Comparative statistical mechanics of myosin molecular motors in rat heart, diaphragm and tracheal smooth muscle

Purpose

Statistical mechanics establishes a link between microscopic properties of matter and its bulk properties. A. Huxley's equations (1957) [1] provide the necessary phenomenological formalism to use statistical mechanics.

Methods

We compared statistical mechanics in rat diaphragm in tetanus (tet; n = 10) and twitch (tw; n = 12) modes, in heart in twitch mode (n = 20), and in tracheal smooth muscle in tetanus mode (TSM; n = 10). This powerful tool makes it possible to determine: (i) statistical entropy (S) which is related to the dispersal of energy and represents a measure of the degree of disorder in muscular system; (ii) thermodynamic force A/T (chemical affinity A and temperature T); (iii) thermodynamic flow (υ); (iv) entropy production rate (A/T × υ), which quantifies irreversible chemical processes generated by myosin crossbridge (CB) molecular motors.

Results

All muscles studied operated near equilibrium, i.e., A << 2500 J/mol and in a stationary linear regime, i.e., A/T varied linearly with υ. The heart operated farther from equilibrium than both diaphragm (tet and tw) and TSM, as attested by its high entropy production rate. S was of the same order of magnitude in heart and TSM but lower in diaphragm (tet and tw).

Conclusion

CB kinetics derived from A. Huxley's equations conferred a characteristic profile in terms of statistical mechanics on each muscle type. All studied muscles differed in terms of statistical entropy, chemical affinity, and entropy production rate. Stimulation mode (tet and tw) modulated CB kinetics and statistical mechanics. All muscle types operated near equilibrium and in a stationary linear regime.     

Increased entropy production in diaphragm muscle of PPAR alpha knockout mice

Peroxisome proliferator activated receptor alpha (PPAR alpha) regulates fatty acid beta-oxidation (FAO) and plays a central role in the metabolic and energetic homeostasis of striated muscles. The thermodynamic consequences of the absence of PPAR alpha were investigated in diaphragm muscle of PPAR alpha knockout mice (KO). Statistical mechanics provides a powerful tool for determining entropy production, which quantifies irreversible chemical processes generated by myosin molecular motors and which is the product of thermodynamic force A/T (chemical affinity A and temperature T) and thermodynamic flow (myosin crossbridge (CB) cycle velocity upsilon). The behavior of both wild type (WT) and KO diaphragm was shown to be near-equilibrium and in a stationary state, but KO was farther from equilibrium than WT. In KO diaphragm, a substantial decrease in contractile function was associated with an increase in both A/T and upsilon and with profound histological injuries such as contraction band necrosis. There were no changes in PPAR delta and gamma expression levels or myosin heavy chain (MHC) patterns. In KO diaphragm, a marked increase in entropy production (A/T x upsilon) accounted for major thermodynamic dysfunction and a dramatic increase in irreversible chemical processes during the myosin CB cycle.     

Ultraslow Myosin Molecular Motors of Placental Contractile Stem Villi in Humans

Human placental stem villi (PSV) present contractile properties. In vitro mechanics were investigated in 40 human PSV. Contraction of PSV was induced by both KCl exposure (n = 20) and electrical tetanic stimulation (n = 20). Isotonic contractions were registered at several load levels ranging from zero-load up to isometric load. The tension-velocity relationship was found to be hyperbolic. This made it possible to apply the A. Huxley formalism for determining the rate constants for myosin cross-bridge (CB) attachment and detachment, CB single force, catalytic constant, myosin content, and maximum myosin ATPase activity. These molecular characteristics of myosin CBs did not differ under either KCl exposure or tetanus. A comparative approach was established from studies previously published in the literature and driven by mean of a similar method. As compared to that described in mammalian striated muscles, we showed that in human PSV, myosin CB rate constants for attachment and detachment were about 10³ times lower whereas myosin ATPase activity was 10⁵ times lower. Up to now, CB kinetics of contractile cells arranged along the long axis of the placental sheath appeared to be the slowest ever observed in any mammalian contractile tissue.     

Liquid chromatographic separation and thermodynamic investigation of lorcaserin hydrochloride enantiomers on immobilized amylose–based chiral stationary phase

A novel liquid chromatographic method was developed for enantiomeric separation of lorcaserin hydrochloride on Chiralpak IA column containing chiral stationary phase immobilized with amylose tris (3.5‐dimethylphenylcarbamate) as chiral selector. Baseline separation with resolution greater than 4 was achieved using mobile phase containing mixture of n‐hexane/ethanol/methanol/diethylamine (95:2.5:2.5:0.1, v/v/v/v) at a flow rate of 1.2 mL/min. The limit of detection and limit of quantification of the S‐enantiomer were found to be 0.45 and 1.5 μg/mL, respectively; the developed method was validated as per ICH guideline. The influence of column oven temperatures studied in the range of 20°C to 50°C on separation was studied; from this, retention, separation, and resolution were investigated. The thermodynamic parameters ΔH°, ΔS°, and ΔG° were evaluated from van't Hoff plots,(Ink′ _versus 1/T) and used to explain the strength of interaction between enantiomers and immobilized amylose–based chiral stationary phase     

Glucose metabolic adaptations in the intrauterine growth-restricted adult female rat offspring

We studied glucose metabolic adaptations in the intrauterine growth-restricted (IUGR) rat offspring to decipher glucose homeostasis in metabolic programming. Glucose futile cycling (GFC), which is altered when there is imbalance between glucose production and utilization, was studied during a glucose tolerance test (GTT) in 2-day-old (n = 8), 2-mo-old (n = 22), and 15-mo-old (n = 22) female rat offspring. The IUGR rats exposed to either prenatal (CM/SP, n = 5 per age), postnatal (SM/CP, n = 6), or pre- and postnatal (SM/SP, n = 6) nutrient restriction were compared with age-matched controls (CM/CP, n = 5). At 2 days, IUGR pups (SP) were smaller and glucose intolerant and had increased hepatic glucose production and increased glucose disposal (P < 0.01) compared with controls (CP). At 2 mo, the GTT, glucose clearance, and GFC did not change. However, a decline in hepatic glucose-6-phosphatase (P < 0.05) and fructose-1,6-biphosphatase (P < 0.05) enzyme activities in the IUGR offspring was detected. At 15 mo, prenatal nutrient restriction (CM/SP) resulted in greater weight gain (P < 0.01) and hyperinsulinemia (P < 0.001) compared with postnatal nutrient restriction (SM/CP). A decline in GFC in the face of a normal GTT occurred in both the prenatal (CM/SP, P < 0.01) and postnatal calorie (SM/CP, P < 0.03) and growth-restricted offspring. The IUGR offspring with pre- and postnatal nutrient restriction (SM/SP) were smaller, hypoinsulinemic (P < 0.03), and hypoleptinemic (P < 0.03), with no change in GTT, hepatic glucose production, GFC, or glucose clearance. We conclude that there is pre- and postnatal programming that affects the postnatal compensatory adaptation of GFC and disposal initiated by changes in circulating insulin concentrations, thereby determining hepatic insulin sensitivity in a phenotype-specific manner.     

Photosynthesis and negative entropy production

The widely held view that the maximum efficiency of a photosynthetic pigment system is given by the Carnot cycle expression (1-T/Tr) for energy transfer from a hot bath (radiation at temperature Tr) to a cold bath (pigment system at temperature T) is critically examined and demonstrated to be inaccurate when the entropy changes associated with the microscopic process of photon absorption and photochemistry at the level of single photosystems are considered. This is because entropy losses due to excited state generation and relaxation are extremely small (DeltaS < T/Tr) and are essentially associated with the absorption-fluorescence Stokes shift. Total entropy changes associated with primary photochemistry for single photosystems are shown to depend critically on the thermodynamic efficiency of the process. This principle is applied to the case of primary photochemistry of the isolated core of higher plant photosystem I and photosystem II, which are demonstrated to have maximal thermodynamic efficiencies of xi > 0.98 and xi > 0.92 respectively, and which, in principle, function with negative entropy production. It is demonstrated that for the case of xi > (1-T/Tr) entropy production is always negative and only becomes positive when xi < (1-T/Tr).     

Hydrophylic surfactant–imidazole derivative association studied by RPLC using a hydroorganic solution

A high-performance liquid chromatographic (HPLC) method for an association study of imidazole derivatives in surfactant micellars using a hydrophilic detergent, i.e. Montanox DF 80 was presented. The thermodynamic results obtained showed that imidazole association in the surfactant micelles was effective over a concentration of surfactant equal to approximatively 4·10⁻⁴ mol/l. In addition, an enthalpy–entropy compensation study revealed that the type of interaction between the solute and the RP18 stationary phase was independent of the molecular structure. The thermodynamic variations observed were considered to be the result of equilibrium displacement between the solute and free ethanol (respectively free surfactant) and its clusters (respectively to micelles) created in the mobile phase.     

Optimization of whey fermentation in a shaken-flask fermenter

Summary A composite design technique was used to optimize the fermentation of whey by Kluyveromyces fragilis IMAT 1872. The experimental variables (temperature T, salts NP, yeast-extract YE and lactose level L), but not pH, were found to be significant at a level of 5%. The optimal operating conditions were determined (T=36.4°C, pH=5.1, NP=0.47% w/v, YE=0.114% w/v, and L=24.75 g/l). Temperature and lactose level exhibited a great influence on the biomass yield about the stationary point. Canonical analysis showed that these variables are not mutually independent. The optimal conditions will be used as starting point for a factorial design on a jar fermenter.     

Neonatal brain: Fabrication of a tissue-mimicking phantom and optimization of clinical Τ1w and T2w MRI sequences at 1.5 T

PurposeTο fabricate a tissue-mimicking phantom simulating the MR relaxation times of neonatal gray and white matter at 1.5 T, for the optimization of clinical Τ1 weighted (T1w) and T2 weighted (T2w) sequences.MethodsNumerous agarose gel solutions, doped with paramagnetic Gadopentetic acid (Gd-DTPA) ions, underwent quantitative relaxometry with a Turbo-Inversion-Recovery Spin-Echo (TIRSE) sequence and a Car-Purcell-Meiboom-Gill (CPMG) sequence for T1 and T2 measurements, respectively. Twenty samples which simulated the spectrum of relaxation times of neonatal brain parenchyma were selected. Reproducibility was tested by refabrication and relaxometry of the relevant samples while stability was tested by six sets of quantitative relaxometry scans during a 12-month period.Results“Neonatal gray matter equivalent”(0.6%w/v agarose-0.10 mM Gd-DTPA), accurately mimicked relaxation times of neonatal gray matter: T1 = (1134 ± 7)ms, T2 = (200 ± 7)ms. “Neonatal white matter equivalent”(0.3%w/v agarose-0.03 mM Gd-DTPA), accurately mimicked relaxation times of neonatal white matter: T1 = (1654 ± 9)ms, T2 = (376 ± 4)ms. Coefficient of variation of T1 and T2 relaxation times measurements remained less than 5% during 12 months. Sequences were modified according to maximum relative contrast (RC) between neonatal gray and white matter equivalents. Optimized T2wTSE and T1wTSE parameters were TR/TE = 9500 ms/280 ms and TR/TE = 1200 ms/10 ms, respectively for a MAGNETOM Vision/Sonata Hybrid 1.5 T system. Quantitative relaxometry at different 1.5 T MR systems resulted in inter-system T1, T2 measurement deviations of 12% and 3%, respectively.ConclusionA precise, stable and reproducible phantom for the neonatal brain was fabricated. Subsequent optimization of clinical T1w and T2w sequences based on maximum RC between neonatal gray and white matter equivalents was scientifically supported with robust relaxometry. The procedure was applicable in different 1.5 T systems.HighlightTR & TE optimization of neonatal brain at 1.5 T was based on relaxometry of a stable, reproducible phantom.     

Effects of acetic acid on the temperature range of ethanol tolerance inCandida shehate growing on D-xylose

Summary The yeastCandida shehatæ, growing on a mineral medium with vitamins and D-xylose as sole carbon and energy source, tolerated acetic acid up to 0.4% (v/v), at pH 4.5, the temperature range of growth narrowing from 5–34°C to 21–27°C, and the growth yield on D-xylose decreasing to 64%; tolerance to added ethanol dropped from 5% (v/v) to 2% (v/v). Acetic acid concertedly shifted the Arrhenius plots of thermal death and growth to lower temperatures, but left unchanged the former dissociative relations in the temperature profile. The entropy coefficient of acetic acid-enhanced thermal death was 183.3 entropy units. M^–1.     

The gross and amino acid compositions of batch and semi-continuous cultures ofIsochrysis sp. (clone T.ISO),Pavlova lutheri andNannochloropsis oculata

Three species of microalgae commonly used in mariculture —Isochrysis sp. (clone T.ISO) Parke,Pavlova lutheri (Droop) Green andNannochloropsis oculata (Droop) Green — were grown in batch and semicontinuous modes to compare their biochemical composition and production rates.In batch mode, logarithmic-phase cultures of all species had high levels of protein (25.2 to 41.1) and low levels of carbohydrate (7.1 to 10.3) and lipid (8.8 to 14.9). At stationary phase, cultures ofIsochrysis sp. (clone T.ISO) andN. oculata contained significantly less protein (21.8 and 20.3, respectively), all species contained more carbohydrate (14.8 to 30.6), andP. lutheri contained more lipid (16.6). In semi-continuous mode, cultures maintained at late logarithmic-phase contained more carbohydrate,Isochrysis sp. (clone T.ISO) contained less protein, andP. lutheri more lipid than logarithmic-phase batch cultures of the same species. Neither growth phase nor harvest regime affected the amino acid composition of the microalgae significantly. However, the concentration of proline inN. oculata was higher in batch cultures in logarithmic phase (9.4), than in either semi-continuous cultures in logarithmic phase (5.8 to 7.9) or batch cultures in stationary phase (5.6 to 5.9).The production rates from batch and semi-continuous logarithmic-phase cultures were not significantly different for any of the species, and there were only minor differences in the production rates of the species (range 12.4 to 17.1 mg algae dry weight 1^–1 d^–1). The different culture and harvest regimes produced significant differences in the proportions of protein and carbohydrate in the microalgae. Which regime is chosen for culturing these microalgae as food will depend on the nutritional requirements of the animal species being fed.     

RNA Thermodynamic Structural Entropy

Conformational entropy for atomic-level, three dimensional biomolecules is known experimentally to play an important role in protein-ligand discrimination, yet reliable computation of entropy remains a difficult problem. Here we describe the first two accurate and efficient algorithms to compute the conformational entropy for RNA secondary structures, with respect to the Turner energy model, where free energy parameters are determined from UV absorption experiments. An algorithm to compute the derivational entropy for RNA secondary structures had previously been introduced, using stochastic context free grammars (SCFGs). However, the numerical value of derivational entropy depends heavily on the chosen context free grammar and on the training set used to estimate rule probabilities. Using data from the Rfam database, we determine that both of our thermodynamic methods, which agree in numerical value, are substantially faster than the SCFG method. Thermodynamic structural entropy is much smaller than derivational entropy, and the correlation between length-normalized thermodynamic entropy and derivational entropy is moderately weak to poor. In applications, we plot the structural entropy as a function of temperature for known thermoswitches, such as the repression of heat shock gene expression (ROSE) element, we determine that the correlation between hammerhead ribozyme cleavage activity and total free energy is improved by including an additional free energy term arising from conformational entropy, and we plot the structural entropy of windows of the HIV-1 genome. Our software RNAentropy can compute structural entropy for any user-specified temperature, and supports both the Turner’99 and Turner’04 energy parameters. It follows that RNAentropy is state-of-the-art software to compute RNA secondary structure conformational entropy. Source code is available at https://github.com/clotelab/RNAentropy/; a full web server is available at http://bioinformatics.bc.edu/clotelab/RNAentropy, including source code and ancillary programs.     

Chitin oligosaccharide binding to a family GH19 chitinase from the moss Bryum coronatum

Substrate binding of a family GH19 chitinase from a moss species, Bryum coronatum (BcChi-A, 22 kDa), which is smaller than the 26 kDa family GH19 barley chitinase due to the lack of several loop regions ('loopless'), was investigated by oligosaccharide digestion, thermal unfolding experiments and isothermal titration calorimetry (ITC). Chitin oligosaccharides [β-1,4-linked oligosaccharides of N-acetylglucosamine with a polymerization degree of n, (GlcNAc)(n), n = 3-6] were hydrolyzed by BcChi-A at rates in the order (GlcNAc)(6) > (GlcNAc)(5) > (GlcNAc)(4) > (GlcNAc)(3). From thermal unfolding experiments using the inactive BcChi-A mutant (BcChi-A-E61A), in which the catalytic residue Glu61 is mutated to Ala, we found that the transition temperature (T(m) ) was elevated upon addition of (GlcNAc)(n) (n = 2-6) and that the elevation (ΔT(m)) was almost proportional to the degree of polymerization of (GlcNAc)(n). ITC experiments provided the thermodynamic parameters for binding of (GlcNAc)(n) (n = 3-6) to BcChi-A-E61A, and revealed that the binding was driven by favorable enthalpy changes with unfavorable entropy changes. The change in heat capacity (ΔC(p)°) for (GlcNAc)(6) binding was found to be relatively small (-105 ± 8 cal·K(-1) ·mol(-1)). The binding free energy changes for (GlcNAc)(6), (GlcNAc)(5), (GlcNAc)(4) and (GlcNAc)(3) were determined to be -8.5, -7.9, -6.6 and -5.0 kcal·mol(-1), respectively. Taken together, the substrate binding cleft of BcChi-A consists of at least six subsites, in contrast to the four-subsites binding cleft of the 'loopless' family 19 chitinase from Streptomyces coelicolor. DATABASE: Chitinase, EC 3.2.1.14.     

Maturational differences between vascular and bladder smooth muscle during ovine development

Maturation rates of vascular and visceral smooth muscle (SM) during ovine development were compared by quantifying contractile protein, myosin heavy chain (MHC) isoform contents, and contractile properties of aortas and bladders from female fetal (n = 19) and postnatal (n = 21) sheep. Actin, myosin, and protein contents rose progressively throughout development in both tissues (P 相似文献   

Thermal stability and thermodynamic analysis of native and methoxypolyethylene glycol modified trypsin

Four methoxypolyethylene glycols (MPEG, molecular masses 350, 750, 2000 and 5000 Da), each activated by nitrophenyl chloroformate, were used to modify trypsin. Compared with the native trypsin, the MPEG-modified trypsin was more stable against temperature between 30°C and 70°C, longer chain of MPEG moiety corresponding to higher thermal stability. The T for the native and the modified trypsin (0.4 mg ml^–1) was increased from 47°C to 66°C. The stabilization effect caused by MPEG modification was the result of decreasing in both the autolysis rate and the thermal denaturation rate. The thermodynamic analysis of the thermal denaturation process showed that the activation free energy (G^*) of the native and the modified trypsin at 60°C was increased from 102.9 to 109.3 kJ mol^–1; the activation enthalpy (H^*) was increased from 57.4 to 86.9 kJ mol^–1; the activation entropy (S^*) was increased from –136 to –67 J molK^–1. A possible explanation for the decreased thermal denaturation rate caused by MPEG modification was also discussed.     

Thermodynamics and muscle contraction. II. Consequences of the principle of maximization of the rate of entropy production]

For non-elastic irreversible mechanochemical machines of the muscular type, the above-mentioned principle (by H. Ziegler) leads to the following results. The velocity of shortening, v, decreases when the force F increases. The mechanical power of the system Fv, is active when 0 greater than v greater than vF=0 or 0 greater than F greater than Fv=0. At F=0 the rate of chemical reaction has the maximum and dQ/dF = -v greater than 0 (where Q is the rate of heat production). At v = 0 the rate of entropy production has the minimum and d/dv = F/A greater than 0 (where A is an affinity of the chemical reaction). The Onsager symmetry relation holds at v=0 only.     

基于核型和分子系统学方法对中国猪尾鼠分类与分布的讨论

猪尾鼠属（Typhlomys）是啮齿类中的孑遗类群,片段化分布于我国南方和越南最北部的山地森林。前期我们基于形态和分子系统学的方法将猪尾鼠属现生类群划分为4个物种。但该分类系统仍存在争议和有待于解决的问题：一方面,有学者对大娄山猪尾鼠等是否应属于种级分类单元抱有疑问;另一方面,秦岭、南岭和广西周边的猪尾鼠种群的分类地位仍未有定论。因此,本研究采用核型分析以及分子系统学分析的方法,对我国猪尾鼠的分类及分布进行进一步梳理。本研究首次报道了中华猪尾鼠和大娄山猪尾鼠的G带核型和Ag-NORs的数目和分布,其中中华猪尾鼠2n=36,核型为14(M, SM) + 20 (A),XY (SM, A),Ag-NORs 6个;大娄山猪尾鼠2n=56,核型为2 (SM) + 52 (A),XX (SM, SM ),Ag-NORs 4个。上述核型与已报道的沙巴猪尾鼠核型（2n=38）存在显著差异,支持上述类群均为独立物种。基于线粒体Cyt b,ND2和COⅠ基因的进化关系分析,秦岭种群应属于大娄山猪尾鼠、南岭种群应属于中华猪尾鼠。而来自红河以东的云南南部的种群以及贵州南部的种群情况复杂,暗示云南、贵州和广西的喀斯特地区可能还存在未知的分类单元。     

Herbage intake and behavioural adaptation of grazing dairy cows by restricting time at pasture under two feeding regimes

The time at pasture of dairy cows is often restricted in the context of extending the grazing season in autumn or at the end of winter. The objective of our study was to evaluate the effects of a restriction of time at pasture on milk production, herbage intake and feeding behaviour in dairy cows according to feeding regime. The four treatments consisted of 4 h or 8 h of time at pasture per day tested under two feeding regimes combining rate of supplementation and herbage allowance: either a high rate of supplementation (10 kg dry matter (DM) of a maize silage-soya bean meal mixture in the ratio 87 : 13 on a % DM basis) with a low herbage allowance (6 kg DM/cow per day above 5 cm), or a low rate of supplementation (5 kg DM of the same supplement) with a high herbage allowance (11 kg DM/cow per day). The study was carried out according to a 4 × 4 Latin square design with four 2-week periods, with 48 mid-lactation Holstein cows. The cows in the 4-h treatment had access to pasture from 0900 h to 1300 h and those in the 8-h treatment from 0900 h to 1700 h. The supplement was given at 1830 h. When time at pasture was reduced from 8 h to 4 h per day, herbage intake decreased (9.9 v. 8.1 kg DM, P < 0.001), along with a fall in milk production (22.3 v. 21.2 kg, P < 0.001) and milk protein concentration (30.1 v. 29.6 g/kg, P < 0.001), while milk fat concentration increased (39.4 v. 39.9 g/kg, P < 0.05). The effect of time at pasture on milk production was slightly more marked on the low-supplement feeding regime (interaction P < 0.06). Reducing time at pasture by 4 h led to a sharp decrease in grazing time (327 v. 209 min, P < 0.001), but strongly increased the pasture intake rate (31 v. 39 g DM/min, P < 0.001) and the proportion of time spent grazing (0.68 v. 0.87, P < 0.001). Cows showed a stronger motivation for grazing when receiving the low-supplement feeding regime. In conclusion, we showed that reducing time at pasture from 8 to 4 h for cows receiving 5 to 10 kg DM of a maize silage-based supplement decreased moderately milk production and herbage intake, because of the capacity for behavioural adaptation by the grazing dairy cows.     

Calculating Stress: From Entropy to a Thermodynamic Concept of Health and Disease

To date, contemporary science has lacked a satisfactory tool for the objective expression of stress. This text thus introduces a new–thermodynamically derived–approach to stress measurement, based on entropy production in time and independent of the quality or modality of a given stressor or a combination thereof. Hereto, we propose a novel model of stress response based on thermodynamic modelling of entropy production, both in the tissues/organs and in regulatory feedbacks. Stress response is expressed in our model on the basis of stress entropic load (SEL), a variable we introduced previously; the mathematical expression of SEL, provided here for the first time, now allows us to describe the various states of a living system, including differentiating between states of health and disease. The resulting calculation of stress response regardless of the type of stressor(s) in question is thus poised to become an entirely new tool for predicting the development of a living system.     

Predicting loop–helix tertiary structural contacts in RNA pseudoknots

Tertiary interactions between loops and helical stems play critical roles in the biological function of many RNA pseudoknots. However, quantitative predictions for RNA tertiary interactions remain elusive. Here we report a statistical mechanical model for the prediction of noncanonical loop–stem base-pairing interactions in RNA pseudoknots. Central to the model is the evaluation of the conformational entropy for the pseudoknotted folds with defined loop–stem tertiary structural contacts. We develop an RNA virtual bond-based conformational model (Vfold model), which permits a rigorous computation of the conformational entropy for a given fold that contains loop–stem tertiary contacts. With the entropy parameters predicted from the Vfold model and the energy parameters for the tertiary contacts as inserted parameters, we can then predict the RNA folding thermodynamics, from which we can extract the tertiary contact thermodynamic parameters from theory–experimental comparisons. These comparisons reveal a contact enthalpy (ΔH) of −14 kcal/mol and a contact entropy (ΔS) of −38 cal/mol/K for a protonated C⁺•(G–C) base triple at pH 7.0, and (ΔH = −7 kcal/mol, ΔS = −19 cal/mol/K) for an unprotonated base triple. Tests of the model for a series of pseudoknots show good theory–experiment agreement. Based on the extracted energy parameters for the tertiary structural contacts, the model enables predictions for the structure, stability, and folding pathways for RNA pseudoknots with known or postulated loop–stem tertiary contacts from the nucleotide sequence alone.