Computational analysis of Asp519 and Glu665 mutations of coagulation factor FVIIIa: Implications for enhanced binding affinity of A2-domain

The A2-domain of blood coagulation factor VIIIa is non-covalently bound to the A1 and A3 domains via weak intermolecular interactions. Functional instability due to rapid dissociation of A2-domain from the active FVIII in blood presents a major hurdle for the therapeutic applications of FVIIIa to treat Hemophilia-A. To identify the ideal hot-spot residues at the interface of A2 and A1/A3 domains that could enhance the structural stability of FVIIIa, we performed a comprehensive computational mutagenesis study of two A2-domain residues, Asp519 and Glu665, that interface the A1 and A3-domains. Each residue was mutated to 15 uncharged amino-acids and the mutant structures were refined by MD simulations. Based on the estimated relative binding affinities of mutant structures, we predict that the mutation of Asp519 to Leu, Gln, Thr, Val and the mutation of Glu665 to Val, Ile, Met, Asn and Trp enhance the A2-domain binding affinity by more than 20 kcal/mol, compared to the WT structure. We anticipate that these predictions will be valuable for enzymatic studies towards the rational design of FVIIIa synthetic constructs with improved A2-domain binding affinity.     

底排药剂燃烧产气量的理论计算

燃烧产气量是底排药剂很重要的参数.采用最小自由能法建立了底排药剂燃烧平衡产物的计算模型,以现役的某烟火型底排药剂配方为对象进行计算,根据计算结果确定出该底排药剂的燃烧产气量.     

Global behavior of the diffusion coefficient for the Van Der Waals binary mixture

We describe the general dependence of the diffusion coefficient associated with the Van der Waals binary mixture on the temperature, number densities, and relative strengths of molecular interaction parameters. The task is facilitated by the fact that for Kac-type intermolecular potentials, in the long-range limit, the diffusion coefficient becomes simply related to the product of a partial compressibility and the curvature of the equilibrium free energy in the space of number densities. Therefore the different kinds of behavior found can be classified according to the scheme of Scott and Van Konynenburg for the global phase diagram of the same model mixture.Paper presented at the Tenth Symposium on Thermophysical Properties, June 20–23, 1988, Gaithersburg, Maryland, U.S.A.     

最小自由能法求解GAP在等压绝热条件下的燃烧产物

采用最小自由能法计算了GAP在等压绝热条件下的燃烧温度以及产物的比例，从理论上说明了GAP的燃烧特点。计算结果显示，GAP燃烧产物中有较多的固态C、气态H2、CO等可以再燃烧的物质存在。     

Effect of FA chain length on normal- and reversed-phase HPLC of phospholipids

Forty-seven saturated synthetic diacyl PA, PC, PE, PG, and PS and five unsaturated diacyl phospholipids (PL) underwent normal- and reversed-phase (RP) HPLC with isocratic isopropanol/hexane/water (5∶4∶1) and methanol/chloroform/acetonitrile/water (79.5∶9∶8∶3.5) mobile phases, respectively. For normal-phase HPLC, capacity factors (k′ _i ) decrease with chain length (n) of the two identical PL FA residues, whereas the opposite occurs with RP (C₁₈)-HPLC. Plots of In k′ _i vs. n for individual PL classes are in general curved, violating the linear free-energy relationship. For PL of the same n but with different head groups, k′ _i with normal-phase HPLC varies as PE<PG<PA<PS<PC, except when n≥16, when the order is PE<PS≈PA≈PG<PC. For RP-HPLC, the order of k′ _i values is PG<_A≈PS≤PC≈PE until n≥16, when it is PA≈PG<PS≪PC≈PE. With normal-phase HPLC, k′ _i values of PL with unsaturated FA of n=18 are ordered as PE<PA<PC. Increasing degrees of unsaturation lead to increasing k′ _i .     

Developing an Updated Strategy for Estimating the Free-Energy Parameters in RNA Duplexes

For the last 20 years, it has been common lore that the free energy of RNA duplexes formed from canonical Watson–Crick base pairs (bps) can be largely approximated with dinucleotide bp parameters and a few simple corrective constants that are duplex independent. Additionally, the standard benchmark set of duplexes used to generate the parameters were GC-rich in the shorter duplexes and AU-rich in the longer duplexes, and the length of the majority of the duplexes ranged between 6 and 8 bps. We were curious if other models would generate similar results and whether adding longer duplexes of 17 bps would affect the conclusions. We developed a gradient-descent fitting program for obtaining free-energy parameters—the changes in Gibbs free energy (ΔG), enthalpy (ΔH), and entropy (ΔS), and the melting temperature (Tm)—directly from the experimental melting curves. Using gradient descent and a genetic algorithm, the duplex melting results were combined with the standard benchmark data to obtain bp parameters. Both the standard (Turner) model and a new model that includes length-dependent terms were tested. Both models could fit the standard benchmark data; however, the new model could handle longer sequences better. We developed an updated strategy for fitting the duplex melting data.     

Development of free-energy-based models for chaperonin containing TCP-1 mediated folding of actin

A free-energy-based approach is used to describe the mechanism through which chaperonin-containing TCP-1 (CCT) folds the filament-forming cytoskeletal protein actin, which is one of its primary substrates. The experimental observations on the actin folding and unfolding pathways are collated and then re-examined from this perspective, allowing us to determine the position of the CCT intervention on the actin free-energy folding landscape. The essential role for CCT in actin folding is to provide a free-energy contribution from its ATP cycle, which drives actin to fold from a stable, trapped intermediate I₃, to a less stable but now productive folding intermediate I₂. We develop two hypothetical mechanisms for actin folding founded upon concepts established for the bacterial type I chaperonin GroEL and extend them to the much more complex CCT system of eukaryotes. A new model is presented in which CCT facilitates free-energy transfer through direct coupling of the nucleotide hydrolysis cycle to the phases of actin substrate maturation.     

催泪弹药剂焚烧销毁参数的确定

为了能安全有效地销毁废旧催泪弹,确定最佳的焚烧销毁参数,根据最小自由能法计算了催泪弹药剂在不同温度,空气过量系数分别为1.2、1.4、1.6、1.8、2.0下发生燃烧反应的平衡产物,验证了焚烧炉焚烧法销毁废旧催泪弹的可行性。并对烟气中相关生成物的浓度变化规律进行了研究和讨论,分析确定了催泪弹药剂安全焚烧销毁所需的最佳焚烧温度为1473 K及空气过量系数为1.6。     

Analysis and Interpretation of the Impact of Missense Variants in Cancer

Large scale genome sequencing allowed the identification of a massive number of genetic variations, whose impact on human health is still unknown. In this review we analyze, by an in silico-based strategy, the impact of missense variants on cancer-related genes, whose effect on protein stability and function was experimentally determined. We collected a set of 164 variants from 11 proteins to analyze the impact of missense mutations at structural and functional levels, and to assess the performance of state-of-the-art methods (FoldX and Meta-SNP) for predicting protein stability change and pathogenicity. The result of our analysis shows that a combination of experimental data on protein stability and in silico pathogenicity predictions allowed the identification of a subset of variants with a high probability of having a deleterious phenotypic effect, as confirmed by the significant enrichment of the subset in variants annotated in the COSMIC database as putative cancer-driving variants. Our analysis suggests that the integration of experimental and computational approaches may contribute to evaluate the risk for complex disorders and develop more effective treatment strategies.     

Mechanisms of ionic conductivity for zwitterionic polymers

In this work, ionic conductivity data of zwitterionic polymers are compared with predictions of the random free-energy barrier model for a.c. conduction in disordered solids. It is shown that conductivity follows a long range delocalized diffusion of charge carriers within an equally probable distribution of free-energy barriers. Accordingly, it follows time–temperature superposition, expressed as a master curve for the normalized conductivity as a function of the non-dimensional frequency. The dielectric behaviour is dominated by ionic conductivity, and results suggest a process of quasi-ideal conduction of the ion carriers, consistent with a large value of the dielectric relaxation time characteristic of delocalized conduction processes. It is further remarked that alternative interpretations to the conduction behaviour in these polymers can also be given by other theories and models.