Thermodynamic descriptors, profiles and driving forces in membrane receptor-ligand interactions

Extension of the (isothermal) Gibbs-Helmholtz equation for the heat capacity terms (ΔC(p)) allows formulating a temperature function of the free (Gibbs) energy change (ΔG). An approximation of the virtually unknown ΔC(p) temperature function enables then to determine and numerically solve temperature functions of thermodynamic parameters ΔH and ΔS (enthalpy and entropy change, respectively). Analytical solutions and respective numeric procedures for several such approximation formulas are suggested in the presented paper. Agreement between results obtained by this analysis with direct microcalorimetric measurements of ΔH (and ΔC(p) derived from them) was approved on selected cases of biochemical interactions presented in the literature. Analysis of several ligand-membrane receptor systems indicates that temperature profiles of ΔH and ΔS are parallel, largely not monotonic, and frequently attain both positive and negative values within the current temperature range of biochemical reactions. Their course is determined by the reaction change of heat capacity: temperature extremes (maximum or minimum) of both ΔH and ΔS occur at ΔC(p)=0, for most of these systems at roughly 285-305 K. Thus, the driving forces of these interactions may change from enthalpy-, entropy-, or enthalpy-entropy-driven in a narrow temperature interval. In contrast, thermodynamic parameters of ligand-macromolecule interactions in solutions (not bound to a membrane) mostly display a monotonic course. In the case of membrane receptors, thermodynamic discrimination between pharmacologically defined groups-agonists, partial agonists, antagonists-is in general not specified and can be achieved, in the best, solely within single receptor groups.     

Thermodynamics of T-cell receptor-peptide/MHC interactions: progress and opportunities

alphabeta T-cell receptors (TCRs) recognize peptide antigens presented by class I or class II major histocompatibility complex molecules (pMHC). Here we review the use of thermodynamic measurements in the study of TCR-pMHC interactions, with attention to the diversity in binding thermodynamics and how this is related to the variation in TCR-pMHC interfaces. We show that there is no enthalpic or entropic signature for TCR binding; rather, enthalpy and entropy changes vary in a compensatory manner that reflects a narrow free energy window for the interactions that have been characterized. Binding enthalpy and entropy changes do not correlate with structural features such as buried surface area or the number of hydrogen bonds within TCR-pMHC interfaces, possibly reflecting the myriad of contributors to binding thermodynamics, but likely also reflecting a reliance on van't Hoff over calorimetric measurements and the unaccounted influence of equilibria linked to binding. TCR-pMHC binding heat capacity changes likewise vary considerably. In some cases, the heat capacity changes are consistent with conformational differences between bound and free receptors, but there is little data indicating these conformational differences represent the need to organize disordered CDR loops. In this regard, we discuss how thermodynamics may provide additional insight into conformational changes occurring upon TCR binding. Finally, we highlight opportunities for the further use of thermodynamic measurements in the study of TCR-pMHC interactions, not only for understanding TCR binding in general, but also for understanding specifics of individual interactions and the engineering of TCRs with desired molecular recognition properties.     

Thermodynamics of Aβ16–21 dissociation from a fibril: Enthalpy,entropy, and volumetric properties

Here, we provide insights into the thermodynamic properties of A dissociation from an amyloid fibril using all‐atom molecular dynamics simulations in explicit water. An umbrella sampling protocol is used to compute potentials of mean force (PMF) as a function of the distance ξ between centers‐of‐mass of the A peptide and the preformed fibril at nine temperatures. Changes in the enthalpy and the entropic energy are determined from the temperature dependence of these PMF(s) and the average volume of the simulation box is computed as a function of ξ. We find that the PMF at 310 K is dominated by enthalpy while the entropic energy does not change significantly during dissociation. The volume of the system decreases during dissociation. Moreover, the magnitude of this volume change also decreases with increasing temperature. By defining dock and lock states using the solvent accessible surface area (SASA), we find that the behavior of the electrostatic energy is different in these two states. It increases (unfavorable) and decreases (favorable) during dissociation in lock and dock states, respectively, while the energy due to Lennard‐Jones interactions increases continuously in these states. Our simulations also highlight the importance of hydrophobic interactions in accounting for the stability of A . Proteins 2015; 83:1963–1972. © 2015 Wiley Periodicals, Inc.     

江西省森林净初级生产力动态变化特征及其驱动因子分析

亚热带森林生态系统具有巨大的固碳潜力。净初级生产力(NPP)在碳循环过程中具有重要的作用, 受到气候变化、大气成分、森林扰动的强度和频度、林龄等因子的综合影响, 然而目前上述各因子对亚热带森林NPP变化的贡献尚不明确, 需要鉴别森林NPP时空变化的主要驱动因子, 以准确认识亚热带森林生态系统碳循环。该文综合气象数据、年最大叶面积指数(LAI)、参考年NPP (BEPS模型模拟)、林龄、森林类型、土地覆盖、数字高程模型(DEM)、土壤质地、CO₂浓度、氮沉降等多源数据, 利用InTEC模型(Integrated Terrestrial Ecosystem Carbon-budget Model)研究亚热带典型地区江西省森林生态系统1901-2010年NPP时空动态变化特征, 通过模拟情景设计, 着重讨论1970-2010年气候变化、林龄、CO₂浓度和氮沉降对森林NPP动态变化的影响。研究结果如下: (1) InTEC模型能较好地模拟研究区NPP的时空变化; (2)江西省森林NPP 1901-2010年为(47.7 ± 4.2) Tg C·a^-1 (平均值±标准偏差), 其中20世纪70年代、80年代、90年代分别为50.7、48.8、45.4 Tg C·a^-1, 2000-2009年平均为55.2 Tg C·a^-1; 随着森林干扰后的恢复再生长, 江西省森林NPP显著上升, 2000-2009年NPP增加的森林面积占森林总面积的60%; (3) 1970-2010年, 仅考虑森林干扰因子和仅考虑非干扰因子(气候、氮沉降、CO₂浓度)情景下NPP分别为43.1和53.9 Tg C·a^-1, 比综合考虑干扰因子和非干扰因子作用下的NPP分别低估7.3 Tg C·a^-1 (低估的NPP与综合考虑干扰因子和非干扰因子作用下NPP的比值为14.5%,下同)和高估3.6 Tg C·a^-1 (7.1%); 气候因子导致平均NPP减少2.0 Tg C·a^-1 (4.7%), 氮沉降导致平均NPP增加4.5 Tg C·a^-1 (10.4%), CO₂浓度变化及耦合效应(氮沉降+ CO₂浓度变化)分别导致平均NPP增加4.4 Tg C·a^-1 (10.3%)和9.4 Tg C·a^-1 (21.8%)。     

新疆玛纳斯河流域2000-2010年土地利用/覆盖变化及影响因素

在2000年和2010年两期遥感影像解译的基础上,从土地利用类型的结构、变化速率、变化方向及土地利用程度等方面分析了玛纳斯河流域土地利用的变化特征,并分析了影响土地利用变化的主要因素及不同因素之间的交互作用。结果表明:(1)近10年来,流域土地利用程度增强,人工绿洲呈扩张趋势,耕地和城乡工矿居民用地大量增加,林地和未利用地减少;上游地区草地和冰川积雪覆盖地面积增加。(2)耕地向内部外部双向扩张,主要来源于林地、荒漠和盐碱地;新增草地以山地裸地和山前荒漠的转变为主;林地主要转变为中游的耕地和城乡工矿居民用地及上游的草地和裸地;城乡工矿居民用地的增加主要来自荒漠、耕地和林地;未利用地变化以向人工绿洲土地类型的转变为主。(3)上游土地利用变化主要受气候变化的影响,降水量增加可能是冰川积雪面积扩张的主要原因;中游人类活动密集,耕地和城乡工矿居民用地扩张,荒漠植被退化;下游受气候和人类活动共同作用,尾闾湖泊萎缩,河岸和湖周植被退化。     

Thermodynamic properties of BPTI variants with highly simplified amino acid sequences

We report the first detailed thermodynamic analysis of simplified proteins by differential scanning calorimetry (DSC). The experiments were carried out with five simplified BPTI variants, whose structures and activities have been reported, in which several residues not essential for specifying the tertiary structure were replaced by alanine. In most aspects, the thermodynamics of simplified proteins were very similar to, if not essentially identical with, those of natural proteins. In particular, they undergo a highly cooperative two-state thermal unfolding process with a large enthalpy change, which is a thermodynamic hallmark of the native state of natural globular proteins. Furthermore, the specific enthalpy and entropy changes upon unfolding at 110 degrees C were close to values invariably observed for small natural globular proteins (55 J g(-1) and ~16 J K(-1) g(-1), respectively). On the other hand, two simplified BPTI variants, BPTI-21 and BPTI-22 (containing 21 and 22 alanine residues), were enthalpically stabilized while entropically destabilized with respect to the reference BPTI-[5,55] molecule. This peculiar type of entropy-enthalpy compensation is in sharp contrast to the usual enthalpy destabilization/entropy stabilization observed in mutational studies of natural proteins. Overall, we conclude that a thermodynamic native state can be achieved by proteins encoded with extensively simplified sequences.     

Protein/DNA interactions involving ATF/AP1-, CCAAT-, and HiNF-D-related factors in the human H3-ST519 histone promoter: cross-competition with transcription regulatory sites in cell cycle controlled H4 and H1 histone genes.

Protein/DNA interactions of the H3-ST519 histone gene promoter were analyzed in vitro. Using several assays for sequence specificity, we established binding sites for ATF/AP1-, CCAAT-, and HiNF-D related DNA binding proteins. These binding sites correlate with two genomic protein/DNA interaction domains previously established for this gene. We show that each of these protein/DNA interactions has a counterpart in other histone genes: H3-ST519 and H4-F0108 histone genes interact with ATF- and HiNF-D related binding activities, whereas H3-ST519 and H1-FNC16 histone genes interact with the same CCAAT-box binding activity. These factors may function in regulatory coupling of the expression of different histone gene classes. We discuss these results within the context of established and putative protein/DNA interaction sites in mammalian histone genes. This model suggests that heterogeneous permutations of protein/DNA interaction elements, which involve both general and cell cycle regulated DNA binding proteins, may govern the cellular competency to express and coordinately control multiple distinct histone genes.     

Pituitary adenylate cyclase-activating polypeptide induces translocation of its G-protein-coupled receptor into caveolin-enriched membrane microdomains, leading to enhanced cyclic AMP generation and neurite outgrowth in PC12 cells

Pituitary adenylate cyclase-activating polypeptide (PACAP), a member of the secretin/glucagon/vasoactive intestinal peptide family expressed throughout the nervous system, binds to the PACAP-specific G-protein-coupled receptor family members to promote both neuronal differentiation and survival. Although the PACAP receptor is known to activate its effector protein, adenylate cyclase (AC), and thus enhance cAMP generation, the molecular mechanism utilized by the receptor to activate AC is lacking. Here, we show that PACAP induces neurite outgrowth in PC12 cells by induction of translocation of the PACAP type 1 receptor (PAC1R) into caveolin-enriched Triton X-100-insoluble microdomains, leading to stronger PAC1R-AC interaction and elevated cAMP production. Moreover, we demonstrate that translocation of PAC1R is blocked by various treatments that selectively disrupt caveolae. As a result, intracellular cAMP level is decreased and consequently the PACAP-induced neurite outgrowth retarded. In contrast, addition of exogenous ganglioside GM1 to the cells shows the opposite effects. These results therefore identify the PACAP-induced translocation of its G-protein-coupled receptor into caveolae, where both AC and the regulating G-proteins reside, as the key molecular event in activating AC and inducing cAMP-mediated differentiation of PC12 cells.     

Influence of Glu-376 --> Gln mutation on enthalpy and heat capacity changes for the binding of slightly altered ligands to medium chain acyl-CoA dehydrogenase

We showed that the alpha-CH(2) --> NH substitution in octanoyl-CoA alters the ground and transition state energies for the binding of the CoA ligands to medium-chain acyl-CoA dehydrogenase (MCAD), and such an effect is caused by a small electrostatic difference between the ligands. To ascertain the extent that the electrostatic contribution of the ligand structure and/or the enzyme site environment modulates the thermodynamics of the enzyme-ligand interaction, we undertook comparative microcalorimetric studies for the binding of 2-azaoctanoyl-CoA (alpha-CH(2) --> NH substituted octanoyl-CoA) and octenoyl-CoA to the wild-type and Glu-376 --> Gln mutant enzymes. The experimental data revealed that both enthalpy (DeltaH degrees ) and heat capacity changes (DeltaC(p) degrees ) for the binding of 2-azaoctanoyl-CoA (DeltaH degrees (298) = -21.7 +/- 0.8 kcal/mole, DeltaC(p) degrees = -0.627 +/- 0.04 kcal/mole/K) to the wild-type MCAD were more negative than those obtained for the binding of octenoyl-CoA (DeltaH degrees (298) = -17.2 +/- 1.6 kcal/mole, DeltaC(p) degrees = -0.526 +/- 0.03 kcal/mole/K). Of these, the decrease in the magnitude of DeltaC(p) degrees for the binding of 2-azaoctanoyl-CoA (vis-à-vis octenoyl-CoA) to the enzyme was unexpected, because the former ligand could be envisaged to be more polar than the latter. To our further surprise, the ligand-dependent discrimination in the above parameters was completely abolished on Glu-376 --> Gln mutation of the enzyme. Both DeltaH degrees and DeltaC(p) degrees values for the binding of 2-azaoctanoyl-CoA (DeltaH degrees (298) = -13.3 +/- 0.6 kcal/mole, DeltaC(p) degrees = -0.511 +/- 0.03 kcal/mole/K) to the E376Q mutant enzyme were found to be correspondingly identical to those obtained for the binding of octenoyl-CoA (DeltaH degrees (298) = -13.2 +/- 0.6 kcal/mole, DeltaC(p) degrees = -0.520 +/- 0.02 kcal/mole/K). However, in neither case could the experimentally determined DeltaC(p) degrees values be predicted on the basis of the changes in the water accessible surface areas of the enzyme and ligand species. Arguments are presented that the origin of the above thermodynamic differences lies in solvent reorganization and water-mediated electrostatic interaction between ligands and enzyme site groups, and such interactions are intrinsic to the molecular basis of the enzyme-ligand complementarity.