蛋白质结构比较的微分几何方法

本文提出了一种利用蛋白质主链结构的微分几何描述实现蛋白质结构比较的新方法,即用主链的曲率和扰率刻划蛋白质结构有局部构象,再按动态规划算法实现最佳比较。通过对珠蛋白,天冬氨酸蛋白酶和丝氨酸蛋白酶的多重比较表明这个方法既适用于近缘同源蛋白又适用于近缘同源蛋白又适用于远缘同源蛋白的结构比较。     

蛋白质柔性复合物的结构预测

将自洽系综最优化方法（ＳＣＥＯ）推广到主链可变的分子体系,并以此来实现蛋白质复合物结合界面的柔性优化。据此,提出了一种模拟蛋白质“诱导契合”过程的计算方法,来实现蛋白质柔性复合物的结构预测。经过三个蛋白质柔性复合物结构预测的检验,表明这种方法是可行的,并且达到了计算精度和计算速度上的兼顾     

新型平均势函数在蛋白质反向折叠中的应用

利用蛋白质主链的极性分数及主链二面角为参量,构建了一种基于蛋白质结构数据库的势函数。将该势函数应用于蛋白质反向折叠研究中,发现该函数可成功地将蛋白质分子的天然构象从构建的构象库中识别出来;将一目标序列与构象库的每一可能的构象匹配,并用该势函数计算相应的能量,结果表明对绝大多数蛋白质分子来说,天然的构象的能量值总是最低。此外,该函数还将一些序列相似性较低,而结构相似性较高的蛋白质分子识别出来。我们认     

紫球藻多糖化学结构解析

为明确紫球藻多糖的化学结构,本文采用化学分析和光谱分析方法对紫球藻多糖的一级糖链结构进行了分析。GC分析表明该多糖由木糖、葡萄糖和半乳糖组成,为一种杂多糖,其摩尔比为:2.96∶1.25∶3.06;红外光谱分析结果显示紫球藻多糖为硫酸化多糖,糖苷键类型为β构型;化学分析结果推断紫球藻多糖糖链连接方式以1→3为主,存在少量1→2,1→4,1→6键型,且半乳糖在支链或主链末端有较大量的存在,木糖和葡萄糖在主链或靠近主链区域有特定分布;NMR分析显示紫球藻多糖的硫酸酯基连在C-6上,且多糖的糖苷键为β型;GC-MS联机分析进一步确定紫球藻多糖为一种主要含有1→3糖苷键,并含有1→4,1→6糖苷键的杂多糖。综合上述分析,推断出紫球藻多糖的糖链主链的重复单元结构。     

蛋白质折叠速度与其拓扑结构关系的研究

以6种不同的方式来定义蛋白质内存在的接触,进而运用分子动力学模拟等不同方法,对10个小蛋白进行分析,研究了不同的接触定义及不同的拓扑参数计算方法下,蛋白质的折叠速度与其拓扑参数的关系.结果表明,用含主链重原子的方式定义接触,所计算的拓扑参数与蛋白质折叠速度的相关性较好;用含侧链原子的方式定义接触,得到的拓扑参数与β型蛋白质的折叠速度的相关性较好.对不同的蛋白质,其拓扑结构与相应折叠速度间的相关程度不同。     

蛋白质结构预测方法探析

首先介绍了蛋白质结构预测中的三种理论方法,然后对同源蛋白质结构预测中侧链构造和环区构建中涉及到的主要方法进行了探讨,对非同源蛋白质结构预测中空间构象搜寻涉及到的主要算法进行了分析比较。     

耐热甜味蛋白brazzein的溶液NMR结构研究——二级结构和分子骨架

brazzein是从非洲西部野生植物PentadiplandrabrazzeanaBaillon的果实中提取的一种甜味蛋白 .在所有已知的甜味蛋白质中 ,brazzein的分子量最小 ,水溶性最好 ,并且具有很好的热稳定性 .利用二维核磁共振 ( 2DNMR)技术研究brazzein的溶液三维结构 ,完成了包括主链和侧链在内的所有质子共振峰的序列归属 .brazzein的二级结构包含一段α螺旋 ( 2 1～ 2 9) ,一段较短的 310 螺旋 ( 1 4～ 1 7)和两股反平行 β折叠 ( 34～ 39,44～ 5 0 ) ,分子N端可能形成了第 3股 β链 ( 5～ 7) .比较研究发现 ,该甜味分子骨架CSαβ与蝎毒、昆虫防卫素和植物抗菌蛋白γ 硫素的分子支架基本相同 .以此为基础 ,讨论了这种多功能分子支架的意义 ,可能的甜味活性中心及其热稳定性的结构基础 .     

黏附细胞中生物大分子结构变化的显微Raman光谱

鉴于细胞黏附作用的重要生物学意义, 选择了T淋巴细胞(Jurkat)为实验对象, 用先进的显微Raman光谱技术, 同时获得用其他方法难以得到的活细胞内数种生物大分子的构象信息. 通过比较单个和黏附细胞的显微Raman光谱的差异发现, 当细胞黏附时, 细胞内生物分子(DNA, 蛋白质, 碳水化合物, 脂类)的构象有不同的变化: (ⅰ) 双链DNA的骨架保持有序的B型或修改的B型构象, 然而它的脱氧核糖和碱基(A, G, C, T)的一些基团被修饰. (ⅱ) 蛋白质构象的主、侧链变化明显不同, 属于a螺旋和b折叠的一些谱线强度下降而b回折的一些谱线强度却明显增加; 酪氨酸和色氨酸从“埋藏状态”变成“暴露状态”; 它的巯基基团的谱线强度也有增加; 二硫键的构象从两种变成3种, 表明细胞黏附引起该蛋白质主链的氢键体系和侧链环境的变化. (ⅲ) 碳水化合物的一些基团同时被修饰. (ⅳ) 膜脂双层的构象变化很明显, 随着黏附细胞数目的增加, 链间侧向相互作用序参数逐渐减少, 提示细胞黏附导致细胞膜的流动性和离子通透性增加.     

蛋白质结构成对比较的新方法

介绍一种蛋白质三维结构的快速比较方法.此方法毋需初始联配,而能自动寻找和智能迭代.利用本程序对珠蛋白、丝氨酸蛋白酶、天冬氨酸蛋白酶、钙结合蛋白和溶菌酶作了系统的结构比较,取得了满意的结果.本文也讨论了衡量联配结果好坏的要素问题.     

碱液提取箬叶多糖的纯化及其结构性质的研究

通过高碘酸氧化、Smith降解、部分酸水解分析、NMR分析等多种方法对以不同浓度的NaOH溶液箬叶中提取的两种多糖FⅢ-a及FⅣ-a进行了研究,结果表明二者均具有多分枝结构,FⅢ-a主链以α(1→3)连接的木糖为主,分子侧链由半乳糖、阿拉伯糖、葡萄糖醛酸构成,葡萄糖醛酸主要位于分子的末端;FⅣ-a主链由α(1→3)木糖和β(1→6)半乳糖构成,以阿拉伯糖、葡萄糖醛酸组成侧链,葡萄糖醛酸主要位于分子的末端.     

Effect of increased convective clearance by on-line hemodiafiltration on all cause and cardiovascular mortality in chronic hemodialysis patients – the Dutch CONvective TRAnsport STudy (CONTRAST): rationale and design of a randomised controlled trial [ISRCTN38365125]

Background

The high incidence of cardiovascular disease in patients with end stage renal disease (ESRD) is related to the accumulation of uremic toxins in the middle and large-middle molecular weight range. As online hemodiafiltration (HDF) removes these molecules more effectively than standard hemodialysis (HD), it has been suggested that online HDF improves survival and cardiovascular outcome. Thus far, no conclusive data of HDF on target organ damage and cardiovascular morbidity and mortality are available. Therefore, the CONvective TRAnsport STudy (CONTRAST) has been initiated.

Methods

CONTRAST is a Dutch multi-center randomised controlled trial. In this trial, approximately 800 chronic hemodialysis patients will be randomised between online HDF and low-flux HD, and followed for three years. The primary endpoint is all cause mortality. The main secondary outcome variables are fatal and non-fatal cardiovascular events.

Conclusion

The study is designed to provide conclusive evidence whether online HDF leads to a lower mortality and less cardiovascular events as compared to standard HD.     

Should We Still Focus That Much on Cardiovascular Mortality in End Stage Renal Disease Patients? The CONvective TRAnsport STudy

Background

We studied the distribution of causes of death in the CONTRAST cohort and compared the proportion of cardiovascular deaths with other populations to answer the question whether cardiovascular mortality is still the principal cause of death in end stage renal disease. In addition, we compared patients who died from the three most common death causes. Finally, we aimed to study factors related to dialysis withdrawal.

Methods

We used data from CONTRAST, a randomized controlled trial in 714 chronic hemodialysis patients comparing the effects of online hemodiafiltration versus low-flux hemodialysis. Causes of death were adjudicated. The distribution of causes of death was compared to that of the Dutch dialysis registry and of the Dutch general population.

Results

In CONTRAST, 231 patients died on treatment. 32% died from cardiovascular disease, 22% due to infection and 23% because of dialysis withdrawal. These proportions were similar to those in the Dutch dialysis registry and the proportional cardiovascular mortality was similar to that of the Dutch general population. cardiovascular death was more common in patients <60 years. Patients who withdrew were older, had more co-morbidity and a lower mental quality of life at baseline. Patients who withdrew had much co-morbidity. 46% died within 5 days after the last dialysis session.

Conclusions

Although the absolute risk of death is much higher, the proportion of cardiovascular deaths in a prevalent end stage renal disease population is similar to that of the general population. In older hemodialysis patients cardiovascular and non-cardiovascular death risk are equally important. Particularly the registration of dialysis withdrawal deserves attention. These findings may be partly limited to the Dutch population.     

Evaluation of an algorithm for the automated sequential assignment of protein backbone resonances: A demonstration of the connectivity tracing assignment tools (CONTRAST) software package

Summary The peptide sequential assignment algorithm presented here was implemented as a macro within the CONnectivity TRacing ASsignment Tools (CONTRAST) computer software package. The algorithm provides a semi- or fully automated global means of sequentially assigning the NMR backbone resonances of proteins. The program's performance is demonstrated here by its analysis of realistic computer-generated data for III^Glc, a 168-residue signal-transducing protein of Escherichia coli [Pelton et al. (1991) Biochemistry, 30, 10043–10057]. Missing experimental data (19 resonances) were generated so that a complete assignment set could be tested. The algorithm produces sequential assignments from appropriate peak lists of nD NMR data. It quantifies the ambiguity of each assignment and provides ranked alternatives. A best first approach, in which high-scoring local assignments are made before and in preference to lower scoring assignments, is shown to be superior (in terms of the current set of CONTRAST scoring routines) to approaches such as simulated annealing that seek to maximize the combined scores of the individual assignments. The robustness of the algorithm was tested by evaluating the effects of imposed frequency imprecision (scatter), added false signals (noise), missing peaks (incomplete data), and variation in userdefined tolerances on the performance of the algorithm.     

荞麦籽粒结构的观察与分析

从荞麦籽粒的和分析中可以看出,荞麦的果皮和种皮容易分开,种子中心巨大的“Ｓ”形胚芽、胚根以及糊粉层虹适量科贮藏蛋白质存在的主要场所。在“Ｓ”形胚芽和胚根两侧是荞麦的两片叶子,由淀粉贮藏细胞组成。该细胞呈长方多棱体,细胞壁极薄且透明,人淀粉粒呈多面球形,大小均匀整齐,淀粉粒间结合紧密、严实,具有一定的几何构形。在淀粉粒间未发现基质蛋白质。     

CONTRAST: a discriminative,phylogeny-free approach to multiple informant <Emphasis Type="Italic">de novo</Emphasis>gene prediction

We describe CONTRAST, a gene predictor which directly incorporates information from multiple alignments rather than employing phylogenetic models. This is accomplished through the use of discriminative machine learning techniques, including a novel training algorithm. We use a two-stage approach, in which a set of binary classifiers designed to recognize coding region boundaries is combined with a global model of gene structure. CONTRAST predicts exact coding region structures for 65% more human genes than the previous state-of-the-art method, misses 46% fewer exons and displays comparable gains in specificity.     

Gaussian-based Alignment of Protein Structures: Deriving a Consensus Superposition when Alternative Solutions Exist

The use of a Gaussian-based representation of protein structures for evaluating protein-structure similarities and deriving three-dimensional superpositions is presented. The approach, as implemented in the program GAPS, is applied to three pairs of proteins with different topological characteristics (rich -helix, mixed -helix/-strand, and rich -strand), low sequence identities (10–30%), and recognized difficulties to define a unique optimum alignment.Validation of the GAPS superpositions is done by comparison with superpositions obtained by the TOP, GA_FIT, and ALIGN programs and those directly extracted from the FSSP database. Results suggest that a Gaussian-based methodology offers an objective means to, depending on the Gaussian-based representation, derive a consensus three-dimensional superposition when alternative superposition solutions exist.     

Structure prediction of the RPE65 protein

The RPE65 protein is located in the retinal pigment epithelial cells and plays an important role in the visual cycle. Although numerous experimental results demonstrate that it participates in the visual cycle, its detailed structure and function are not clear yet because of difficulties in isolation and crystallization. This paper describes a computational modeling study to propose a three-dimensional (3D) structure and suggest a possible mechanism for the function of the protein. The 3D-PSSM server is used to obtain the preliminary 3D structural model of the RPE65 protein. The coordinates of the side chains are obtained from the SCWRL program. Finally, two software packages, Jackal and Tinker with the CHARMM force field are used to fix and refine the preliminary structural model. Based on the obtained 3D structural model, a possible mechanism for the protein function is discussed.     

Effect of increased convective clearance by on-line hemodiafiltration on all cause and cardiovascular mortality in chronic hemodialysis patients - the Dutch CONvective TRAnsport STudy (CONTRAST): rationale and design of a randomised controlled trial [ISRCTN38365125

BACKGROUND: The high incidence of cardiovascular disease in patients with end stage renal disease (ESRD) is related to the accumulation of uremic toxins in the middle and large-middle molecular weight range. As online hemodiafiltration (HDF) removes these molecules more effectively than standard hemodialysis (HD), it has been suggested that online HDF improves survival and cardiovascular outcome. Thus far, no conclusive data of HDF on target organ damage and cardiovascular morbidity and mortality are available. Therefore, the CONvective TRAnsport STudy (CONTRAST) has been initiated. METHODS: CONTRAST is a Dutch multi-center randomised controlled trial. In this trial, approximately 800 chronic hemodialysis patients will be randomised between online HDF and low-flux HD, and followed for three years. The primary endpoint is all cause mortality. The main secondary outcome variables are fatal and non-fatal cardiovascular events. CONCLUSION: The study is designed to provide conclusive evidence whether online HDF leads to a lower mortality and less cardiovascular events as compared to standard HD.     

Evolutionary computer programming of protein folding and structure predictions

In order to understand the mechanism of protein folding and to assist the rational de-novo design of fast-folding, non-aggregating and stable artificial enzymes it is very helpful to be able to simulate protein folding reactions and to predict the structures of proteins and other biomacromolecules. Here, we use a method of computer programming called "evolutionary computer programming" in which a program evolves depending on the evolutionary pressure exerted on the program. In the case of the presented application of this method on a computer program for folding simulations, the evolutionary pressure exerted was towards faster finding deep minima in the energy landscape of protein folding. Already after 20 evolution steps, the evolved program was able to find deep minima in the energy landscape more than 10 times faster than the original program prior to the evolution process.     

A rapid protein structure alignment algorithm based on a text modeling technique

Structural alignment of proteins is widely used in various fields of structural biology. In order to further improve the quality of alignment, we describe an algorithm for structural alignment based on text modelling techniques. The technique firstly superimposes secondary structure elements of two proteins and then, models the 3D-structure of the protein in a sequence of alphabets. These sequences are utilized by a step-by-step sequence alignment procedure to align two protein structures. A benchmark test was organized on a set of 200 non-homologous proteins to evaluate the program and compare it to state of the art programs, e.g. CE, SAL, TM-align and 3D-BLAST. On average, the results of all-against-all structure comparison by the program have a competitive accuracy with CE and TM-align where the algorithm has a high running speed like 3D-BLAST.