Engineering proteins with enhanced mechanical stability by force-specific sequence motifs

Use of atomic force microscopy (AFM) has recently led to a better understanding of the molecular mechanisms of the unfolding process by mechanical forces; however, the rational design of novel proteins with specific mechanical strength remains challenging. We have approached this problem from a new perspective that generates linear physical–chemical properties (PCP) motifs from a limited AFM data set. Guided by our linear sequence analysis, we designed and analyzed four new mutants of the titin I1 domain with the goal of increasing the domain's mechanical strength. All four mutants could be cloned and expressed as soluble proteins. AFM data indicate that at least two of the mutants have increased molecular mechanical strength. This observation suggests that the PCP method is useful to graft sequences specific for high mechanical stability to weak proteins to increase their mechanical stability, and represents an additional tool in the design of novel proteins besides steered molecular dynamics calculations, coarse grained simulations, and ?‐value analysis of the transition state. Proteins 2012; © 2011 Wiley Periodicals, Inc.     

Collagen adhesin–nanoparticle interaction impairs adhesin's ligand binding mechanism

Background

Pathogenic bacteria specifically recognize extracellular matrix (ECM) molecules of the host (e.g. collagen, fibrinogen and fibronectin) through their surface proteins known as MSCRAMMs (Microbial Surface Components Recognizing Adhesive Matrix Molecules) and initiate colonization. On implantation, biomaterials easily get coated with these ECM molecules and the MSCRAMMs mediate bacterial adherence to biomaterials. With the rapid rise in antibiotic resistance, designing alternative strategies to reduce/eliminate bacterial colonization is absolutely essential.

Methods

The Rhusiopathiae surface protein B (RspB) is a collagen‐binding MSCRAMM of Erysipelothrix rhusiopathiae. It also binds to abiotic surfaces. The crystal structure of the collagen‐binding region of RspB (rRspB_31–348) reported here revealed that RspB also binds collagen by a unique ligand binding mechanism called “Collagen Hug” which is a common theme for collagen‐binding MSCRAMMs of many Gram-positive bacteria. Here, we report the interaction studies between rRspB_31–348 and silver nanoparticles using methods like gel shift assay, gel permeation chromatography and circular dichroism spectroscopy.

Results

The “Collagen Hug” mechanism was inhibited in the presence of silver nanoparticles as rRspB_31–348 was unable to bind to collagen. The total loss of binding was likely because of rRspB_31–348 and silver nanoparticle protein corona formation and not due to the loss of the structural integrity of rRspB_31–348 on binding with nanoparticles as observed from circular dichroism experiments.

General significance

Interaction of rRspB_31–348 with silver nanoparticle impaired its ligand binding mechanism. Details of this inhibition mechanism may be useful for the development of antimicrobial materials and antiadhesion drugs.     

Rheological and structural properties of starches from γ-irradiated and stored potatoes

Starch was extracted from irradiated and stored potato tubers and the properties were compared to CIPC (chlorpropham) treated tubers. The granule properties and dynamic viscoelasticity in temperature ramp and frequency sweep modes were studied while heating the samples. Starch structural characteristics were investigated by high performance anion exchange chromatography (HPAEC) and Fourier transform infrared spectroscopy (FTIR). Gamma-irradiation of potato tubers at a dosage of 0.1 kGy induced some degradation of starch molecules, resulting in earlier swelling of starch granules, and greater extents of amylose and total carbohydrate leaching. The early swelling phenomenon was also enhanced with tuber storage time. The retrogradation rate and extent for a concentrated starch gel also increased with tuber storage time whereas γ-irradiation delayed the gel retrogradation. Sprout inhibiting methods could be selected based on the specific processing and texture requirements of the end products.     

Crystallization behavior and hydrophobic properties of biodegradable ethyl cellulose-g-poly(3-hydroxybutyrate-co-3-hydroxyvalerate): The influence of the side-chain length and grafting density

The copolymerization of grafting poly(3-hydroxybutyrate-co-3-hydroxyvalerate) (PHBV) onto ethyl cellulose (EC) was carried out through the homogeneous acylation reaction between EC as a backbone and telechelic OH-terminated PHBV oligomer as side chains in 1,2-dichloroethane by using 1,6-hexamethylene diisocyanate (HDI) as a coupling agent and dibutyltin dilaurate as catalyst. The resulting copolymers were studied by using NMR, FT-IR, WAXD, DSC, and contact angle measurements. It is found that with the increasing of the HDI/PHBV fraction, a transition exhibition occurred on crystallization behavior and hydrophobic properties, which could be modulated through controlling the lengths and grafting densities of PHBV side chains. Compared with those of neat PHBV, the degree of crystallinity for EC-g-PHBV_1.8 decreased from 58.1% to 39.1%, the maximum decomposition temperature increased from 259.6 to 266.3 °C, and the contact angle increased from 60.1° to 95.7°.     

有机肥和化肥配施对不同熟期大白菜土壤生物特性及产量品质的影响

以早熟和晚熟品种大白菜为试材,根据化肥氮(尿素)、有机肥氮(生物有机肥)配施比例设置4个施肥处理,测定不同施肥处理下不同熟期大白菜土壤酶活性、可培养微生物数量及产量、品质的变化特征.结果 表明:早熟品种'德高16'大白菜莲座期和结球紧实期均以配施1/2生物有机肥(T2)处理的土壤蔗糖酶、土壤脲酶、土壤过氧化氢酶活性较强...     

不同灌水量下限对高羊茅绿期及抗寒性生理指标的影响

采用盆栽试验的方法,研究了秋末冬初不同灌水量下限\[分别占田间持水量(FC)的80%、70%、60%、50%\]对高羊茅绿期及抗寒性生理指标的影响.结果表明：在冬季低温条件下,80%和70%FC灌水处理使高羊茅叶片相对含水量、保护酶(SOD、POD和CAT)活性、叶绿素、可溶性糖和游离脯氨酸含量维持在较高水平,丙二醛含量和电解质外渗率降低,高羊茅的抗寒性增强.80%FC灌水处理分别较70%、60%和50%FC处理的草坪草绿期延长4、22和28 d,到达枯黄休眠的时间最晚,完成返青的时间最早.综合考虑节水和提高水分利用效率等多种因素,70%FC灌水处理为高羊茅秋末冬初季节最佳的灌水下限.     

α-亚麻酸甾醇酯的理化特性及氧化稳定性研究

本文研究了采用无溶剂直接酯化法合成得到的α-亚麻酸甾醇酯的理化特性、脂溶性、结晶特性、油脂氧化稳定性。结果表明,α-亚麻酸甾醇酯具有理想的理化特性,酸价和过氧化值分别为1.2 mg KOH/g和0.56meq/kg,反式脂肪酸含量小于0.1%,在不同植物油脂中的溶解性达到30%以上,结晶温度区间在-25.9～-29.6℃之间。α-亚麻酸甾醇酯在大豆油、油菜籽油和亚麻籽油中的浓度分别小于0.1%、0.1%和0.3%,油脂的氧化诱导时间随浓度增加而增加。因此α-亚麻酸甾醇酯良好的理化特性表明其在不同形态食品、保健品和医药产品等中将具有较广的应用范围,是一种具有较高营养价值的功能性食品添加剂。     

高温胁迫对枇杷果皮热伤害的抗氧化特性影响

为探讨枇杷[Eriobotrya japonica(Thunb.)Lindl.]对高温胁迫的响应,对‘红种’枇杷果皮热伤害的抗氧化特性进行研究。结果表明,在自然光下,枇杷果皮热伤害的阈值为40℃(1.5 h),且果皮热伤害与温度和持续时间关系密切,光照可促进热伤害的发生。枇杷果皮受热伤害程度与果实本身的营养状态有关,果肉维生素C(Vc)、钙(Ca)含量越低,果皮热伤害级数越高。与25℃相比,40℃高温处理增加了果皮的超氧阴离子和丙二醛(MDA)含量,而超氧化物歧化酶(SOD)、过氧化物酶(POD)的活性呈下降趋势。这揭示了高温胁迫下枇杷果皮对热伤害的抗氧化响应机制。     

Characterization of protein primary sequences based on partial ordering

In this paper, we present a new approach to characterize protein sequences. Based on orderings of the 20 natural amino acids which reflect some of their physico-chemical properties, we construct an augmented Hasse matrix for each protein sequence. Furthermore, the normalized leading eigenvalues of these matrices are computed and considered as invariants for the protein sequences. Finally, we make a comparison for the similarity/diversity of nine different protein sequences.     

Non-management of Natural Resources: The Case of Inland Fisheries in the Mayan Zone,Quintana Roo,México

This study explores the management of inland fisheries on common lands (ejidos) within the Mayan Zone of Quintana Roo, Mexico. Qualitative survey data are used to examine whether there are (a) ongoing fishery conservation activities; (b) local caretakers of fishing sites; (c) restrictions on where fishing can take place; and (d) particular groups of individuals who lack the right to fish within the ejidos. Results indicate that in contrast to other local resources, fisheries in the ejidos have less defined use rights, being viewed as largely “open access”. In particular, most feel that outsiders can fish in an ejido if they abide by local rules (notably not damaging the local water bodies, asking consent to fish, and having a friend or relative in the community). However, there are within-community differences in views concerning management and conservation, with those more dependent on fishing being more likely to support exclusion of outsiders.