Spring mechanics of {{alpha}}-helical polypeptide

To design protein- and polymer-based micro-machineries, it isimportant to understand the mechanical properties of basic structuralelements such as the     

Side-chain conformations in 4-{{alpha}}-helical bundles

The distribution of the ₁, ₂ dihedral angles in a dataset consistingof 12 unrelated 4--helical bundle proteins was determined andqualitatively compared with that observed in globular proteins.The analysis suggests that the 4--helical bundle motif couldoccasionally impose steric constraints on side chains: (i) theside-chain conformations are limited to only a subset of theconformations observed in globular proteins and for some aminoacids they are sterically more constrained than those in helicalregions of globular proteins; (ii) aspartic acid and asparagineoccasionally adopt rotamers that have not been previously reportedfor globular or helical proteins; (iii) some rotamers of tyrosineand isoleucine are predominantly or exclusively associated withhydrophobic core positions (a, d); (iv) mutations in the hydrophobiccore occur preferentially between residue types which amongother physicochemical properties also share a predominant rotamer.     

Organization of regions with amphiphilic {{alpha}}-helical potential within the three-dimensional structure of {beta}-sheet proteins

The observation that strong amphiphilic -helical potential existsin all proteins, including ß-sheet proteins, has givenrise to the idea that -helical intermediates may be criticalto the folding paths of all proteins. Here we report that regionswith amphiphilic -helical potential in ß-sheet proteinsare regularly spaced within the native structure of the proteinsat an average interval of about 13 Å. This regular spacingdid not occur when the location of amphiphilic regions was randomlyassigned (p = 0.0056), suggesting some degree of organizationwith respect to the native fold. However, in the native structureof various non-homologous proteins that contain the same fold,the location of the regions with amphiphilic -helical potentialwas not conserved. Further, there was no apparent associationof amphiphilic -helical potential with any particular type ofsecondary structure, confirming that this potential is not involvedin maintenance of native structure and suggesting that it maybe associated with a highly adaptable process.     

Activation of the low oxygen affinity-inducing potential of the Asn108({beta}){->}Lys mutation of Hb-Presbyterian on intramolecular {{alpha}}{{alpha}}-fumaryl cross-bridging

The Asn108ßLys mutation in hemoglobin (HbPresbyterianmutation) endows a low O₂ affinity-inducing propensity to theprotein. Introduction of a fumaryl cross-bridge between itstwo 99 lysine residues also induces a low O₂ affinity into HbA.We have now engineered an -fumaryl cross-bridge into Hb-Presbyterianto determine the synergy or additivity, if any, that can beachieved between these two low O₂ affinity-inducing structuralperturbations. Despite the presence of the additional -aminogroup of Lys108(ß) within the central cavity, the-amino group of Lys99() of deoxy Hb-Presbyterian retained highselectivity for -fumaryl cross-bridging, with an overall efficiencycomparable to that with HbA. The -fumaryl cross-linking of Hb-Presbyterianreduced its O₂ affinity much more significantly than that observedwith HbA, indicating a synergy between the two low O₂ affinity-inducingstructural perturbations. Apparently, the -fumaryl cross-bridgein Hb-Presbyterian activates part of the latent low O₂ affinity-inducingpotential of Lys108(ß) that is generally activatedin the presence of chloride. The synergy between the Asn108(ß)Lysmutation and the -fumaryl cross-bridging was conserved in thepresence of chloride, but not in the presence of DPG. Furthermore,in the presence of chloride and DPG, -fumaryl Hb-Presbyterianaccessed a low O₂ affinity T-state that is accessed by HbA,-HbA and Hb-Presbyterian only in the presence of IHP. Isoelectricfocusing analysis suggested that the -fumaryl cross-linkingof Hb-Presbyterian induces changes in the ionization behaviorof one or more of the functional groups neighboring Lys99()and Lys108(ß) [presumably His103() and/or Glu101(ß)]to compensate for the extra positive charge of Lys108(ß).Molecular modeling studies identified two potential chloridebinding sites per ß dimer within the middle of thecentral cavity of -fumaryl HbA involving residues His103(),Arg104(ß) and Asn108(ß). The affinity ofthese sites is increased in -fumaryl Hb-Presbyterian as a resultof the Asn108(ß)Lys mutation. Thus, the results ofthe present study suggest that the enhanced neutralization ofthe positive charges in the middle of the central cavity ofHb achieved by these two electrostatic modifications, one (the-fumaryl cross-bridge) acting directly and the other (the Presbyterianmutation) acting indirectly through the mediation of chlorideion binding, facilitates the - fumaryl-Hb Presbyterian to accessa low O₂ affinity T-state structure much more readily than eitherHb-Presbyterian or -fumaryl HbA.     

Structural consequences of replacement of an {alpha}-helical Pro residue in Escherichia coli thioredoxin

While it is well known that introduction of Pro residues intothe interior of protein     

利福霉素S的固液相平衡和溶解热力学

在288.15—323.15 K温度范围内,采用静态法测定了利福霉素S在5种纯有机溶剂(乙醇、异丙醇、正丁醇、乙酸乙酯和乙酸丁酯)中的溶解度,结果显示:利福霉素S在5种溶剂中的溶解度均随温度的升高而增大。使用修正Apelblat方程对溶解度的实验值进行了关联,并采用X射线衍射仪测定利福霉素S的晶型。在范特霍夫方程的基础上,对溶解过程中相关的热力学参数进行了估算,所得的溶解焓和吉布斯自由能均为正值,从而说明该过程是吸热的,而当溶液饱和后继续溶解是需要吸收能量的;并且分析了溶解过程中不同溶剂条件下焓与熵的贡献率。为制得纯度更高的利福霉素S,整体优化利福平合成工艺提供了理论指导。     

热力循环水加酸工艺处理实例

宣钢动力厂在热力车间循环水系统中更换循环水稳剂配方,并采用循环水加酸工艺提高了循环水浓缩倍数,在提高循环水的浓缩倍率(由1.9上升至3.3)的同时,控制加酸后循环水的pH,使系统新鲜水补水量由154.53t/h降至105.03t/h。实现了节水降耗的目的,取得了良好的经济效益。     

Copper binding to the neurotoxic peptide PrP106-126: thermodynamic and structural studies

The human prion protein fragment PrP(106-126) is a highly fibrillogenic peptide, resistant to proteinases and toxic to neurons; it derives from the normal prion protein (PrP(C)), with which it can interact, thus inhibiting its superoxide dismutase-like activity. The same properties are also shown by the abnormal isoform of the prion protein (PrP(Sc)), and this similarity makes PrP(106-126) an interesting model for the neurotoxic action of PrP(Sc). A role for copper in PrP(106-126) aggregation and toxicity has recently been evidenced, and the interaction of terminal Lys, His and Met residues with the copper ion at neutral pH has been suggested. In order to shed more light on the complex-formation equilibria of PrP(106-126) with the copper ion, a thorough investigation has been carried out by means of several experimental techniques: potentiometry, solution calorimetry, VIS spectrophotometry, circular dichroism, EPR and NMR spectroscopy. A shorter and more soluble fragment-PrP(106-113), which lacks the hydrophobic C-terminal domain of PrP(106-126) but contains all the potential donor groups-has also been considered for the sake of comparison. The involvement of terminal amino, imidazolic and amido nitrogens in complex formation has been confirmed, while no evidence was found for the interaction of side chains of Met and Lys residues with the copper ion. Solution structures for the main complexes are suggested.     

{alpha}-Helix folding by Monte Carlo simulated annealing in isolated C-peptide of ribonuclease A

Conformation of the C-peptide fragment of RNase A is calculatedby Monte Carlo simulated annealing. We adopt the total potentialenergy as given by the sum of generic interatomic energies whoseparameters are determined separately for each amino acid withoutreferring to the empirical structure of the C-peptide. The simulationis carried out in a completely unrestricted way without imposingany weight towards given final destinations. Starting from completelyrandom initial conformations and minimizing the total potentialenergy with respect to main-chain dihedral angles and side-chaintorsion angles, we have obtained partial -helix structure witha high probability ({small tilde}40%). The energetically mostfavourable structure exhibits a 2.5-turn -helix at the locationidentical with that of the 3-turn -helix in the native enzymemolecule. Classification of conformations obtained in the simulationinto clusters of similar structure shows that our simulationindeed predicts the -helix structure for the isolated C-peptidewith specific charged residues. The results of simulation withvarious amino acid substitutions are also found to be consistentwith the experimental implication for the importance of intramolecularionic interactions for -helix stability for this peptide.     

Characterization of peptide and amino acid profile in casein hydrolysates

The nutritional quality of protein hydrolysates has been related in several reports to their di- and tripeptide contents. In the present work different hydrolytic conditions were tested using papain in order to prepare casein hydrolysates with a suitable peptide profile for being used in special diets. The hydrolysates were fractionated by size-exclusion HPLC and the rapid Correct Fraction Area method was used for quantifying the peptides. Among the five hydrolytic conditions studied, three of them gave rise to preparations having nutritionally similar peptide profiles. However, the use of the temperature of 37 degrees C and enzyme:substrate ratio (E:S) of 2% may probably be the most economical condition for industrial production.     

Structural basis for the difference in thermodynamic properties between the two cysteine proteinase inhibitors human stefins A and B

Homology modelling has been used to model stefin A based onthe X-ray structure of stefin B. Several models have been producedby interactive modelling or positioning of the side chains byMonteCarlo procedure with simulated annealing.The quality of modelswas evaluated by calculation of the free energy of hydration,3D-1D potential or buried area of surface accessibility. StefinA is a thermostable protein, exhibiting a two-state denaturation,while stefin B denaturesat a 40°C lower temperature andforms a stable molten globule intermediate under mild denaturingconditions. From the tertiary structures, thermodynamic functionswere predicted, conforming closely to the experimental calorimetrkresults. Polar and apolar buried areas of surface accessibilitywere obtained by structural deconvolution of the thermograms.It is suggested that the bask difference between the stefinsis the domination of hydrophobic interaction in the stabilizationof stefin B, which is due to its non-specific nature leadingto the formation of a molten globule intermediate. Modellingof stefin A predicts increased numbers of hydrogen bonds whichstabilize it and the increase the cooperativity of its denaturation.     

Factors affecting the formation of alpha and beta polymorphs in glutaric acid aerosols

Dicarboxylic acids are prevalent in the atmosphere and frequently investigated by aerosol and atmospheric scientists. Glutaric acid, being a water-soluble dicarboxylic acid, is commonly used to model water activity in dicarboxylic acid aerosols. Different values associated with glutaric acid aerosols, specifically DRH and hygroscopic data, have been reported by several groups. We hypothesize that this variability is caused by its polymorphism. Glutaric acid exhibits dimorphism, meaning the molecule can form into two different types of crystal structures, an alpha and a beta polymorph. Glutaric acid naturally forms the beta polymorph, which is more stable. The alpha polymorph is the metastable phase. These polymorphs manifest themselves as a bimodal aerosol size distribution when analyzed by Scanning Mobility Particle Sizers or other aerosol mobility sizing methods. In this article, we discuss the formation of the nanoscale alpha glutaric acid polymorph generated from an aqueous glutaric acid solution. The formation of both polymorphs from an aqueous solution has not been documented elsewhere. We have found that the alpha polymorph forms at faster crystallization speeds, with a lower aqueous solution concentration and a lower solution flow rate into the atomizer. This identification of the presence of polymorphism in glutaric acid aerosols under common laboratory generation conditions could explain the variability present in studies associated with glutaric acid aerosols. Understanding the conditions at which the alpha polymorph is present will allow researchers to avoid it when using glutaric acid as a dicarboxylic acid standard and explain previously noted discrepancies.

Copyright © 2019 American Association for Aerosol Research     

Potentiometric and thermodynamic studies of vinylacetic acid and its metal complexes in monomeric and polymeric forms

Proton–monomeric ligand dissociation and metal–monomeric ligand stability constants of vinylacetic acid (VA) with some metal ions were calculated potentiometrically in 0.1M KCl. Also, in the presence of 2,2′‐azobisisobutyronitrile as initiator, the proton–polymeric ligand dissociation and metal–polymeric ligand stability constants were calculated. The effect of temperature on the dissociation of VA and the stability of its formed complexes were studied in monomeric and polymeric forms. The corresponding thermodynamic functions were derived and discussed. The dissociation process was nonspontaneous, endothermic, and entropically unfavorable. The formation of the metal complexes was found to be spontaneous, endothermic, and entropically favorable. © 2005 Wiley Periodicals, Inc. J Appl Polym Sci 97: 952–956, 2005     

三氟乙酸及甲酸体系下重组人促红素液质肽图的比较

目的探讨流动相中添加三氟乙酸(trifluoroacetic acid,TFA)或甲酸(formic acid,FA)时,重组人促红素(erythropoietin,EPO)液质肽图中各肽段的保留时间、峰面积及离子化效率的差异。方法将重组人EPO样品进行酶切,分别在含0.1%TFA及0.1%FA的流动相体系下测定液质肽图。通过分析质谱数据对各色谱峰进行定性,记录并计算各肽段的保留时间、峰面积及质谱信号强度。结果两种添加剂体系下,各肽段的保留时间存在差异,大部分肽段的保留时间变化在1 min左右,个别肽段超过2 min;TFA体系下各肽段的峰面积相对较小,约为FA体系下的84%;FA体系下各肽段离子化效率较高,信号强度一般为TFA体系的6倍,个别肽段高达10倍以上。结论两种体系下重组人EPO的液质肽图存在较大差异,应根据实验目的选择合适的流动相添加物。     

Transport phenomena in the system ion-exchange membranes/sulfuric acid solutions. Non-equilibrium thermodynamic approach

Transport processes in the systems sulfonic acid membranes (NAFION-120 or MRF-26)/sulfuric acid solutions are discussed applying non-equilibrium thermodynamic approach. For this purpose the phenomenological resistance and friction as well as coupling coefficients were calculated. The coefficients were extended to all the components, i.e. hydrogen ions, sulfuric acid anions, water, and polymer network. As the most important feature determining transport phenomena, the interaction between anions and the polymer network, having a maximum at the same relative concentration of sorbed acid to that of fixed charges in both membranes, was recognized. The second factor is the specificity of hydrogen ions, resulting in a small interaction of those ions with the polymer network, as well as essential coupling of large hydrogen ions and water streams.