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Protein Folding

Protein Folding

Proteins are chains of amino acids linked together by peptide bonds. Upon synthesis, a protein folds into a three-dimensional conformation, critical to its biological function. Interactions between its constituent amino acids guide protein folding, and hence the protein structure is primarily dependent on its amino acid sequence.
Protein Structure Is Critical to Its Biological Function
Proteins perform a wide range of biological functions such as catalyzing chemical reactions, providing...

Protein Folding

Protein Folding

Molecular Chaperones and Protein Folding

Molecular Chaperones and Protein Folding

The native conformation of a protein is formed by interactions between the side chains of its constituent amino acids. When the amino acids cannot form these interactions, the protein cannot fold by itself and needs chaperones. Notably, chaperones do not relay any additional information required for the folding of polypeptides; the native conformation of a protein is determined solely by its amino acid sequence. Chaperones catalyze protein folding without being a part of the folded protein.
The...

Molecular Chaperones and Protein Folding

Molecular Chaperones and Protein Folding

Protein Folding Quality Check in the RER

Protein Folding Quality Check in the RER

ER is the primary site for the maturation and folding of soluble and transmembrane secretory proteins. The calnexin cycle is a specific chaperone system that folds and assesses the confirmation of N-glycosylated proteins before they can exit the ER lumen. The primary players of this quality check pipeline are the lectins, ER-resident chaperones, and a glucosyl transferase enzyme. In case the calnexin system in the lumen fails to salvage a misfolded protein, it is transported to the cytoplasm...

Conservation of Protein Domains Over Different Proteins

Conservation of Protein Domains Over Different Proteins

Protein domains are small structurally independent units that are part of a single amino acid chain. Although these domains are often structurally independent, they may rely on synergistic effects to perform their functions as part of a larger protein. Protein domains may be conserved within the same organism, as well as across different organisms.
A limited set of protein domains often duplicate and recombine during evolution. These domains can be organized in different combinations to...

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Updated: Jan 9, 2026

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

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

Published on: July 14, 2015

使用进化背景来分类难以折叠的蛋白质.

Jimin Pei^1,2,3, R Dustin Schaeffer², Qian Cong^1,2,3

¹Eugene McDermott Center for Human Growth and Development, University of Texas Southwestern Medical Center, Dallas, Texas, United States of America.

PLoS computational biology

|December 1, 2025

概括

此摘要是机器生成的。

蛋白质结构预测的进步揭示了新的蛋白质域. 整合结构和进化方法,如DPAM,有助于分类这些领域,并发现遥远的进化联系.

更多相关视频

Creating and Applying a Reference to Facilitate the Discussion and Classification of Proteins in a Diverse Group

Creating and Applying a Reference to Facilitate the Discussion and Classification of Proteins in a Diverse Group

Published on: August 16, 2017

A Protocol for Computer-Based Protein Structure and Function Prediction

A Protocol for Computer-Based Protein Structure and Function Prediction

Published on: November 3, 2011

相关实验视频

Last Updated: Jan 9, 2026

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

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

Published on: July 14, 2015

Creating and Applying a Reference to Facilitate the Discussion and Classification of Proteins in a Diverse Group

Creating and Applying a Reference to Facilitate the Discussion and Classification of Proteins in a Diverse Group

Published on: August 16, 2017

A Protocol for Computer-Based Protein Structure and Function Prediction

A Protocol for Computer-Based Protein Structure and Function Prediction

Published on: November 3, 2011

科学领域:

结构生物学是结构生物学.
生物信息学是一种生物信息学.
进化生物学是进化的生物学.

背景情况:

最近的蛋白质结构预测工具,如AlphaFold2,已经确定了许多具有独特结构的新型蛋白质域.
域名百科全书 (TED) 项目根据结构分类编目了超过7400个候选新 (CNF) 域名.

研究的目的:

使用一种新方法分析TED CNF领域的进化和结构背景.
将TED和DPAM的域解析结果进行比较,以了解它们之间的关系并完善蛋白质域分类.

主要方法:

应用DPAM (AlphaFold模型的域解析器),它将AlphaFold信任分数与序列和结构相似性搜索集成.
在包含TED CNF域的AlphaFold模型中解析域.
在TED和DPAM之间比较域边界和分类.

主要成果:

确定了8044个与TED CNF域重叠的DPAM域;2490个在ECOD层次结构中被安全地分类.
有相当一部分TED CNF域是已知的ECOD域的远方同类.
在TED和DPAM之间观察到不同的域边界模式,TED域经常嵌入DPAM域内,表明插入或扩展.

结论:

结构和进化方法是蛋白质域注释的补充.
像DPAM这样的整合方法对于完善复杂蛋白质折叠的分类和识别远程进化关系来说非常强大.
这项研究完善了我们对新型蛋白质折叠及其进化联系的理解.