肽链的折叠方式不是蛋白质多样性的直接原因

从蛋白质的分子结构、翻译后的蛋白质质量控制、蛋白质结构预测方法 3个方面阐述肽链的折叠方式不是引起蛋白质结构和功能多样性的直接原因:在氨基酸序列确定的情况下,肽链的折叠方式是保守的;肽链一旦折叠错误,蛋白质质量控制系统会对其进行纠正或降解清除,若质量控制失败,错误折叠的蛋白质便会引起疾病;从氨基酸序列出发利用分子力学模拟方法和建模软件预测蛋白质三维构象的研究技术侧面印证了氨基酸序列确定的肽链其折叠方式具有保守性。     

传染性蛋白的“负面”和“正面”(1)

蛋白质是生命活动的执行者,除了催化数千种化学反应,蛋白质还在生物的身体结构、信息传递、生物防卫等方面起不可或缺的作用。不同的生理功能不仅需要不同的蛋白质,还需要蛋白质分子形成各自的结构和形状。而蛋白质分子是由不分支的肽链组成的,从新合成的肽链到具有特定三维结构和有生理功能的蛋白质,需要复杂精细的肽链折叠过程。由于各种折叠方式之间的能量差别甚小,许多因素,包括自身浓度的变化、分子中一部分肽链缺失或者延长、基因突变引起的氨基酸残基改变、环境中酸碱度改变、离子浓度变化、周围的分子环境变化等,都能使肽链的折叠方式发生改变。肽链折叠方式改变的后果之一,就是形成特殊的β-折叠:肽链中彼此平行而又方向相反的区段以氢键联系,形成片状结构,多个分子的这种片状结构还能逐层叠加,形成纤维状的聚合物。不仅如此,这样的"异常"结构还会使"正常"的蛋白也改变折叠方式,变成和自己一样的结构,因此这些"异常"结构的蛋白质具有"传染性",即能复制自己的结构,统称"传染性蛋白",词源是从英文的Prion一词意译而来。在许多情况下,这种"折叠错误"的蛋白会丧失原有的生理功能,且其聚合物对细胞有害,引起疾病,包括疯牛病、痒羊病(Scrapie)、人类的克-雅氏病、老年痴呆、帕金森氏症、杭廷顿氏症等中枢神经系统病症。除了这些疾病,折叠错误的蛋白还可沉积在身体各处,引起各种"淀粉样变性病"(Amyloidosis)。另一方面,Prion型的蛋白由于其稳定性和特殊结构,又可获得新的生理功能,在生物材料的建造,物质储存、作为黑色素和牙釉质合成时的模板、动物的长期记忆,以及免疫系统的信息传输中发挥重要作用,即一些传染性蛋白也能发挥正常的、甚至不可替代的生理功能。本文以3个部分分别介绍传染性蛋白被发现的历史和形成机制、传染性蛋白所引起的疾病(负面),以及传染性蛋白执行的正常生理功能(正面)。     

传染性蛋白的“负面”和“正面”(2)

蛋白质是生命活动的执行者,除了催化数千种化学反应,蛋白质还在生物的身体结构、信息传递、生物防卫等方面起不可或缺的作用。不同的生理功能不仅需要不同的蛋白质,还需要蛋白质分子形成各自的结构和形状。而蛋白质分子是由不分支的肽链组成的,从新合成的肽链到具有特定三维结构和有生理功能的蛋白质,需要复杂精细的肽链折叠过程。由于各种折叠方式之间的能量差别甚小,许多因素,包括自身浓度的变化、分子中一部分肽链缺失或者延长、基因突变引起的氨基酸残基改变、环境中酸碱度改变、离子浓度变化、周围的分子环境变化等,都能使肽链的折叠方式发生改变。肽链折叠方式改变的后果之一,就是形成特殊的β-折叠:肽链中彼此平行而又方向相反的区段以氢键联系,形成片状结构,多个分子的这种片状结构还能逐层叠加,形成纤维状的聚合物。不仅如此,这样的"异常"结构还会使"正常"的蛋白也改变折叠方式,变成和自己一样的结构,因此这些"异常"结构的蛋白质具有"传染性",即能复制自己的结构,统称"传染性蛋白",词源是从英文的Prion一词意译而来。在许多情况下,这种"折叠错误"的蛋白会丧失原有的生理功能,且其聚合物对细胞有害,引起疾病,包括疯牛病、痒羊病(Scrapie)、人类的克-雅氏病、老年痴呆、帕金森氏症、杭廷顿氏症等中枢神经系统病症。除了这些疾病,折叠错误的蛋白还可沉积在身体各处,引起各种"淀粉样变性病"(Amyloidosis)。另一方面,Prion型的蛋白由于其稳定性和特殊结构,又可获得新的生理功能,在生物材料的建造,物质储存、作为黑色素和牙釉质合成时的模板、动物的长期记忆,以及免疫系统的信息传输中发挥重要作用,即一些传染性蛋白也能发挥正常的、甚至不可替代的生理功能。本文以3个部分分别介绍传染性蛋白被发现的历史和形成机制、传染性蛋白所引起的疾病(负面),以及传染性蛋白执行的正常生理功能(正面)。     

传染性蛋白的“负面”和“正面”(10)

蛋白质是生命活动的执行者,除了催化数千种化学反应,蛋白质还在生物的身体结构、信息传递、生物防卫等方面起不可或缺的作用。不同的生理功能不仅需要不同的蛋白质,还需要蛋白质分子形成各自的结构和形状。而蛋白质分子是由不分支的肽链组成的,从新合成的肽链到具有特定三维结构和有生理功能的蛋白质,需要复杂精细的肽链折叠过程。由于各种折叠方式之间的能量差别甚小,许多因素,包括自身浓度的变化、分子中一部分肽链缺失或者延长、基因突变引起的氨基酸残基改变、环境中酸碱度改变、离子浓度变化、周围的分子环境变化等,都能使肽链的折叠方式发生改变。肽链折叠方式改变的后果之一,就是形成特殊的β-折叠:肽链中彼此平行而又方向相反的区段以氢键联系,形成片状结构,多个分子的这种片状结构还能逐层叠加,形成纤维状的聚合物。不仅如此,这样的"异常"结构还会使"正常"的蛋白也改变折叠方式,变成和自己一样的结构,因此这些"异常"结构的蛋白质具有"传染性",即能复制自己的结构,统称"传染性蛋白",词源是从英文的Prion一词意译而来。在许多情况下,这种"折叠错误"的蛋白会丧失原有的生理功能,且其聚合物对细胞有害,引起疾病,包括疯牛病、痒羊病(Scrapie)、人类的克-雅氏病、老年痴呆、帕金森氏症、杭廷顿氏症等中枢神经系统病症。除了这些疾病,折叠错误的蛋白还可沉积在身体各处,引起各种"淀粉样变性病"(Amyloidosis)。另一方面,Prion型的蛋白由于其稳定性和特殊结构,又可获得新的生理功能,在生物材料的建造,物质储存、作为黑色素和牙釉质合成时的模板、动物的长期记忆,以及免疫系统的信息传输中发挥重要作用,即一些传染性蛋白也能发挥正常的、甚至不可替代的生理功能。本文以3个部分分别介绍传染性蛋白被发现的历史和形成机制、传染性蛋白所引起的疾病(负面),以及传染性蛋白执行的正常生理功能(正面)。     

传染性蛋白的“负面”和“正面”(6)

蛋白质是生命活动的执行者,除了催化数千种化学反应,蛋白质还在生物的身体结构、信息传递、生物防卫等方面起不可或缺的作用。不同的生理功能不仅需要不同的蛋白质,还需要蛋白质分子形成各自的结构和形状。而蛋白质分子是由不分支的肽链组成的,从新合成的肽链到具有特定三维结构和有生理功能的蛋白质,需要复杂精细的肽链折叠过程。由于各种折叠方式之间的能量差别甚小,许多因素,包括自身浓度的变化、分子中一部分肽链缺失或者延长、基因突变引起的氨基酸残基改变、环境中酸碱度改变、离子浓度变化、周围的分子环境变化等,都能使肽链的折叠方式发生改变。肽链折叠方式改变的后果之一,就是形成特殊的β-折叠:肽链中彼此平行而又方向相反的区段以氢键联系,形成片状结构,多个分子的这种片状结构还能逐层叠加,形成纤维状的聚合物。不仅如此,这样的"异常"结构还会使"正常"的蛋白也改变折叠方式,变成和自己一样的结构,因此这些"异常"结构的蛋白质具有"传染性",即能复制自己的结构,统称"传染性蛋白",词源是从英文的Prion一词意译而来。在许多情况下,这种"折叠错误"的蛋白会丧失原有的生理功能,且其聚合物对细胞有害,引起疾病,包括疯牛病、痒羊病(Scrapie)、人类的克-雅氏病、老年痴呆、帕金森氏症、杭廷顿氏症等中枢神经系统病症。除了这些疾病,折叠错误的蛋白还可沉积在身体各处,引起各种"淀粉样变性病"(Amyloidosis)。另一方面,Prion型的蛋白由于其稳定性和特殊结构,又可获得新的生理功能,在生物材料的建造,物质储存、作为黑色素和牙釉质合成时的模板、动物的长期记忆,以及免疫系统的信息传输中发挥重要作用,即一些传染性蛋白也能发挥正常的、甚至不可替代的生理功能。本文以3个部分分别介绍传染性蛋白被发现的历史和形成机制、传染性蛋白所引起的疾病(负面),以及传染性蛋白执行的正常生理功能(正面)。     

传染性蛋白的“负面”和“正面”(7)

蛋白质是生命活动的执行者,除了催化数千种化学反应,蛋白质还在生物的身体结构、信息传递、生物防卫等方面起不可或缺的作用。不同的生理功能不仅需要不同的蛋白质,还需要蛋白质分子形成各自的结构和形状。而蛋白质分子是由不分支的肽链组成的,从新合成的肽链到具有特定三维结构和有生理功能的蛋白质,需要复杂精细的肽链折叠过程。由于各种折叠方式之间的能量差别甚小,许多因素,包括自身浓度的变化、分子中一部分肽链缺失或者延长、基因突变引起的氨基酸残基改变、环境中酸碱度改变、离子浓度变化、周围的分子环境变化等,都能使肽链的折叠方式发生改变。肽链折叠方式改变的后果之一,就是形成特殊的β-折叠:肽链中彼此平行而又方向相反的区段以氢键联系,形成片状结构,多个分子的这种片状结构还能逐层叠加,形成纤维状的聚合物。不仅如此,这样的"异常"结构还会使"正常"的蛋白也改变折叠方式,变成和自己一样的结构,因此这些"异常"结构的蛋白质具有"传染性",即能复制自己的结构,统称"传染性蛋白",词源是从英文的Prion一词意译而来。在许多情况下,这种"折叠错误"的蛋白会丧失原有的生理功能,且其聚合物对细胞有害,引起疾病,包括疯牛病、痒羊病(Scrapie)、人类的克-雅氏病、老年痴呆、帕金森氏症、杭廷顿氏症等中枢神经系统病症。除了这些疾病,折叠错误的蛋白还可沉积在身体各处,引起各种"淀粉样变性病"(Amyloidosis)。另一方面,Prion型的蛋白由于其稳定性和特殊结构,又可获得新的生理功能,在生物材料的建造,物质储存、作为黑色素和牙釉质合成时的模板、动物的长期记忆,以及免疫系统的信息传输中发挥重要作用,即一些传染性蛋白也能发挥正常的、甚至不可替代的生理功能。本文以3个部分分别介绍传染性蛋白被发现的历史和形成机制、传染性蛋白所引起的疾病(负面),以及传染性蛋白执行的正常生理功能(正面)。     

传染性蛋白的“负面”和“正面”(9)

蛋白质是生命活动的执行者,除了催化数千种化学反应,蛋白质还在生物的身体结构、信息传递、生物防卫等方面起不可或缺的作用。不同的生理功能不仅需要不同的蛋白质,还需要蛋白质分子形成各自的结构和形状。而蛋白质分子是由不分支的肽链组成的,从新合成的肽链到具有特定三维结构和有生理功能的蛋白质,需要复杂精细的肽链折叠过程。由于各种折叠方式之间的能量差别甚小,许多因素,包括自身浓度的变化、分子中一部分肽链缺失或者延长、基因突变引起的氨基酸残基改变、环境中酸碱度改变、离子浓度变化、周围的分子环境变化等,都能使肽链的折叠方式发生改变。肽链折叠方式改变的后果之一,就是形成特殊的β-折叠:肽链中彼此平行而又方向相反的区段以氢键联系,形成片状结构,多个分子的这种片状结构还能逐层叠加,形成纤维状的聚合物。不仅如此,这样的"异常"结构还会使"正常"的蛋白也改变折叠方式,变成和自己一样的结构,因此这些"异常"结构的蛋白质具有"传染性",即能复制自己的结构,统称"传染性蛋白",词源是从英文的Prion一词意译而来。在许多情况下,这种"折叠错误"的蛋白会丧失原有的生理功能,且其聚合物对细胞有害,引起疾病,包括疯牛病、痒羊病(Scrapie)、人类的克-雅氏病、老年痴呆、帕金森氏症、杭廷顿氏症等中枢神经系统病症。除了这些疾病,折叠错误的蛋白还可沉积在身体各处,引起各种"淀粉样变性病"(Amyloidosis)。另一方面,Prion型的蛋白由于其稳定性和特殊结构,又可获得新的生理功能,在生物材料的建造,物质储存、作为黑色素和牙釉质合成时的模板、动物的长期记忆,以及免疫系统的信息传输中发挥重要作用,即一些传染性蛋白也能发挥正常的、甚至不可替代的生理功能。本文以3个部分分别介绍传染性蛋白被发现的历史和形成机制、传染性蛋白所引起的疾病(负面),以及传染性蛋白执行的正常生理功能(正面)。     

传染性蛋白的“负面”和“正面”(4)

蛋白质是生命活动的执行者,除了催化数千种化学反应,蛋白质还在生物的身体结构、信息传递、生物防卫等方面起不可或缺的作用。不同的生理功能不仅需要不同的蛋白质,还需要蛋白质分子形成各自的结构和形状。而蛋白质分子是由不分支的肽链组成的,从新合成的肽链到具有特定三维结构和有生理功能的蛋白质,需要复杂精细的肽链折叠过程。由于各种折叠方式之间的能量差别甚小,许多因素,包括自身浓度的变化、分子中一部分肽链缺失或者延长、基因突变引起的氨基酸残基改变、环境中酸碱度改变、离子浓度变化、周围的分子环境变化等,都能使肽链的折叠方式发生改变。肽链折叠方式改变的后果之一,就是形成特殊的β-折叠:肽链中彼此平行而又方向相反的区段以氢键联系,形成片状结构,多个分子的这种片状结构还能逐层叠加,形成纤维状的聚合物。不仅如此,这样的"异常"结构还会使"正常"的蛋白也改变折叠方式,变成和自己一样的结构,因此这些"异常"结构的蛋白质具有"传染性",即能复制自己的结构,统称"传染性蛋白",词源是从英文的Prion一词意译而来。在许多情况下,这种"折叠错误"的蛋白会丧失原有的生理功能,且其聚合物对细胞有害,引起疾病,包括疯牛病、痒羊病(Scrapie)、人类的克-雅氏病、老年痴呆、帕金森氏症、杭廷顿氏症等中枢神经系统病症。除了这些疾病,折叠错误的蛋白还可沉积在身体各处,引起各种"淀粉样变性病"(Amyloido-sis)。另一方面,Prion型的蛋白由于其稳定性和特殊结构,又可获得新的生理功能,在生物材料的建造,物质储存、作为黑色素和牙釉质合成时的模板、动物的长期记忆,以及免疫系统的信息传输中发挥重要作用,即一些传染性蛋白也能发挥正常的、甚至不可替代的生理功能。本文以3个部分分别介绍传染性蛋白被发现的历史和形成机制、传染性蛋白所引起的疾病(负面),以及传染性蛋白执行的正常生理功能(正面)。     

传染性蛋白的“负面”和“正面”(5)

蛋白质是生命活动的执行者,除了催化数千种化学反应,蛋白质还在生物的身体结构、信息传递、生物防卫等方面起不可或缺的作用。不同的生理功能不仅需要不同的蛋白质,还需要蛋白质分子形成各自的结构和形状。而蛋白质分子是由不分支的肽链组成的,从新合成的肽链到具有特定三维结构和有生理功能的蛋白质,需要复杂精细的肽链折叠过程。由于各种折叠方式之间的能量差别甚小,许多因素,包括自身浓度的变化、分子中一部分肽链缺失或者延长、基因突变引起的氨基酸残基改变、环境中酸碱度改变、离子浓度变化、周围的分子环境变化等,都能使肽链的折叠方式发生改变。肽链折叠方式改变的后果之一,就是形成特殊的β-折叠:肽链中彼此平行而又方向相反的区段以氢键联系,形成片状结构,多个分子的这种片状结构还能逐层叠加,形成纤维状的聚合物。不仅如此,这样的"异常"结构还会使"正常"的蛋白也改变折叠方式,变成和自己一样的结构,因此这些"异常"结构的蛋白质具有"传染性",即能复制自己的结构,统称"传染性蛋白",词源是从英文的Prion一词意译而来。在许多情况下,这种"折叠错误"的蛋白会丧失原有的生理功能,且其聚合物对细胞有害,引起疾病,包括疯牛病、痒羊病(Scrapie)、人类的克-雅氏病、老年痴呆、帕金森氏症、杭廷顿氏症等中枢神经系统病症。除了这些疾病,折叠错误的蛋白还可沉积在身体各处,引起各种"淀粉样变性病"(Amyloidosis)。另一方面,Prion型的蛋白由于其稳定性和特殊结构,又可获得新的生理功能,在生物材料的建造,物质储存、作为黑色素和牙釉质合成时的模板、动物的长期记忆,以及免疫系统的信息传输中发挥重要作用,即一些传染性蛋白也能发挥正常的、甚至不可替代的生理功能。本文以3个部分分别介绍传染性蛋白被发现的历史和形成机制、传染性蛋白所引起的疾病(负面),以及传染性蛋白执行的正常生理功能(正面)。     

传染性蛋白的“负面”和“正面”(8)

蛋白质是生命活动的执行者,除了催化数千种化学反应,蛋白质还在生物的身体结构、信息传递、生物防卫等方面起不可或缺的作用。不同的生理功能不仅需要不同的蛋白质,还需要蛋白质分子形成各自的结构和形状。而蛋白质分子是由不分支的肽链组成的,从新合成的肽链到具有特定三维结构和有生理功能的蛋白质,需要复杂精细的肽链折叠过程。由于各种折叠方式之间的能量差别甚小,许多因素,包括自身浓度的变化、分子中一部分肽链缺失或者延长、基因突变引起的氨基酸残基改变、环境中酸碱度改变、离子浓度变化、周围的分子环境变化等,都能使肽链的折叠方式发生改变。肽链折叠方式改变的后果之一,就是形成特殊的β-折叠:肽链中彼此平行而又方向相反的区段以氢键联系,形成片状结构,多个分子的这种片状结构还能逐层叠加,形成纤维状的聚合物。不仅如此,这样的"异常"结构还会使"正常"的蛋白也改变折叠方式,变成和自己一样的结构,因此这些"异常"结构的蛋白质具有"传染性",即能复制自己的结构,统称"传染性蛋白",词源是从英文的Prion一词意译而来。在许多情况下,这种"折叠错误"的蛋白会丧失原有的生理功能,且其聚合物对细胞有害,引起疾病,包括疯牛病、痒羊病(Scrapie)、人类的克-雅氏病、老年痴呆、帕金森氏症、杭廷顿氏症等中枢神经系统病症。除了这些疾病,折叠错误的蛋白还可沉积在身体各处,引起各种"淀粉样变性病"(Amyloidosis)。另一方面,Prion型的蛋白由于其稳定性和特殊结构,又可获得新的生理功能,在生物材料的建造,物质储存、作为黑色素和牙釉质合成时的模板、动物的长期记忆,以及免疫系统的信息传输中发挥重要作用,即一些传染性蛋白也能发挥正常的、甚至不可替代的生理功能。本文以3个部分分别介绍传染性蛋白被发现的历史和形成机制、传染性蛋白所引起的疾病(负面),以及传染性蛋白执行的正常生理功能(正面)。     

The entropic nature of protein thermal stabilization

We performed thermodynamic analysis of temperature-induced unfolding of mesophilic and thermophilic proteins. It was shown that the variability in protein thermostability associated with pH-dependent unfolding or linked to the substitution of amino acid residues on the protein surface is evidence of the governing role of the entropy factor. Numerical values of conformational components in enthalpy, entropy and free energy which characterize protein unfolding in the “gas phase” were obtained. Based on the calculated absolute values of entropy and free energy, a model of protein unfolding is proposed in which the driving force is the conformational entropy of native protein, as an energy of the heat motion (T·S^NC) increasing with temperature and acting as an factor devaluating the energy of intramolecular weak bonds in the transition state.     

Structural details of urea binding to barnase: a molecular dynamics analysis.

BACKGROUND: The molecular mechanism of urea-induced protein unfolding has not been established. It is generally thought that denaturation results from the stabilizing interactions of urea with portions of the protein that are buried in the native state and become exposed upon unfolding of the protein. RESULTS: We have performed molecular dynamics simulations of barnase (a 110 amino acid RNase from Bacillus amyloliquefaciens) with explicit water and urea molecules at 300 K and 360 K. The native conformation was unaffected in the 300 K simulations at neutral and low pH. Two of the three runs at 360 K and low pH showed some denaturation, with partial unfolding of the hydrophobic core 2. The first solvation shell has a much higher density of urea molecules (water/urea ratio ranging from 2.07 to 2.73) than the bulk (water/urea ratio of 4.56). About one half of the first-shell urea molecules are involved in hydrogen bonds with polar or charged groups on the barnase surface, and between 15% and 18% of the first-shell urea molecules participate in multiple hydrogen bonds with barnase. The more stably bound urea molecules tend to be in crevices or pockets on the barnase surface. CONCLUSIONS: The simulation results indicate that an aqueous urea solution solvates the surface of a polypeptide chain more favorably than pure water. Urea molecules interact more favorably with nonpolar groups of the protein than water does, and the presence of urea improves the interactions of water molecules with the hydrophilic groups of the protein. The results suggest that urea denaturation involves effects on both nonpolar and polar groups of proteins.     

The dominant interaction between peptide and urea is electrostatic in nature: a molecular dynamics simulation study

The conformational equilibrium of a blocked valine peptide in water and aqueous urea solution is studied using molecular dynamics simulations. Pair correlation functions indicate enhanced concentration of urea near the peptide. Stronger hydrogen bonding of urea-peptide compared to water-peptide is observed with preference for helical conformation. The potential of mean force, computed using umbrella sampling, shows only small differences between urea and water solvation that are difficult to quantify. The changes in solvent structure around the peptide are explained by favorable electrostatic interactions (hydrogen bonds) of urea with the peptide backbone. There is no evidence for significant changes in hydrophobic interactions in the two conformations of the peptide in urea solution. Our simulations suggest that urea denatures proteins by preferentially forming hydrogen bonds to the peptide backbone, reducing the barrier for exposing protein residues to the solvent, and reaching the unfolded state.     

Non-linear effects of temperature and urea on the thermodynamics and kinetics of folding and unfolding of hisactophilin

Extensive measurements and analysis of thermodynamic stability and kinetics of urea-induced unfolding and folding of hisactophilin are reported for 5-50 degrees C, at pH 6.7. Under these conditions hisactophilin has moderate thermodynamic stability, and equilibrium and kinetic data are well fit by a two-state transition between the native and the denatured states. Equilibrium and kinetic m values decrease with increasing temperature, and decrease with increasing denaturant concentration. The betaF values at different temperatures and urea concentrations are quite constant, however, at about 0.7. This suggests that the transition state for hisactophilin unfolding is native-like and changes little with changing solution conditions, consistent with a narrow free energy profile for the transition state. The activation enthalpy and entropy of unfolding are unusually low for hisactophilin, as is also the case for the corresponding equilibrium parameters. Conventional Arrhenius and Eyring plots for both folding and unfolding are markedly non-linear, but these plots become linear for constant DeltaG/T contours. The Gibbs free energy changes for structural changes in hisactophilin have a non-linear denaturant dependence that is comparable to non-linearities observed for many other proteins. These non-linearities can be fit for many proteins using a variation of the Tanford model, incorporating empirical quadratic denaturant dependencies for Gibbs free energies of transfer of amino acid constituents from water to urea, and changes in fractional solvent accessible surface area of protein constituents based on the known protein structures. Noteworthy exceptions that are not well fit include amyloidogenic proteins and large proteins, which may form intermediates. The model is easily implemented and should be widely applicable to analysis of urea-induced structural transitions in proteins.     

Molecular dynamics simulations of urea and thermal-induced denaturation of S-peptide analogue

Molecular dynamics simulations of the S-peptide analogue AETAAAKFLREHMDS in water at 278 and 358 K, and in 8 M urea at 278 K were performed. The results show agreement with experiments. The helix is stable at low temperature (278 K), while at 358 K, unfolding is observed. The effects of urea on protein stability have been studied. The data support a model in which urea denatures proteins by: (1) diminishing the hydrophobic effect by displacing water molecules from the solvent shell around nonpolar groups; and (2) binding directly to amide units (NH and CO groups) via hydrogen bonds. The results of cluster analysis and essential dynamics analysis suggest that the mechanism of urea and thermal-induced denaturation may not be the same.     

Effect of Substitutions in Surface Amino Acid on Energy Profile of Apomyoglobin

Studies on the process of spontaneous protein folding into a unique native state are an important issue of molecular biology. Apomyoglobin from the sperm whale is a convenient model for these studies in vitro. Here, we present the results of equilibrium and kinetic experiments carried out in a study on the folding and unfolding of eight mutant apomyoglobin forms of with hydrophobic amino acid substitutions on the protein surface. Calculated values of apparent constants of folding/unfolding rates, as well as the data on equilibrium conformational transitions in the urea concentration range of 0–6 M at 11°C are given. Based on the obtained information on the kinetic properties of the studied proteins, a Φ-value analysis of the transition state has been performed and values of urea concentrations corresponding to the midpoint of the transition from the native to intermediate state have been determined for the given forms of mutant apomyoglobin. It has been found that a significant increase in the stability of the native state can be achieved by a small number of amino acid substitutions on the protein surface. It has been shown that the substitution of only one amino acid residue exclusively affects the height of the energy barrier that separates different states of apomyoglobin.     

On the role of some conserved and nonconserved amino acid residues in the transitional state and intermediate of apomyoglobin folding

The contributions of some amino acid residues in the A, B, G, and H helices to the formation of the folding nucleus and folding intermediate of apomyoglobin were estimated. The effects of point substitutions of Ala for hydrophobic amino acid residues on the structural stability of the native (N) protein and its folding intermediate (I), as well as on the folding/unfolding rates for four mutant apomyoglobin forms, were studied. The equilibrium and kinetic studies of the folding/unfolding rates of these mutant proteins in a wide range of urea concentrations demonstrated that their native state was considerably destabilized as compared with the wild-type protein, whereas the stability of the intermediate state changed moderately. It was shown that the amino acid residues in the A, G, and H helices contributed insignificantly to the stabilization of the apomyoglobin folding nucleus in the rate-limiting I ? N transition, taking place after the formation of the intermediate, whereas the residue of the B helix was of great importance in the formation of the folding nucleus in this transition.     

Structural basis of urea-induced unfolding of Fasciola gigantica glutathione S-transferase

Glutathione S-transferases (GSTs) are enzymes that are involved in the detoxification of harmful electrophilic endogenous and exogenous compounds by conjugating with glutathione (GSH). The liver fluke GSTs have multifunctional roles in the host–parasite interaction, such as general detoxification and bile acid sequestration to synthase activity. The GSTs have been highlighted as vaccine candidates towards parasitic flukes. In this study, we have thoroughly examined the urea-induced unfolding of a mu-class Fasciola gigantica GST1 ( FgGST1) using spectroscopic techniques and molecular dynamic simulations. FgGST1 is a highly cooperative molecule, because during urea-induced equilibrium unfolding, a concurrent unfolding of the protein without stabilization of any folded intermediate was observed. The protein was stabilized with conformational free energy of about ~12.36 kcal/mol. The protein loses its activity with increasing urea concentration, as the GSH molecule is not able to bind to the protein. We also studied the fluorescence quenching of Trp residues and the obtained K _SV data that provided additional information on the unfolding of FgGST1. Molecular dynamic trajectories simulated in different urea concentrations and temperatures indicated that urea destabilizes FgGST1 structure by weakening hydrophobic interactions and the hydrogen bond network. We observed a precise correlation between the in vitro and in silico studies.     

An equilibrium folding intermediate detected in the thermal unfolding transition of ribonuclease S by circular dichroism

The thermal-denaturation transition of ribonuclease S (RNAase S) is measured by circular dichroism at 225 nm. Only conformational transitions involving the S-peptide–S-protein complex are detected at this wavelength. Different pathways of thermal unfolding at high and low concentrations are apparent: at low concentrations the temperature of half-completion of denaturation (T_m) varies with concentration. Above a total enzyme concentration of 50 μM, T_m remains constant. The observed data can be explained on the basis of a model where the association–dissociation step occurs between S-peptide and thermally (at least partly) unfolded S-protein. The complex as a whole undergoes a major folding–unfolding transition in the course of which the S-peptide μ-helix appears to be formed. The unfolded complex is well populated in the unfolding transition region for enzyme concentrations of 100 μM or more. The model succeeds in deducing thermodynamic parameters from the thermal denaturation curves in various different ways. The values thus obtained are fully self-consistent and, moreover, consistent with the values for the apparent association constant and apparent association enthalpy as measured in enzyme-dilution experiments and by batch calorimetry.     

Structure of collagen with a new net of hydrogen bonds]

A conformational variability of the collagen triple helix was studied with the methods of molecular mechanics. The Rich-Crick model with one hydrogen bond per tripeptide fragment or the model with two hydrogen bonds per tripeptide fragment were used for tripeptides forming the primary structure of the protein. Imino acid and amino acid residues were located in the second position of the tripeptide fragments in the first and second cases, respectively. Conformations on domain boundaries, which had alternating structures with one and two hydrogen bonds per tripeptide, were particularly studied. Essentially all types of collagen backbone composed of amino acid residues most frequently occurring in this protein were considered. A new model was suggested that combined elements of the Rich-Crick model and our new approach. This was shown to be stereochemically valid, energetically advantageous, and consistent with the experimental data. It was conclusively demonstrated that the primary structure of collagen determines its tertiary structure.