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相关概念视频

Tail-anchoring of Proteins in the ER Membrane01:45

Tail-anchoring of Proteins in the ER Membrane

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Tail-anchored, or TA, proteins are estimated to make up to 3-5% of membrane proteins found in the eukaryotic cell. Such proteins have a single transmembrane domain located approximately 30 amino acid residues upstream from the C-terminal end. As a result, the signal recognition particle (SRP) cannot guide a TA protein to the ER membrane for cotranslational insertion. Hence, they are integrated into the ER membrane post-translationally using their C-terminal end as the anchor. TA proteins...
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Ligand Binding Sites02:40

Ligand Binding Sites

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Proteins are dynamic macromolecules that carry out a wide variety of essential processes; however, the activities of most proteins depend on their interactions with other molecules or ions, known as ligands.
Protein-ligand interactions are quite specific; even though numerous potential ligands surround a cellular protein at any given time, only a particular ligand can bind to that protein. Moreover, a ligand binds only to a dedicated area on the surface of the protein, known as the...
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Ligand Binding and Linkage00:49

Ligand Binding and Linkage

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Allosteric proteins have more than one ligand binding site; the binding of a ligand to any of these sites influences the binding of ligands to the other sites. When a protein is allosteric, its binding sites are called coupled or linked.  In the case of enzymes, the site that binds to the substrate is known as the active site and the other site is known as the regulatory site. When a ligand binds to the regulatory site, this leads to conformational changes in the protein that can influence...
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Protein-protein Interfaces02:04

Protein-protein Interfaces

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Many proteins form complexes to carry out their functions, making protein-protein interactions (PPIs) essential for an organism's survival. Most PPIs are stabilized by numerous weak noncovalent chemical forces. The physical shape of the interfaces determines the way two proteins interact. Many globular proteins have closely-matching shapes on their surfaces, which form a large number of weak bonds. Additionally, many PPIs occur between two helices or between a surface cleft and a...
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Lipids as Anchors01:32

Lipids as Anchors

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In the plasma membrane, the lipids forming the bilayer can also act as an anchor to tether proteins to the membrane. The three main types of lipid anchors found in eukaryotes are – prenyl groups, fatty acyl groups, and glycosylphosphatidylinositol or GPI groups. Prenyl and fatty acyl groups act as anchors on the cytosolic surface of the membrane, whereas GPI anchors proteins on the extracellular side.
The carboxy-terminal of most of the prenylated proteins, such as Ras proteins, contains...
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Assembly of Signaling Complexes01:30

Assembly of Signaling Complexes

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Multiprotein signaling complexes are formed in a dynamic process involving protein-protein interactions at the cytoplasmic domain of transmembrane receptors or enzymatic and non-enzymatic proteins associated with the receptor. These complexes ensure the activation and propagation of intracellular signals that regulate cell functions.
Interaction domains in cell signaling
Interaction domains recognize exposed features of their binding partners containing post-translationally modified sequences,...
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Development of Inhibitors of Protein-protein Interactions through REPLACE: Application to the Design and Development Non-ATP Competitive CDK Inhibitors
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解锁金属蛋白的精密对接方式

Camila M Clemente1, Juan M Prieto1, Marcelo Martí1

  • 1Departamento de Química Biológica, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires (FCEyN-UBA) e Instituto de Química Biológica de la Facultad de Ciencias Exactas y Naturales (IQUIBICEN) CONICET, Pabellón 2 de Ciudad Universitaria, Ciudad de Buenos Aires C1428EHA, Argentina.

Journal of chemical information and modeling
|February 19, 2024
PubMed
概括

金属蛋白偏差对接 (MBD) 通过提高预测与金属蛋白相互作用的准确性和精度来改善连接物发现. 这种新方法优于这些关键生物分子的传统对接.

科学领域:

  • 生物化学和分子生物学
  • 计算化学的计算化学
  • 药物发现 药物发现 药物发现

背景情况:

  • 金属蛋白在许多生物过程中是必不可少的.
  • 由于工具和数据有限,发现金属蛋白的高亲缘关系联体具有挑战性.
  • 分子对接方法与金属蛋白中独特的连接体-金属键作斗争.

研究的目的:

  • 引入一种新的知识驱动的对接方法,金属蛋白偏差对接 (MBD),以克服对接金属蛋白的局限性.
  • 为了评估MBD与传统对接 (CD) 的性能,以检测金属蛋白-连接体相互作用.

主要方法:

  • 汇集了15个金属蛋白家族 (Ca,Co,Fe,Mg,Mn,Zn) 的金属蛋白-连接体复合物的综合数据集.
  • 通过扩展AutoDock偏差技术开发了MBD.
  • 使用已建立的数据集,与AutoDock4 (CD) 进行MBD性能比较.

主要成果:

  • MBD在准确性,选择性和精确性方面显著超过CD,用于连接体姿势预测.
  • 在MBD预测的连接体自由能量和实验值之间观察到正相关性.
  • 在各种金属蛋白标上,MBD表现出卓越的性能.

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结论:

  • MBD是增强金属蛋白-连接体相互作用的探索的宝贵工具.
  • 开发的方法为金属蛋白药物发现的虚拟查提供了更高的准确性和效率.
  • MBD解决了涉及金属蛋白的计算研究中的关键挑战.