In Silico Investigation of Potential Applications of Gamma Carbonic Anhydrases as Catalysts of CO2 Biomineralization Processes: A Visit to the Thermophilic Bacteria Persephonella hydrogeniphila,Persephonella marina,Thermosulfidibacter takaii,and Thermus thermophilus

Carbonic anhydrases (CAs) have been identified as ideal catalysts for CO₂ sequestration. Here, we report the sequence and structural analyses as well as the molecular dynamics (MD) simulations of four γ-CAs from thermophilic bacteria. Three of these, Persephonella marina, Persephonella hydrogeniphila, and Thermosulfidibacter takaii originate from hydrothermal vents and one, Thermus thermophilus HB8, from hot springs. Protein sequences were retrieved and aligned with previously characterized γ-CAs, revealing differences in the catalytic pocket residues. Further analysis of the structures following homology modeling revealed a hydrophobic patch in the catalytic pocket, presumed important for CO₂ binding. Monitoring of proton shuttling residue His69 (P. marina γ-CA numbering) during MD simulations of P. hydrogeniphila and P. marina’s γ-CAs (γ-PhCA and γ-PmCA), showed a different behavior to that observed in the γ-CA of Escherichia coli, which periodically coordinates Zn²⁺. This work also involved the search for hotspot residues that contribute to interface stability. Some of these residues were further identified as key in protein communication via betweenness centrality metric of dynamic residue network analysis. T. takaii’s γ-CA showed marginally lower thermostability compared to the other three γ-CA proteins with an increase in conformations visited at high temperatures being observed. Hydrogen bond analysis revealed important interactions, some unique and others common in all γ-CAs, which contribute to interface formation and thermostability. The seemingly thermostable γ-CA from T. thermophilus strangely showed increased unsynchronized residue motions at 423 K. γ-PhCA and γ-PmCA were, however, preliminarily considered suitable as prospective thermostable CO₂ sequestration agents.     

Chemical-Shift Perturbations Reflect Bile Acid Binding to Norovirus Coat Protein: Recognition Comes in Different Flavors

Bile acids have been reported as important cofactors promoting human and murine norovirus (NoV) infections in cell culture. The underlying mechanisms are not resolved. Through the use of chemical shift perturbation (CSP) NMR experiments, we identified a low-affinity bile acid binding site of a human GII.4 NoV strain. Long-timescale MD simulations reveal the formation of a ligand-accessible binding pocket of flexible shape, allowing the formation of stable viral coat protein–bile acid complexes in agreement with experimental CSP data. CSP NMR experiments also show that this mode of bile acid binding has a minor influence on the binding of histo-blood group antigens and vice versa. STD NMR experiments probing the binding of bile acids to virus-like particles of seven different strains suggest that low-affinity bile acid binding is a common feature of human NoV and should therefore be important for understanding the role of bile acids as cofactors in NoV infection.     

金刚石膜的计算机虚拟制备技术中的分子动力学模拟

综述了近年来金刚石薄膜形成过程的分子动力学（Molecular Dynamics，简称MD）模拟研究，详细地阐述了原子间相互作用势的选取，总结了不同沉积条件下MD的计算模型和几种典型情况下的模拟结果。研究表明：在原子尺度上，MD方法能较全面地提供有关膜生长的信息，对进一步了解金刚石膜形成的微观机制以及为细观层次仿真提供基本信息均具有重要意义。     

基于双因子认证技术的网络身份识别

本文提出了一种基于动态双因子认证技术的网络身份识别方法,用户每次登录的口令是利用系统时间和用户ID通过MD5加密算法计算得到,其通过MD5加密后生成的登录口令是随机的,这将进一步提高开放网络环境下身份识别的可靠性和安全性。同时,本文还提出网络身份识别技术可以应用到各类网站的服务器上,用来完成对用户身份的识别,以提高网络系统的安全性。     

RSA数字签名技术在信息化工程监理流程E化中的研究

提出的信息化工程监理流程的E化过程就是将监理流程通过现有的IT技术进行重新梳理、再造,达到电子化、网络化。将对在E化过程中数字签名的应用进行研究,以应对E化容易出现的伪造这一网络安全问题。主要讲述hash签名技术中单向散列函数对文件进行摘要处理,然后使用RSA公钥加密算法对摘要进行加密。也会对签名过程和验证过程给予解说。     

Molecular Dynamics Simulations Based on 1-Phenyl-4-Benzoyl-1-Hydro-Triazole ERRα Inverse Agonists

Estrogen-related receptor α (ERRα), which is overexpressed in a variety of cancers has been considered as an effective target for anticancer therapy. ERRα inverse agonists have been proven to effectively inhibit the migration and invasion of cancer cells. As few crystalline complexes have been reported, molecular dynamics (MD) simulations were carried out in this study to deepen the understanding of the interaction mechanism between inverse agonists and ERRα. The binding free energy was analyzed by the MM-GBSA method. The results show that the total binding free energy was positively correlated with the biological activity of an inverse agonist. The interaction of the inverse agonist with the hydrophobic interlayer composed of Phe328 and Phe495 had an important impact on the biological activity of inverse agonists, which was confirmed by the decomposition of energy on residues. As Glu331 flipped and formed a hydrogen bond with Arg372 in the MD simulation process, the formation of hydrogen bond interaction with Glu331 was not a necessary condition for the compound to act as an inverse agonist. These rules provide guidance for the design of new inverse agonists.     

基于IPv6的视频资源服务平台构建

介绍了基于IPv6视频资源服务平台的工作原理和关键技术,设计并开发了基于IPv6的视频资源服务平台,该平台能实现视频教学、影视娱乐、交流答疑、视频直播、视频点播等功能。     

基于Blowfish和MD5的混合加密方案*

针对Blowfish算法在实际应用中存在的等价密钥、重复初始化等问题,提出Blowfish与MD5算法相结合,将MD5算法的生成值作为密钥的一部分对Blowfish算法进行初始化,使用概率统计方法证明该方案弥补了Blowfish算法的实际应用缺陷。计算结果表明,混合加密方案具有更高的安全性、更快的速度。     

MD5散列算法的研究

借鉴了M.M.J.Stevens的碰撞思路,重新编写了MD5碰撞算法中的核心循环,主要提供一对MD5碰撞产生的过程以及碰撞的完成。通过实验统计分析,利用改进的MD5碰撞算法找到一对碰撞信息所用平均时间不多于60s,且该算法较之传统的MD5碰撞算法具有更好的可读性和可移植性。