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相关概念视频

Noncovalent Attractions in Biomolecules02:35

Noncovalent Attractions in Biomolecules

Noncovalent attractions are associations within and between molecules that influence the shape and structural stability of complexes. These interactions differ from covalent bonding in that they do not involve sharing of electrons.
Four types of noncovalent interactions are hydrogen bonds, van der Waals forces, ionic bonds, and hydrophobic interactions.
Hydrogen bonding results from the electrostatic attraction of a hydrogen atom covalently bonded to a strong-electronegative atom like oxygen,...
Conserved Binding Sites01:49

Conserved Binding Sites

Many proteins’ biological role depends on their interactions with their ligands, small molecules that bind to specific locations on the protein known as ligand-binding sites. Ligand-binding sites are often conserved among homologous proteins as these sites are critical for protein function.
Binding sites are often located in large pockets, and if their location on a protein’s surface is unknown, it can be predicted using various approaches. The energetic method computationally analyses the...
Cooperative Allosteric Transitions01:58

Cooperative Allosteric Transitions

Cooperative allosteric transitions can occur in multimeric proteins, where each subunit of the protein has its own ligand-binding site. When a ligand binds to any of these subunits, it triggers a conformational change that affects the binding sites in the other subunits; this can change the affinity of the other sites for their respective ligands. The ability of the protein to change the shape of its binding site is attributed to the presence of a mix of flexible and stable segments in the...
Coupled Reactions01:17

Coupled Reactions

Cellular processes such as building and breaking down complex molecules occur through stepwise chemical reactions. Some of these chemical reactions are spontaneous and release energy, whereas others require energy to proceed. Cells often couple the energy-releasing reaction with the energy-requiring one to carry out important cell functions. 
Energy in adenosine triphosphate or ATP molecules is easily accessible to do work. ATP powers the majority of energy-requiring cellular reactions. Cells...
Conserved Binding Sites01:49

Conserved Binding Sites

Many proteins’ biological role depends on their interactions with their ligands, small molecules that bind to specific locations on the protein known as ligand-binding sites. Ligand-binding sites are often conserved among homologous proteins as these sites are critical for protein function.
Binding sites are often located in large pockets, and if their location on a protein’s surface is unknown, it can be predicted using various approaches. The energetic method computationally analyses the...
Noncovalent Attractions in Biomolecules02:35

Noncovalent Attractions in Biomolecules

Noncovalent attractions are associations within and between molecules that influence the shape and structural stability of complexes. These interactions differ from covalent bonding in that they do not involve sharing of electrons.
Four types of noncovalent interactions are hydrogen bonds, van der Waals forces, ionic bonds, and hydrophobic interactions.
Hydrogen bonding results from the electrostatic attraction of a hydrogen atom covalently bonded to a strong-electronegative atom like oxygen,...

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相关实验视频

Updated: Jun 6, 2026

Optimization of Synthetic Proteins: Identification of Interpositional Dependencies Indicating Structurally and/or Functionally Linked Residues
07:08

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Published on: July 14, 2015

从功能上重要的残留物来自于同进化动态合的图形分析.

Manming Xu1, Sarath Chandra Dantu2, James A Garnett3

  • 1UCL School of Pharmacy, London, United Kingdom.

eLife
|March 28, 2025
PubMed
概括

DyNoPy集成了共同进化和分子动力学来预测蛋白质功能. 这种方法揭示了蛋白质动态上的进化影响,有助于在抗生素耐药性等挑战的药物设计中.

关键词:
这是Dynopy.共同进化的共同进化分子生物物理学分子生物物理学分子动力学分子动力学结构生物学结构生物学

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11:22

Using Three-color Single-molecule FRET to Study the Correlation of Protein Interactions

Published on: January 30, 2018

相关实验视频

Last Updated: Jun 6, 2026

Optimization of Synthetic Proteins: Identification of Interpositional Dependencies Indicating Structurally and/or Functionally Linked Residues
07:08

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Published on: July 14, 2015

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09:51

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Published on: July 16, 2017

Using Three-color Single-molecule FRET to Study the Correlation of Protein Interactions
11:22

Using Three-color Single-molecule FRET to Study the Correlation of Protein Interactions

Published on: January 30, 2018

科学领域:

  • 计算生物学 计算生物学
  • 蛋白质动力学 蛋白质动力学
  • 进化生物学 进化生物学

背景情况:

  • 蛋白质动态对于生物功能和药物开发至关重要.
  • 目前用于预测功能残留的方法忽视了进化对动态的影响.
  • 进化过程通过补偿突变微调蛋白质动态.

研究的目的:

  • 介绍DynoPy,一种新的计算方法.
  • 模拟进化对蛋白质动态的影响.
  • 为了揭示功能网站之间的隐藏的相关性.

主要方法:

  • DyNoPy将残留物共进化分析与分子动力学模拟相结合.
  • 构建了残留物-残留物相互作用的图形模型.
  • 共同发达的动态合被利用来识别关键位置.

主要成果:

  • DyNoPy成功地预测和分析了蛋白质的演变和动态.
  • 功能部位之间隐藏的相关性被揭示出来.
  • 对SHV-1和PDC-3β-乳酸酶的有效性得到证明.

结论:

  • DyNoPy提供了一种强大的方法来理解蛋白质动力学和进化.
  • 该方法有可能为药物设计提供信息.
  • DyNoPy可以帮助解决医疗保健挑战,例如抗生素耐药性.