities in cyclic voltammetry experiments, has been measured as a function of the temperature from 5 to 65 degrees C, at different ionic strength (I = 0.01-0.2 M). The temperature profile of the pKapp values is biphasic and yields two distinct sets of DeltaH degrees 'AT and DeltaS degrees 'AT values below and above approximately 40 degrees C. In the low-temperature range, the process is endothermic and is accompanied by a small positive entropy change, while at higher temperatures it becomes less endothermic and involves a pronounced entropy loss. The temperature dependence of the transition thermodynamics is most likely the result of the thermal transition of native ferricytochrome c from a low-T to an high-T conformer which occurs at alkaline pH values at a temperature comparable with above (Ikeshoji, T., Taniguchi, I., and Hawkridge, F. M. (1989) J. Electroanal. Chem. 270, 297-308; Battistuzzi, G., Borsari, M., Sola, M., and Francia, F. (1997) Biochemistry 36, 16247-16258). Thus, it is apparent that the transitions of the two native conformers to the corresponding alkaline form(s) are thermodynamically distinct processes. It is suggested that this difference arises from either peculiar transition-induced changes in the hydration sphere of the protein or to the preferential binding of different lysines to the heme iron in the two temperature ranges. Extrapolation of the Kapp values at null ionic strength allowed the determination of the thermodynamic equilibrium constants (Ka) at each temperature, hence of the "true" standard thermodynamic parameters of the transition. The pKa value at 25 degrees C was found to be 8.0. A pKapp value of 14.4 was calculated for the alkaline transition of ferrocytochrome c at 25 degrees C and I = 0.1 M. The much greater relative stabilization of the native state in the reduced as compared to the oxidized form turns out to be almost entirely enthalpic in origin, and is most likely due to the greater affinity of the methionine sulfur for the Fe(II) ion. Finally, it is found that the Debye-Hückel theory fits the ionic strength dependence of the pKapp values, at least qualitatively, as observed previously for the ionic strength dependence of the reduction potential of this protein class. It is apparent that the increase in the pKapp values with increasing ionic strength is for the most part an entropic effect.

Animals↗

PubMed1991

THERM: a computer code for estimating thermodynamic properties for species important to combustion and reaction modeling.

A computer package has been developed called THERM, an acronym for THermodynamic property Estimation for Radicals and Molecules. THERM is a versatile computer code designed to automate the estimation of ideal gas phase thermodynamic properties for radicals and molecules important to combustion and reaction-modeling studies. Thermodynamic properties calculated include heat of formation and entropies at 298 K and heat capacities from 300 to 1500 K. Heat capacity estimates are then extrapolated to above 5000 K, and NASA format polynomial thermodynamic property representations valid from 298 to 5000 K are generated. This code is written in Microsoft Fortran version 5.0 for use on machines running under MSDOS. THERM uses group additivity principles of Benson and current best values for bond strengths, changes in entropy, and loss of vibrational degrees of freedom to estimate properties for radical species from parent molecules. This ensemble of computer programs can be used to input literature data, estimate data when not available, and review, update, and revise entries to reflect improvements and modifications to the group contribution and bond dissociation databases. All input and output files are ASCII so that they can be easily edited, updated, or expanded. In addition, heats of reaction, entropy changes, Gibbs free-energy changes, and equilibrium constants can be calculated as functions of temperature from a NASA format polynomial database.

Databases, Factual↗

PubMedDate not supplied

In silico analysis of the thermodynamic stability changes of psychrophilic and mesophilic alpha-amylases upon exhaustive single-site mutations.

Identifying sequence modifications that distinguish psychrophilic from mesophilic proteins is important for designing enzymes with different thermodynamic stabilities and to understand the underlying mechanisms. The PoPMuSiC algorithm is used to introduce, in silico, all the single-site mutations in four mesophilic and one psychrophilic chloride-dependent alpha-amylases and to evaluate the changes in thermodynamic stability. The analysis of the distribution of the sequence positions that could be stabilized upon mutation shows a clear difference between the three domains of psychrophilic and mesophilic alpha-amylases. Most of the mutations stabilizing the psychrophilic enzyme are found in domains B and C, contrary to the mesophilic proteins where they are preferentially situated in the catalytic domain A. Moreover, the calculations show that the environment of some residues responsible for the activity of the psychrophilic protein has evolved to reinforce favorable interactions with these residues. In the second part, these results are exploited to propose rationally designed mutations that are predicted to confer to the psychrophilic enzyme mesophilic-like thermodynamic properties. Interestingly, most of the mutations found in domain C strengthen the interactions with domain A, in agreement with suggestions made on the basis of structural analyses. Although this study focuses on single-site mutations, the thermodynamic effects of the recommended mutations should be additive if the mutated residues are not close in space.

Amino Acid Sequence↗

PubMed2002

Thermodynamic correlation analysis: hydration and perturbation sensitivity of RNA secondary structures.

The thermodynamic parameters DeltaH, DeltaS, T(m), and DeltaG of a total of 36 RNA strands, 22 tetralooped 22mers, and 14 heptalooped 25mers (same stem sequence) were analyzed with respect to enthalpy-entropy compensation (EEC). The EEC plots [DeltaH, DeltaS] were compared with collected literature data from protein and nucleic acid unfolding studies (3224 and 241 datapoints, respectively) which all proved to be remarkably linear. The similarity of the compensation slopes and intercepts for all compounds indicate that, irrespective of the chemical nature and stability of the folding solutes, the exothermicity DeltaH and entropic penalty T x DeltaS of folding are strongly dominated by the rearrangement and formation of hydration layers around the solutes, while it is well-known that the stability of folding results only from the difference (DeltaG) and ratio (T(m)) of both parameters. EEC plots [DeltaH, DeltaS] are presented in an extended context, as 3D plots [DeltaH, DeltaS, T(m)] allowing for a correct analytical description of the enthalpy-entropy relationship and for more practical interpretations of large amounts of thermodynamic data when replotted as [DeltaH, T(m)] or [DeltaG(T), T(m)]. The introduction of a variety of mismatches into nucleic acids, or limited irreguliarities into any supramolecular complex, and the analysis of the involved thermodynamics as shown in this study-i.e., scanning the "enthalpy-entropy space" of whole macromolecular subgroups-should permit to extract and quantify more "hidden information", such as hydration extent and sensitivity of macromolecular frameworks toward desolvation and structural perturbation, from thermodynamic analyses of large sample sizes.

Nucleic Acid Conformation↗

PubMed2005

Scan-rate-dependent melting transitions of interleukin-1 receptor (type II): elucidation of meaningful thermodynamic and kinetic parameters of aggregation acquired from DSC simulations.

The role of thermal unfolding as it pertains to thermodynamic properties of proteins and their stability has been the subject of study for more than 50 years. Moreover, exactly how the unfolding properties of a given protein system may influence the kinetics of aggregation has not been fully characterized. In the study of recombinant human Interleukin-1 receptor type II (rhuIL-1R(II)) aggregation, data obtained from size exclusion chromatography and differential scanning calorimetry (DSC) were used to model the thermodynamic and kinetic properties of irreversible denaturation. A break from linearity in the initial aggregation rates as a function of 1/T was observed in the vicinity of the melting transition temperature (T(m) approximately 53.5 degrees C), suggesting significant involvement of protein unfolding in the reaction pathway. A scan-rate dependence in the DSC experiment testifies to the nonequilibrium influences of the aggregation process. A mechanistic model was developed to extract meaningful thermodynamic and kinetic parameters from an irreversibly denatured process. The model was used to simulate how unfolding properties could be used to predict aggregation rates at different temperatures above and below the T(m) and to account for concentration dependence of reaction rates. The model was shown to uniquely identify the thermodynamic parameters DeltaC(P) (1.3 +/- 0.7 kcal/mol-K), DeltaH(m) (74.3 +/- 6.8 kcal/mol), and T(m) with reasonable variances.

Calorimetry, Differential Scanning↗

PubMed2006

Regioselectivity and equilibrium thermodynamics for addition of Rh-OH to olefins in water.

Rhodium(III) tetra(p-sulfonato phenyl) porphyrin ((TSPP)Rh) aquo and hydroxo complexes react with a series of olefins in water to form beta-hydroxyalkyl complexes. Addition reactions of (TSPP)Rh-OH to unactivated terminal alkenes invariably occur with both kinetic and thermodynamic preferences to place rhodium on the terminal carbon to form (TSPP)Rh-CH(2)CH(OH)R complexes. Acrylic and styrenic olefins initially react to place rhodium on the terminal carbon to form Rh-CH(2)CH(OH)X as the kinetically preferred isomer but subsequently proceed to an equilibrium distribution of regioisomers where Rh-CH(CH(2)OH)X is the predominant thermodynamic product. Equilibrium constants for reactions of the diaquo rhodium(III) compound ([(TSPP)Rh(III)(H(2)O)(2)](-3)) in water with a series of terminal olefins that form beta-hydroxyalkyl complexes were directly evaluated and used in deriving thermodynamic values for addition of the Rh-OH unit to olefins. The DeltaG degrees for reactions of the Rh-OH unit with olefins in water is approximately 3 kcal mol(-1) less favorable than the comparable Rh-H reactions in water. Comparisons of the regioisomers and thermodynamics for addition reactions of olefins with Rh-H and Rh-OH units in water are presented and discussed.

Alkenes↗

PubMed2006

Quantum chemical analysis of the thermodynamics of 2D cluster formation of n-carboxylic acids at the air/water interface.

Within the framework of PM3 molecular orbital approximation the thermodynamic function characteristics for the formation and geometrical structure of monomers, dimers, trimers, and tetramers of nondissociated n-carboxylic acids C(n)H(2n+1)COOH with n = 5-15 are calculated. It is shown that spontaneous aggregation of homologous fatty acids for the homologues with carbon atoms numbers n > or = 13 at the air/water interface can take place, leading to the formation of infinite plane rectangular clusters, whereas for the homologues with n < 11 spontaneous decomposition of large aggregates is energetically preferable. At the same time, the formation of trimers is more probable for the lower homologues (8 < n < 13). These results agree well both with the experimental data reported by various authors and with thermodynamic models developed earlier for soluble and insoluble monolayers. The slopes of the regressions calculated for the dependencies of the thermodynamic parameters on the alkyl chain length for all the clusters considered are all equal to each other. This fact indicates that the contributions of the CH2 groups to the thermodynamic characteristics of alcohols and acids are the same, and the differences in the formation of clusters by these substances should be attributed only to the differences in the structure and interactions of relevant functional groups. Therefore, it enables one to describe both acids and alcohols within the framework of the developed method, and it makes it possible to extend the proposed approach onto other classes of amphiphilic compounds.

Air↗

PubMedDate not supplied

Physical stability and solubility advantage from amorphous celecoxib: the role of thermodynamic quantities and molecular mobility.

Glassy pharmaceuticals, characterized by excess thermodynamic properties, are theoretically more soluble than their crystalline counterparts. The practical solubility advantage of the amorphous form of celecoxib (CEL) is lost due to its proclivity to lose energy and undergo solvent-mediated devitrification. Theoretical assessment of solubility advantage using differences in isobaric heat capacities (Cp) revealed a 7-21-fold enhancement in the solubility of the amorphous form over that of the crystalline state of CEL. The present study attempts to unveil these differences between experimental and theoretical solubility using thermodynamic parameters such as free energy, enthalpy, and entropy. Amorphous CEL exhibited 1.3-1.5 times enhancement in Cp over that for the crystalline form. The zero and critical molecular mobility regions, represented by Kauzmann temperature (TK) and glass transition temperature (Tg), were found to lie near 246 and 323 K, respectively, for amorphous CEL. The fictive temperature (Tf), an indicator of the configurational entropy of glass, was determined for glassy CEL, signifying the retention of considerable molecular mobility in the glassy phase that may favor nucleation even below Tg. Further, the estimation of various thermodynamic quantities and strength/fragility parameters (D = 11.5 and m = 67.0) postulated the classification of glassy CEL into moderately fragile liquid, as per Angell's classification. A comprehensive understanding of such thermodynamic facets of amorphous form would help in rationalizing the approaches toward development of stable glassy pharmaceuticals with adequate solubility advantage.

Celecoxib↗

PubMed2005

Variable temperature infrared spectroscopy: a convenient tool for studying the thermodynamics of weak solid-gas interactions.

This tutorial review describes the use of variable temperature infrared spectroscopy of adsorbed species (VTIR), a recent method for studying the thermodynamics of weak solid-gas interactions. Examples show how a fundamental relationship of thermodynamics (the van't Hoff equation, used long since in several fields of physical chemistry) can describe equilibrium processes at the solid-gas interface. The VTIR method is fully exploited by measuring absorbance of an IR band, temperature and pressure over a wide temperature range: an estimation of the interaction energy is, however, possible even ignoring the equilibrium pressure. Precise thermodynamic characterization of solid-gas interactions is required in several fields: on the applied side, gas sensing, separation and storage, which involve such areas as work-place security, air pollution control and the energy sector; regarding fundamental knowledge, weak solid-gas interactions are relevant to a number of fields, including hydrogen bonding, coordination chemistry and surface phenomena in a broad sense. Infrared (IR) spectroscopy of (gas) molecules adsorbed on a solid is frequently used to characterize both, the adsorbed species and the adsorbing centres at the solid surface. The potential of the technique can be greatly enhanced by obtaining IR spectra over a temperature range, and simultaneously measuring IR absorbance, temperature and equilibrium pressure. When this is done, variable temperature infrared (VTIR) spectroscopy can be used not only for a more detailed surface characterization, but also for precise studies on the thermodynamics of solid-gas interactions. Furthermore, when weak interactions are concerned, the technique shows favourable features compared to adsorption calorimetry, or to other classical methods. The potential of the VTIR method is highlighted by reviewing recently reported studies on dihydrogen, dinitrogen and carbon monoxide adsorption on zeolites. To facilitate understanding, an outline of the basis of the method is also given, together with an appraisal of the critical points involved in its practical use.

Adsorption↗

PubMed2005

Predictive thermodynamics for condensed phases.

Thermodynamic information is central to assessment of the stability and reactivity of materials. However, because of both the demanding nature of experimental thermodynamics and the virtually unlimited number of conceivable compounds, experimental data is often unavailable or, for hypothetical materials, necessarily impossible to obtain. We describe simple procedures for thermodynamic prediction for condensed phases, both ionic and organic covalent, principally via formula unit volumes (or density); our volume-based approach (VBT) provides a new thermodynamic tool for such assessment. These methods, being independent of detailed knowledge of crystal structures, are applicable to liquids and amorphous materials as well as to crystalline solids. Examples of their use are provided.

Algorithms↗

PubMedDate not supplied

Quantitative and thermodynamic studies of erythrocytic ABO antigens.

This paper presents recent data from quantitative and thermodynamic investigations on A and B erythrocyte antigens. In regard to weak A phenotypes on the basis of quantitative data, practically no gap is observed from the weakest Aend to the strongest A3. Weak B phenotypes give a similar distribution. However, a more precise structural analysis including kinetics and thermodynamic measurements provides convincing evidence for the heterogeneity of each type of weak B reactive structures. Weak B antigens appear to be different from one to another, but similar inside one family. However, thermodynamics failed to demonstrate a qualitative difference between the weak B antigen in BX groups and the enhanced B antigen in ABX heterozygote, phenomenon that occurs in some very rare families. The same data were obtained from kinetic and thermodynamic analysis of B reactivity in cis AB samples; it can be assumed that such mutants are all different.

ABO Blood-Group System↗

PubMed2006

Fragility and thermodynamics in nonpolymeric glass-forming liquids.

For nonpolymeric supercooled liquids, the empirical correlation m = 56Tg DeltaCp(Tg)/DeltaHm provides a reliable means of correlating dynamic and thermodynamic variables. The dynamics are characterized by the fragility or steepness index m and the glass transition temperature Tg, while thermodynamics enter in terms of the heat capacity step DeltaCp at Tg and the melting enthalpy DeltaHm. The combination of the above correlation with the 23 rule for the Tg/Tm ratio yields an expression, m = 40DeltaCp(Tg)/DeltaSm, which was rationalized as the correlation of the thermodynamic and kinetic fragilities. Defining a thermodynamic fragility via DeltaCp(Tg)/DeltaSm also reveals that the slopes in Kauzmann's original DeltaS(T)/DeltaSm versus T/Tm plot reflect the fragility concept [Chem. Rev. 43, 219 (1948)], so long as Tm/Tg = 1.5. For the many liquids whose excess heat capacity is a hyperbolic function of temperature, we deduce that the fragility cannot exceed m = 170, unless the Tg/Tm = 2/3 rule breaks down.

Chemical Phenomena↗

PubMed2005

Enthalpy of helix-coil transition: missing link in rationalizing the thermodynamics of helix-forming propensities of the amino acid residues.

It is known that different amino acid residues have effects on the thermodynamic stability of an alpha-helix. The underlying mechanism for the thermodynamic helical propensity is not well understood. The major accepted hypothesis is the difference in the side-chain configurational entropy loss upon helix formation. However, the changes in the side-chain configurational entropy explain only part of the thermodynamic helical propensity, thus implying that there must be a difference in the enthalpy of helix-coil transition for different residues. This work provides an experimental test to this hypothesis. Direct calorimetric measurements of folding of a model host peptide in which the helix formation is induced by metal binding is applied to a wide range of residue types, both naturally occurring and nonnatural, at the guest site. Based on the calorimetric results for 12 peptides, it was found that indeed there is a difference in the enthalpy of helix-coil transition for different amino acid residues, and simple empirical rules that define these differences are presented. The obtained difference in the enthalpies of helix-coil transition complement the differences in configurational entropies and provide the complete thermodynamic characterization of the helix-forming tendencies.

Amino Acid Sequence↗

PubMed2006

Conserved thermodynamic contributions of backbone hydrogen bonds in a protein fold.

Backbone-backbone hydrogen-bonding interactions are a ubiquitous and highly conserved structural feature of proteins that adopt the same fold (i.e., have the same overall backbone topology). This work addresses the question of whether or not this structural conservation is also reflected as a thermodynamic conservation. Reported here is a comparative thermodynamic analysis of backbone hydrogen bonds in two proteins that adopt the same fold but are unrelated at the primary amino acid sequence level. With amide-to-ester bond mutations introduced by total chemical synthesis methods, the thermodynamic consequences of backbone-backbone hydrogen-bond deletions at five different structurally equivalent positions throughout the beta-alpha-alpha fold of Arc repressor and CopG were assessed. The ester bond-containing analogues all folded into native-like three-dimensional structures that were destabilized from 2.5 to 6.0 kcal/(mol dimer) compared with wild-type controls. Remarkably, the five paired analogues with amide-to-ester bond mutations at structurally equivalent positions were destabilized to exactly the same degree, regardless of the degree to which the mutation site was buried in the structure. The results are interpreted as evidence that the thermodynamics of backbone-backbone hydrogen-bonding interactions in a protein fold are conserved.

Amino Acid Sequence↗