The Structural Stability of Alpha-Helix Determined by the Preference of Amino Acids

To accomplish their functions, proteins have to achieve different conformations accompanied by conformational transitions. However, the relationship between the preference of amino acids and the stability of the secondary structure is still unclear. Here we perform molecular simulations on a series of helical structures. Our data show that the dissociation energy of the helical structure is related to the preference of amino acids, and the electrostatic repulsion of the residue i and i ＋ 3/4 with the same sign of charge destabilizes the alpha helix.

Detecting Periodicity Associated with the Alpha-Helix Structure Using Fourier Transform

Alpha helix is a common type of secondary structure in the protein structure that consists of repeating helical turns. Patterns in the protein sequences that cause this repetitive pattern in the structure have long been sought. We used the discrete Fourier transform (DFT) to detect the periodicity signals correlated to the helical structure. We studied the distribution of multiple properties along the protein sequence, and found a property that showed strong periodicity correlated with the helical structure. Using a short-time Fourier transform (STFT) method, we investigated the amplitude of the periodical signals at each amino acid position. The results show that residues in the helix structure tend to display higher amplitudes than residues outside of the helices. This tendency is dramatically strengthen when sequence profiles obtained from multiple alignment were used to detect the periodicity. A simple method that predicted helices based on the amplitude yielded overall true positive rate (TPR) of 63%, 49% sensitivity, 72% specificity, and 0.22 Matthews Correlation Coefficient (MCC). The performance seemed to depend on the length of helices that the proteins had.

α螺旋蛋白质螺旋线模型的三孤立子效应

根据有机分子链的内部作用机制，在α螺旋蛋白质螺旋线模型的基础上，给出了改进的α螺旋蛋白质螺旋线模型，研究了分子螺旋链中的集体激发———三孤子特征。

Interactive association between processing induced molecular structure changes and nutrient delivery on a molecular basis,revealed by cutting-edge vibrational biomolecular spectroscopy

Background:This study was conducted to determine protein molecular structure profiles and quantify the relationship between protein structural features and protein metabolism and bioavailability of blend pel eted products(BPP)based on co-products(canola or carinata)from processing with different proportions of pulse pea screenings and lignosulfonate chemical compound.Method:The protein molecular structures were determined using the non-invasive advanced vibrational molecular spectroscopy(ATR-FT/IR)in terms of chemical structure and biofunctional groups of amides(ⅠandⅡ),α-helix andβ-sheet.Results:The results showed that increasing the level of the co-products in BPP significantly increased the spectral intensity of the amide area and amide height.The products exhibited similar protein secondaryα-helix toβ-sheet ratio.The protein molecular structure profiles(amidesⅠandⅡ,α-helix toβ-sheet)were highly associated with protein degradation kinetics and intestinal digestion.In conclusion,the non-invasive vibrational molecular spectroscopy(ATR-FT/IR)could be used to detect inherent structural make-up characteristics in BPP.Conclusion:The molecular structural features related to protein biopolymer were highly associated with protein utilization and metabolism.

蛋白质分子α螺旋结构的发现

笔者具体介绍了蛋白质分子α螺旋结构的发现过程。鲍林是怎样在了解蛋白质组成和X射线研究的实验成果的基础上,从结构化学的角度认识到在蛋白质中氢键的性质和作用,揭示了肽基的刚性平面性质,从而发现了蛋白质分子的α螺旋结构的。

α螺旋蛋白质螺旋链模型方程组的精确解

采用修正映射法求解α螺旋蛋白质螺旋链运动模型的耦合非线性薛定谔方程组,得到该方程的耦合行波精确解,包括孤波解和Jacobi椭圆函数解.该法的优点是,不必预先给出函数的具体形式,就可以得到较多的函数解,可为进一步研究α螺旋蛋白质螺旋链运动提供参考.

用Riccati方程方法解α螺旋蛋白质螺旋链模型方程组

应用Riccati方程方法求解α螺旋蛋白质螺旋链运动模型的耦合非线性薛定谔方程组,得到了一些新的精确解,其中有冲击波解和孤立波解,为研究α螺旋蛋白质螺旋链运动提供参考。

T辅助细胞亚群在大鼠非酒精性脂肪性肝病模型中的变化

目的:探讨T辅助细胞亚群Th1/Th2和Treg在非酒精性脂肪性肝病(nonalcoholic fatty liver disease,NAFLD)发病机制中的意义.方法:SD大鼠正常喂养1wk后,随机分为正常组(n=20)和高脂饮食组(n=20).正常组大鼠以普通饲料喂养,高脂饮食组以高脂饲料喂养.实验第8、16周分批处死大鼠.观察肝组织的病理改变,荧光定量PCR方法检测肝脏TNF-a、IFN-γ、IL-4和Foxp3的基因表达.结果:高脂饮食8wk大鼠肝细胞脂肪变明显,无明显炎症改变,IFN-γ、IL-4在肝脏的基因表达与正常组比较无明显变化,TNF-α稍升高,但无统计学意义,Foxp3 mRNA的表达比正常组明显降低(ct值:26.12±0.69 vs 24.22±0.62,P<0.05).高脂饮食16wk大鼠脂肪肝明显,炎症明显,IFN-γ和TNF-α基因表达均显著升高(ct值:24.52±0.87 vs 29.94±1.44,24.31±1.13 vs 28.88±1.95,均P<0.05),IL-4与正常组相比较无明显变化,Foxp3基因表达较正常组和高脂饮食8wk时均显著降低(ct值:32.57±1.54 vs 24.29±1.08,26.12±0.69,P<0.05).结论:高脂饮食大鼠肝脏Foxp3和Treg表达减少可能是高脂饮食NAFLD发生发展的重要因素.IFN-γ和TNF-α的联合作用加重了肝脏的炎症损伤.

Spontaneous Unfolding and Refolding of Plantaricin α-Helix in Molecular Dynamics Simulation

Antimicrobial peptides are promising therapeutic agents in view of increasing resistance to conventional antibiotics. Antimicrobial peptides usually fold in α-helical, β-sheet, and extended/random-coil structures. The α-helical antimicrobial peptides are often unstructured in aqueous solution but become structured on bacterial membrane. The α-helical structure allows the partitioning into bacterial membrane. Therefore it is important to understand the mechanism of unfolding and refolding of α-helical structure in antimicrobial peptides. It is not very easy to obverse and study the process of unfolding and refolding of α-helical antimicrobial peptides because of their rapidity. Therefore, molecular simulation provides a way to observe and explain this phenomenon. Plantaricin A is a 26 amino-acid antimicrobial pheromone peptide and can spontaneously unfold and refold under physiological condition. This study demonstrated the unfolding and refolding of plantaricin A by means of molecular simulation, and its mechanism was discussed with its implication to the Levinthal paradox.

More precise model of <i>α</i>-helix and transmembrane <i>α</i>-helical peptide backbone structure

The 3-D structure of the β-adrenergic receptor with a molecular weight of 55,000 daltons is available from crystallographic data. Within one of the seven transmembrane ion channel helices in the β2-receptor, one loop of a helix ACADL has previously been proposed as the site that explains β2 activity (fights acute bronchitis) whereas ASADL in the β1-receptor at the corresponding site explains β1-activity (cardiac stimulation). The α-agonist responsible for this selective reaction is only 0.5% of the receptor molecular weight, and only 1.5% of the weight of the trans-membrane portion of the receptor. The understanding of the mechanism by which a small molecule on binding to a site on one single loop of a helix produces a specific agonist activity on an entire transmembrane ion channel is uncertain. A model of an α-helix is presented in which of pitch occurs at angles both smaller and larger than 180° n. Consequently, atomic coordinates in a peptide backbone α-helix match the data points of individual atom (and atom types) in the backbone. More precisely, eleven atoms in peptide backbone routinely equal one loop of a helix, instead of eleven amino acid residues equaling three loops of a helix;therefore, an α-helix can begin (or end) at any specific atom in a peptide backbone, not just at any specific amino acid. Wavefront Topology System and Finite Element Methods calculate this specific helical shape based only upon circumference, pitch, and phase. Only external forces which specifically affect circumference, pitch and/or phase (e.g. from agonist binding) can/will alter the shape of an α-helix.

人的α螺旋和β折叠片断中亲疏水氨基酸多肽片断

本文选取人的 α螺旋和 β折叠规则二级结构 ,计算其中所含亲 -疏水性氨基酸的多肽片断 ,找出多肽片断分布规律 。

猪心肌高铁肌红蛋白分子结构解析

本研究分别运用十二烷基硫酸钠-聚丙烯酰胺凝胶电泳（sodium dodecyl sulfate-polyacrylamide gelelectropHoresis,SDS-PAGe）、紫外光谱、氨基酸分析、质谱和分子信息技术,比较中国山猪心肌高铁肌红蛋白（pig metmyoglobin,pMetMb）分子信息和三维结构。结果表明：pMetMb肽链至少含有133种氨基酸组分,但较hMb缺少脯氨酸（Pro）和精氨酸（Arg）;与美国国家生物技术信息中心（national Center for Biotechnology Information,nCBI）数据库猪野生型gi｜494385比对,其匹配度79.7%（置信度100%）,故推测肽链长度在133~153之间。pMetMb含有7个α螺旋和2个310螺旋,由于310螺旋存在（马Mb没有）,使肽链中疏水基团作用加强,形成更加紧密盘叠的球状亚基;第6和7螺旋的His64和His93的咪唑基团N（Im n—）与Fe2＋/Fe3＋键合,构成核心heme-Fe功能域;它镶嵌于蛋白质内部疏水结构内,更便于电子传递和Fe2＋/Fe 3＋氧化还原反应,维系肉色。

隐藏高分子界面及生物界面分子结构的和频振动光谱研究(英文)

界面的分子结构决定界面的性质.为了以优化界面的结构来改进材料的性质,原位实时地研究界面的分子结构是很重要的.近年来和频振动光谱已发展成为一个很有效及独特的手段来研究隐藏界面的分子结构,例如液/液界面、固/液界面及固/固界面等.这篇综述讨论了和频振动光谱在研究高分子界面及生物界面等复杂界面的分子结构上的应用.具体说来,本文论述了高分子表面在水里的分子结构变化,高分子及模型粘合促进剂硅烷在界面相互作用的分子机理和隐藏的高分子/高分子及高分子/金属界面的结构.另外,此文还将介绍不同二级结构的多肽及几个有代表性的蛋白分子在界面的结构.界面在诸如化学、生物、物理、材料科学及工程和纳米技术等许多领域都很重要.发展一个独特的能原位研究隐藏界面的分子结构的技术会有力地促进这些领域的研究及跨学科研究的发展.

KcsA一种新型的K离子通道

DeclanADoyleetal于 1998年利用X射线结晶分析在Streptomyceslividans(变铅青链霉菌 )中发现的KcsA(K+conductionandselectivityarchitecture)是一种新型的K+ 通道 .它由四个亚基组成 ,每个亚基含有两个α 螺旋 ,在KcsA的中央有一个选择性滤膜 ,对K+ 具有特殊的通透性 .本文仅对KcsA的结构及其对K+ 选择性介导的作用机制进行综述 .

Identification of Secondary Structure of Extracellular Signal Regulated Kinase (ERK) Interacting Proteins and Their Domain: An in Silico Study

ERK is involved in multiple cell signaling pathways through its interacting proteins. By in silico analysis, earlier we have identified 22 putative ERK interacting proteins namely;ephrin type-B receptor 2 isoform 2 precursor (EPHB2), mitogen-activated protein kinase 1 (MAPK1), interleukin-17 receptor D precursor (IL17RD), WD repeat domain containing 83 (WDR83), tescalcin (Tesc), mitogen-activated protein kinase kinase kinase 4 (MAPP3K4), kinase suppressor of Ras2 (KSR2), mitogen-activated protein kinase kinase 6 (MAP3K6), UL16 binding protein 2 (ULBP2), UL16 binding protein 1 (ULBP1), dual specificity phosphatase 14 (DUSP14), dual specificity phosphatase 6 (DUSP6), hyaluronan-mediated motility receptor (RHAMM), kinase D interacting substrate of 220 kDa (KININS220), membrane-associated guanylate kinase (MAGI3), phosphoprotein enriched in astrocytes 15 (PEA15), typtophenyl-tRNA synthetase, cytoplasmic (WARS), dual specificity phosphatase 9 (DUSP9), mitogen-activated protein kinase kinase kinase 1 (MAP3K1), UL16 binding protein 3 (ULBP3), SLAM family member 7 isoform a precursor (SLAMMF7) and mitogen activated protein kinase kinase kinase 11 (MAP3K11) (Table 1). However, prediction of secondary structure and domain/motif present in aforementioned ERK interacting proteins is not studied. In this paper, in silico prediction of secondary structure of ERK interacting proteins was done by SOPMA and motif/domain identification using motif search. Briefly, SOPMA predicted higher random coil and alpha helix percentage in these proteins (Table 2) and motif scan predicted serine/threonine kinases active site signature and protein kinase ATP binding region in majority of ERK interacting proteins. Moreover, few have commonly dual specificity protein phosphatase family and tyrosine specific protein phosphatase domains (Table 3). Such study may be helpful to design engineered molecules for regulating ERK dependent pathways in disease condition.