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相关概念视频

Protein Organization01:24

Protein Organization

6.3K
Proteins are polymers of amino acid residues. They are versatile and responsible for different cellular functions, including DNA replication, molecular transport, catalysis, and structural support. Proteins have a hierarchical structure comprising at least three levels of organization: primary, secondary, and tertiary structure. Some large proteins have a quaternary structure where individual protein subunits are linked together.
The primary structure of a protein is its amino acid sequence....
6.3K
Globular and Fibrous Proteins02:21

Globular and Fibrous Proteins

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Many proteins can be classified into two distinct subtypes - globular or fibrous. These two types differ in their shapes and solubilities.
Globular proteins are also known as spheroproteins and typically are approximately round in shape. They contain a mix of amino acid types and contain differing sequences in their primary structures. Globular proteins have many different functions, such as enzymes, cellular messengers, and molecular transporters. These roles often require the proteins to be...
43.4K
Protein Families02:47

Protein Families

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Protein families are groups of homologous proteins; that is, they have similarities in amino acid sequences and three-dimensional structures. Protein families usually occur because of gene duplication, where an additional copy of a gene is inserted into the genome of an organism.   Mutations that change the amino acids but still allow the protein to be properly synthesized, will lead to new protein family members.   If these new proteins contain similar amino acids in key...
15.3K
Protein and Protein Structure02:15

Protein and Protein Structure

78.7K
Proteins are one of the most abundant organic molecules in living systems and have the most diverse range of functions of all macromolecules. Proteins may be structural, regulatory, contractile, or protective. They may serve in transport, storage, or membranes; or they may be toxins or enzymes. Their structures, like their functions, vary greatly. They are all, however, amino acid polymers arranged in a linear sequence.
A protein's shape is critical to its function. For example, an enzyme...
78.7K
Gene Families01:57

Gene Families

8.8K
Gene families consist of groups of genes proposed to have originated from a common ancestor. Typically these arise through events in which a gene or genes are mistakenly duplicated during cell division. Unlike their parent genes (which are subject to selection pressure to maintain function), these gene copies do not need to preserve their sequences and may evolve at a relatively faster rate.
Occasionally these regions can be adapted to take on new roles within the organism, becoming novel genes...
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Protein Folding01:22

Protein Folding

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Overview
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相关实验视频

Updated: Jun 9, 2025

Investigating Protein Sequence-structure-dynamics Relationships with Bio3D-web
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Investigating Protein Sequence-structure-dynamics Relationships with Bio3D-web

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蛋白质数据库中的无水结构.

Alexander Wlodawer1, Zbigniew Dauter1, Pawel Rubach2

  • 1Center for Structural Biology, National Cancer Institute, Frederick, MD 21702, USA.

IUCrJ
|October 28, 2024
PubMed
概括

蛋白质数据库 (PDB) 中许多蛋白质晶体结构缺乏预期的水分子,这表明数据质量或精细化存在潜在问题. 这凸显了关于溶剂建模的PDB数据更好的验证的需要.

关键词:
这是PDB-REDO.蛋白质数据库 蛋白质数据库在X射线晶体学.电子密度 的电子密度.建模错误是因为建模错误.蛋白质水化 蛋白质水化蛋白质结构 蛋白质结构结构因素统计的结构因素统计.结构-质量统计数据.

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Protein WISDOM: A Workbench for In silico De novo Design of BioMolecules
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Protein WISDOM: A Workbench for In silico De novo Design of BioMolecules

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A Protocol for Computer-Based Protein Structure and Function Prediction
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相关实验视频

Last Updated: Jun 9, 2025

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科学领域:

  • 结构生物学 结构生物学
  • 生物化学 生物化学
  • 数据科学数据科学数据科学

背景情况:

  • 水分子对蛋白质结构和功能至关重要,预计将与水溶液中结晶的蛋白质结合.
  • 蛋白质数据库 (PDB) 是蛋白质晶体结构的主要存储库,但其内容可能不能完全代表生物现实关于溶剂的存在.

研究的目的:

  • 为了研究预期的水分子存在与它们在沉积的蛋白质晶体结构中的缺席之间的差异.
  • 识别数据收集,精制或沉积过程中的潜在问题,导致缺失或不准确的溶剂建模.

主要方法:

  • 在蛋白质数据库 (PDB) 中分析蛋白质晶体结构模型.
  • 在不同分辨率下检查水分子与氨基酸残留的比率.
  • 详细审查缺乏或异常建模的溶剂分子的结构.

主要成果:

  • 在PDB中,大量的高分辨率蛋白质晶体结构 (800+在≥2.5 Å) 在没有任何水分子的情况下沉积.
  • 观察到的水占用量的变化表明,与衍射数据,精炼或沉积存在潜在问题.
  • 水分子与残留物的比例随分辨率而有很大变化,从原子分辨率>1.5到2.5 Å的0.25.

结论:

  • 在PDB结构中缺少或不准确的水分子建模可能表明潜在的数据或处理问题.
  • PDB应实施系统来标记和解决与存储模型中的溶剂结构相关的问题.
  • 存储者需要确保在蛋白质晶体结构中准确地表示溶剂,以改善生物解释.