サイクロチドにおける分子内二硫化物ペアリングのマルコヴィア時間スケール
Jayapriya Venkatesan1, Durba Roy1
1Department of Chemistry, Birla Institute of Technology and Science, Pilani, Hyderabad Campus, Hyderabad, India.
Proteins
|August 28, 2025
まとめ
この研究は,植物毒素であるサイクロビオラシンO1 (CyO1) の折り畳み動態をモデル化しています. 隠されたマルコフモデルは,固有のペプチド構造の達成に不可欠な,素早い分子内二酸化炭素結合の形成を明らかにする.
科学分野:
- バイオ物理学
- コンピュータ化学
- 分子生物学
背景:
- タンパク質とペプチドの構造と機能には,分子内二硫化結合の形成が不可欠である.
- サイクロヴィオラシンO1 (CyO1) は,サイクルシスティンノード (CCK) を特徴とする複雑なサイクル構造を持つ植物毒素である.
- CyO1における二硫化物ペアリングの動態を理解すると,タンパク質の折り畳みメカニズムに関する洞察が得られる.
研究 の 目的:
- CyO1における分子内二硫化物ペアリングの動態を調査する.
- 縮小状態 (ペプチド-D) から原生状態 (ペプチド-N) への折り畳み経路の運動モデルを開発する.
- ディスルファイド結合形成の時間スケールと最も可能性のある経路を決定する.
主な方法:
- 隠されたマルコフモデル (HMM) を構築するために分子ダイナミクス (MD) シミュレーション軌道を利用しました.
- 構造的進化と二硫化物のペアリング傾向を追跡するためにマルコフ連鎖分析を使用した.
- 最も可能性のある折り畳み経路を特定するために,適用されたレートネットワークと移行経路理論.
主要な成果:
- HMMは,CyO1の進化を,その縮小された形態から原生のような状態へと成功的にモデル化しました.
- CyO1における二硫化物結合の形成は,計算された速度の定数で約10^6s^1であることが判明した.
- 1つ,2つまたは3つの二硫化物ペアの形成を制御する主要な中間物質と経路を特定した.
結論:
- この研究は,CyO1の折り畳みの詳細な運動モデルを提供し,分子内二硫化物ペアリングの速度を強調しています.
- この発見は,他の二硫化物を含むタンパク質における実験的観測と一致する.
- 開発されたモデルと分析方法は,他の複雑なペプチドにおける二硫化結合形成を研究するための枠組みを提供します.
関連する概念動画
Preparation and Reactions of Sulfides
5.1K
Sulfides are the sulfur analog of ethers, just as thiols are the sulfur analog of alcohol. Like ethers, sulfides also consist of two hydrocarbon groups bonded to the central sulfur atom. Depending upon the type of groups present, sulfides can be symmetrical or asymmetrical. Symmetrical sulfides can be prepared via an SN2 reaction between 2 equivalents of an alkyl halide and one equivalent of sodium sulfide.
5.1K
Spin–Spin Coupling: Three-Bond Coupling (Vicinal Coupling)
1.1K
Vicinal or three-bond coupling is commonly observed between protons attached to adjacent carbons. Here, nuclear spin information is primarily transferred via electron spin interactions between adjacent C‑H bond orbitals. This generally favors the antiparallel arrangement of spins, so 3J values are usually positive.
The extent of coupling depends on the C‑C bond length, the two H‑C‑C angles, any electron-withdrawing substituents, and the dihedral angle between the...
The extent of coupling depends on the C‑C bond length, the two H‑C‑C angles, any electron-withdrawing substituents, and the dihedral angle between the...
1.1K
Thermal Sigmatropic Reactions: Overview
2.1K
Sigmatropic rearrangements are a class of pericyclic reactions in which a σ bond migrates from one part of a π system to another. These are intramolecular rearrangements where the total number of σ and π bonds remain unchanged.
Sigmatropic shifts are classified based on an order term [i, j ], where i and j indicate the number of atoms across which each end of the σ bond migrates. Below are examples of a [3,3] sigmatropic shift in...
Sigmatropic shifts are classified based on an order term [i, j ], where i and j indicate the number of atoms across which each end of the σ bond migrates. Below are examples of a [3,3] sigmatropic shift in...
2.1K
Woodward–Hoffmann Selection Rules and Microscopic Reversibility
3.3K
Electrocyclic reactions, cycloadditions, and sigmatropic rearrangements are concerted pericyclic reactions that proceed via a cyclic transition state. These reactions are stereospecific and regioselective. The stereochemistry of the products depends on the symmetry characteristics of the interacting orbitals and the reaction conditions. Accordingly, pericyclic reactions are classified as either symmetry-allowed or symmetry-forbidden. Woodward and Hoffmann presented the selection criteria for...
3.3K
Stability of Substituted Cyclohexanes
13.0K
This lesson discusses the stability of substituted cyclohexanes with a focus on energies of various conformers and the effect of 1,3-diaxial interactions.
The two chair conformations of cyclohexanes undergo rapid interconversion at room temperature. Both forms have identical energies and stabilities, each comprising equal amounts of the equilibrium mixture. Replacing a hydrogen atom with a functional group makes the two conformations energetically non-equivalent.
For example, in...
The two chair conformations of cyclohexanes undergo rapid interconversion at room temperature. Both forms have identical energies and stabilities, each comprising equal amounts of the equilibrium mixture. Replacing a hydrogen atom with a functional group makes the two conformations energetically non-equivalent.
For example, in...
13.0K
Meiosis II
46.3K
Meiosis II entails cell division and segregation of the sister chromatids, resulting in the production of four unique haploid gametes. The steps for meiosis II are similar to mitosis, except that meiosis II occurs in haploid cells, whereas mitosis occurs in diploid cells.
The timing and cell division patterns of meiosis differ between males and females. In male meiosis, the centrosomes are part of the formation of the meiotic spindle. However, in oocytes, including that of humans, Drosophila,...
The timing and cell division patterns of meiosis differ between males and females. In male meiosis, the centrosomes are part of the formation of the meiotic spindle. However, in oocytes, including that of humans, Drosophila,...
46.3K


