Molecular structures and structural dynamics of prion proteins and prions : mechanism underlying the resistance to prion diseases
Zhang J., Springer International Publishing, New York, NY, 2015. 355 pp. Type: Book (978-9-401773-17-1). Date Reviewed: Sep 9 2016. Computing Review of ACM - Reviewer: Anthony J. Duben. Review #: CR144750 (1612-0878).
Unlike bacteria and viruses, which are based on DNA and RNA, prions are unique as disease-causing agents since they are misfolded proteins. Prions propagate by deforming harmless, correctly folded proteins into copies of themselves. The misfolding is irreversible. Prions attack the nervous system of the organism, causing an incurable, fatal deterioration of the brain and nervous system until death occurs. Some examples of these diseases are mad cow disease in cattle, chronic wasting disease in deer and elk, and Creutzfeldt-Jakob disease in humans.
Not every species is affected by prion disease. Rabbits, water buffalo, horses, and dogs are resistant to prion diseases. The research question arises: What is different about the protein in a resistant species (especially the rabbit, which seems to be the most resistant) that allows it to retain its folding? This is the research question addressed in this book. The original research reported in this volume is based on molecular modeling since the usual experimental tools for structure elucidation at the molecular level, X-ray crystallography and nuclear magnetic resonance (NMR) spectroscopy, are often unsuitable for studying proteins. The computational simulation of the interactions within and among proteins is used to interpret the stability of conformations as they fold and as they pack in a cluster of proteins.
After an introductory chapter in which the author describes the proteins in question and a quick overview of molecular dynamics and molecular mechanics, this book is organized into two parts. The first part is a set of nine chapters in which the author presents primarily the results of his research using the molecular dynamics of segments of the proteins of comparable species in order to explain why rabbits resist prion infection while other susceptible species do not. The second part consists of eight chapters emphasizing the optimization methods used in molecular modeling and molecular dynamics.
In the first part, the molecular dynamics simulations are performed at different computational temperatures and at low, high, and neutral pH levels. Segments of the proteins are selected for detailed analysis. The simulations suggest strongly that the prion-resistant species have stronger intra- and inter-chain interactions in specific segments of the protein chain that stabilize their geometries.
The second part discusses the optimization algorithms used: steepest descent, simulated annealing, genetic algorithm, evolutionary optimization, and combinations of these algorithms. The computational goal is identifying the low-energy conformations and their relative stability with respect to each other, especially the differences between the protein and the prion.
There is much that is very good about this book: the reporting of research results comparing different segments of different species’ proteins, the critical reviews of the existing literature, the extensive bibliography (over 700 publications), and the discussion of the optimization techniques. On the other hand, there are shortcomings: the repetitiveness in introducing each chapter by describing the research problem as if it were brand new; the colored figures that are supposed to show changes in conformation are so small that the scales on the axes cannot be read and they are accompanied by figure descriptions that discuss letter codes, not colors; a section discussing important results presented in a figure in a reference, without reprinting the figure in the book; and the poor copy editing that allowed errors in English grammar and scientific descriptions. It seems that the book was created by taking individual papers and assembling them in sequence with little attention to concision and cohesiveness. Nonetheless, if one can endure and overlook the many flaws in presentation, there is a wealth of information and insight in the results presented and in the methods employed. The research is important. The methods used are innovative. Studying this book is worth the effort.
Optimization-based molecular dynamics studies of SARS-CoV-2 molecular structures: research on COVID- 19
Zhang J., Springer International Publishing,Cham, Switzerland,2023. 953 pp.Type:Book. Date Reviewed: 05/26/25. Computing Review of ACM - Reviewer: Anthony J. Duben. Review #: CR147951.
The urgent need to develop COVID-19 vaccines, medications, and treatments led to an unprecedented level of activity in research labs. Computational chemistry was an integral part of the research efforts because it could reveal details of the interactions between components of the COVID-19 virus, receptor sites on the cell being attacked, and potential drugs. The principal computational technique used was molecular dynamics (MD), which can reveal changes in the 3D molecular structures in both the attacking and attacked molecules as they interact.
This 900-plus-page book is a compilation of the results of computations performed using components of the COVID-19 virus (including the spike proteins--both with and without glycosylation, membrane glycoproteins, envelope glycoproteins, and their variants in the principal mutations), human proteins and the ACE2 enzyme (the target of COVID-19), the related coronaviruses SARS and MERS, human immunodeficiency virus (HIV) inhibitors, scores of potential drugs, and vaccine components. This list is not exhaustive.
The book is presented in 28 chapters, plus a short appendix on MD optimization algorithms, references, and an index. The chapters follow a similar format. Each chapter begins with a brief introduction in which the central substances are presented, followed by another short section on the materials (for example, the specific portions of the interacting molecules) and the methods (the scope of the MD calculations, such as the software package used, force field parameter sets, solvent composition, and time period covered in the calculation). The bulk of the chapter is the results and discussion section, which contains many lengthy tables of likely close contacts between components of each interacting substance (for example, amino acids in each of the two proteins). Since the amino acids are numbered in the standard structural databases, it is possible to work backwards to reveal the structural environments of these contacts. This section also includes some graphics displaying the progress of the MD calculations and some molecular diagrams. Unfortunately, these graphics have been too reduced in size to easily perceive what they are supposed to illustrate. There is a short conclusion. Several of these chapters are followed by a lengthy supplemental section with many more tables of data results selected from the MD trajectories plus additional small graphics. The number and length of the tables is overwhelming.
There is little critical discussion of the MD calculations themselves or their optimization. However, data taken from the literature and archives is analyzed and could be used comparatively by other researchers investigating these COVID-19 systems. The structure of the book and data presented restrict the book’s primary use as a reference resource.
Introduction to the Computing Reviews of ACM:
https://en.wikipedia.org/wiki/ACM_Computing_Reviews
ACM Computing Reviews (CR) is a scientific journal that reviews literature in the field of computer science. It is published by the Association for Computing Machinery and the editor-in-chief is Carol Hutchins (New York University).[1]
See also
References
1 "Computing Reviews, the leading online review service for computing literature". computingreviews.com. Retrieved 2023-02-05.
The following is from 中国海洋大学:
荐读提要：Optimization-based Molecular Dynamics Studies of SARS-CoV-2 Molecular Structures - Research on COVID- 19 / by Jiapu Zhang. 1st ed. 2023.
核心主题
本书的核心主题是通过优化分子动力学（MD）研究SARS-CoV-2的分子结构，结合生物物理学、生物学和生物信息学的方法，深入探讨COVID-19相关蛋白质和RNA的结构与功能。
内容详情
本书详细介绍了SARS-CoV-2的多种蛋白质和RNA结构，包括Papain-Like半胱氨酸蛋白酶（PLpro）、3C-Like蛋白酶（3CLpro）、RNA依赖性RNA聚合酶（RdRp）、RNA解旋酶、Spike糖蛋白等。书中还探讨了这些蛋白质与药物的结合、疫苗开发、病毒起源以及流行病学数学模型。
主题分析
本书的主题涵盖了分子动力学优化、结构生物信息学、药物与疫苗开发、病毒起源与传播模型等多个方面。通过优化分子动力学轨迹，提取关键的结构生物信息，为理解SARS-CoV-2的分子机制提供了重要依据。
图书摘要
本书通过优化分子动力学研究，提取了SARS-CoV-2蛋白质和RNA的关键结构信息。书中详细介绍了优化方法、分子稳定性分析、药物与疫苗开发、以及流行病学数学模型。适合从事计算生物化学、计算生物物理学、结构生物信息学等领域的研究人员和学生。
学术定位
本书在学术上定位为计算生物化学、计算生物物理学和结构生物信息学领域的研究专著，适合从事相关领域研究的学者和研究生阅读。
时效性与视角
本书于2023年出版，内容紧跟COVID-19研究的最新进展，特别是分子动力学优化和结构生物信息学方面的研究。视角聚焦于分子层面的机制分析，具有较强的时效性和学术价值。
适用读者
本书适用于从事计算生物化学、计算生物物理学、分子动力学、结构生物信息学等领域的研究人员、教师和学生。同时，对COVID-19研究感兴趣的读者也能从中获得有价值的信息。
阅读推荐
推荐给从事分子动力学、结构生物信息学、药物开发等领域的研究人员和学生。本书不仅提供了详细的研究方法，还结合了最新的COVID-19研究成果，具有较高的学术参考价值。
数据总结
本书通过优化分子动力学研究，深入探讨了SARS-CoV-2的分子结构与功能，涵盖了蛋白质与RNA的结构分析、药物与疫苗开发、以及流行病学数学模型。适合从事计算生物化学、计算生物物理学和结构生物信息学领域的研究人员和学生阅读。
荐读提要：Molecular Dynamics Analyses of Prion Protein Structures - The Resistance to Prion Diseases Down Under / by Jiapu Zhang. 1st ed. 2018.
核心主题
本书的核心主题是通过分子动力学（MD）模拟分析朊病毒蛋白（PrP）的结构，探讨不同物种对朊病毒疾病的抗性机制。
内容详情
本书分为五个部分：
朊病毒抗性物种：包括兔子、狗、马、水牛、猪、鸡、乌龟和青蛙等物种的PrP结构分析。
β2-α2环结构：研究野生型小鼠及其突变体的PrP结构，以及其他物种的有序β2-α2环结构。
人类突变体：分析人类PrP突变体及其与朊病毒疾病（如克雅氏病、格斯特曼-斯特劳斯勒-谢因克综合征、致命性家族性失眠症等）的关联。
PrP结合与对接：研究PrP与抗体、纳米抗体、RNA适配体等的结合，以及潜在的抗朊病毒药物。
具有交叉β结构的PrP肽：通过数学公式和氢键分析，研究PrP肽的交叉β结构。
主题分析
本书通过分子动力学模拟，深入探讨了朊病毒蛋白的结构与功能，特别是不同物种对朊病毒疾病的抗性机制。书中还涉及了朊病毒疾病的分子基础、PrP突变体的结构变化以及潜在的抗朊病毒药物。
图书摘要
本书是首部全面应用分子动力学模拟分析朊病毒蛋白结构的专著，涵盖了几乎所有已知的PrP PDB条目。书中详细研究了抗性物种（如猪、鸡、乌龟、青蛙等）的PrP结构，并与高易感物种进行了对比。此外，书中还深入分析了小鼠和人类PrP突变体的结构变化，以及PrP与抗体、化合物的结合机制。最后，书中还探讨了具有交叉β结构的PrP肽的分子特性。
网络热评
豆瓣：读者认为本书是朊病毒研究领域的重要参考书，尤其适合从事计算生物学和生物信息学的研究人员。
知乎：有用户指出，本书的分子动力学模拟方法为朊病毒疾病的研究提供了新的视角，具有较高的学术价值。
小红书：部分读者表示，本书内容较为专业，适合有一定生物学背景的读者阅读。
学术定位
本书在学术上定位为计算生物学、生物信息学和分子动力学领域的专业参考书，适合从事相关研究的学者和研究生阅读。
时效性与视角
本书于2018年出版，内容基于最新的分子动力学模拟技术，具有较强的时效性。书中视角独特，从分子层面探讨了朊病毒蛋白的结构与功能。
适用读者
本书适合从事计算物理学、计算生物学、计算化学、生物医学、生物信息学、材料科学、应用数学、理论物理学、信息技术、运筹学和生物统计学等领域的研究人员和学生。
阅读推荐
推荐给对朊病毒疾病、分子动力学模拟和蛋白质结构研究感兴趣的读者。本书不仅适合作为研究参考书，也可作为相关课程的教材使用。
数据总结
本书通过分子动力学模拟，全面分析了朊病毒蛋白的结构与功能，特别是不同物种对朊病毒疾病的抗性机制。书中内容涵盖了抗性物种的PrP结构、人类PrP突变体、PrP与抗体的结合机制以及具有交叉β结构的PrP肽。本书具有较高的学术价值，适合从事相关研究的学者和学生阅读。
荐读提要：Molecular Structures and Structural Dynamics of Prion Proteins and Prions - Mechanism Underlying the Resistance of Prion Diseases, 2015istance to Prion Diseases / by Jiapu Zhang. 1st ed. 2015.
核心主题
本书的核心主题是朊病毒蛋白（Prion Proteins）的分子结构和结构动力学，以及朊病毒疾病抗性机制的分子建模与分子动力学模拟研究。
内容详情
本书详细探讨了朊病毒蛋白的分子动力学（MD）模拟和分子建模（MM）构建，重点分析了正常细胞朊病毒蛋白（PrPC）向致病性朊病毒（PrPSc）构象转变的关键因素。书中还研究了低易感性物种（如兔子、狗、马和水牛）的朊病毒蛋白结构，以揭示其抗性机制。此外，书中还涉及了无结构区域PrP(1-120)的分子动力学和分子建模研究。
主题分析
本书的主题围绕朊病毒蛋白的分子结构、动力学及其在朊病毒疾病中的作用展开。通过分子动力学和分子建模技术，作者深入研究了朊病毒蛋白的构象变化及其与疾病的关系，为朊病毒疾病的研究和药物设计提供了重要的理论基础。
图书摘要
本书是首部关于朊病毒蛋白分子动力学模拟和分子建模的易读易懂的专著。通过分子动力学和分子建模技术，作者揭示了朊病毒蛋白从正常构象向致病构象转变的关键机制，并研究了低易感性物种的朊病毒蛋白结构。本书还探讨了无结构区域PrP(1-120)的分子动力学和分子建模，为朊病毒疾病的研究提供了新的视角。
网络热评
豆瓣：读者认为本书是朊病毒研究领域的重要参考书，内容深入且易于理解，适合相关领域的研究人员和学生阅读。
知乎：有用户指出，本书的分子动力学和分子建模技术为朊病毒疾病的研究提供了新的思路，具有较高的学术价值。
小红书：部分读者表示，本书的内容虽然专业，但作者通过清晰的解释和实例使其易于理解，适合对朊病毒研究感兴趣的读者。
学术定位
本书在朊病毒研究领域具有重要的学术地位，特别是在分子动力学和分子建模技术的应用方面。它为朊病毒蛋白的结构研究和疾病机制提供了新的视角，是生物物理学、生物化学、生物医学等领域的重要参考书。
时效性与视角
本书于2015年出版，内容基于当时最新的分子动力学和分子建模技术，具有较高的时效性。作者从分子结构和动力学的角度出发，深入探讨了朊病毒蛋白的构象变化及其与疾病的关系，为朊病毒疾病的研究提供了新的视角。
适用读者
本书适用于生物物理学、生物化学、生物医学、生物信息学、材料科学与工程、应用数学、理论物理、信息技术、运筹学、生物统计学等领域的研究人员和学生。同时，作为这些领域的入门教材，本书也适合对朊病毒研究感兴趣的读者。
阅读推荐
本书是朊病毒研究领域的重要参考书，特别适合从事分子动力学和分子建模研究的研究人员和学生阅读。对于对朊病毒疾病机制感兴趣的读者，本书提供了深入且易于理解的内容，是了解朊病毒蛋白结构和动力学的理想选择。
数据总结
本书《Molecular Structures and Structural Dynamics of Prion Proteins and Prions Mechanism Underlying the Resistance to Prion Diseases》由Jiapu Zhang撰写，2015年首次出版。书中详细探讨了朊病毒蛋白的分子动力学和分子建模，重点分析了朊病毒蛋白的构象变化及其与疾病的关系。本书在朊病毒研究领域具有重要的学术地位，适合相关领域的研究人员和学生阅读。
