Comprehensive experimental and computational analysis of binding energy hot spots at the NF-κB essential modulator/IKKβ protein-protein interface.
Comprehensive experimental and computational analysis of binding energy hot spots at the NF-κB essential modulator/IKKβ protein-protein interface.
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DOI：
10.1021/ja400914z
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发表时间：
2013-04-24
影响因子：
15
通讯作者：
Whitty, Adrian
中科院分区：
文献类型：
--
作者：
Golden, Mary S.;Cote, Shaun M.;Sayeg, Marianna;Zerbe, Brandon S.;Villar, Elizabeth A.;Beglov, Dmitri;Sazinsky, Stephen L.;Georgiadis, Rosina M.;Vajda, Sandor;Kozakov, Dima;Whitty, Adrian
我们报告了一个全面的分析结合能热点之间的蛋白质-蛋白质相互作用（PPI）的接口NF-κB必需调节剂（NEMO）和IκB激酶β亚基（IKKβ），一个相互作用是关键的NF-κB途径信号，使用实验丙氨酸扫描诱变和FTMap方法的计算片段筛选。实验结果证实，先前鉴定的IKKβ NBD区域含有最高浓度的热点残基，其中最强的是W739、W741和L742（ΔΔG分别= 4.3、3.5和3.2 kcal/mol）。这些残基所占据的区域定义了NEMO上的潜在药物结合位点，其延伸约16 bp，以额外包括结合IKKβ L737和F734的区域。NBD残基D 738和S740对于结合也是重要的，但不与NEMO直接接触，而是可能起到稳定周围残基的活性构象的作用。我们还发现了两个以前未知的热点区域，集中在IKKβ残基L708/V709和L719/I723。计算方法成功地识别了IKKβ上的所有三个热点区域。此外，该方法能够准确地量化涉及直接接触NEMO的所有热点残留物的能量重要性。我们的研究结果提供了新的信息，以指导发现的小分子抑制剂，针对NEMO/IKKβ的相互作用。他们还澄清了“口袋形成”和“口袋占据”热点残基之间的结构和能量互补性，并进一步验证了计算片段映射作为识别PPI界面热点的方法。
We report a comprehensive analysis of binding energy hot spots at the protein-protein interaction (PPI) interface between NF-κB Essential Modulator (NEMO) and IκB kinase subunit β (IKKβ), an interaction that is critical for NF-κB pathway signaling, using experimental alanine scanning mutagenesis and also the FTMap method for computational fragment screening. The experimental results confirm that the previously identified NBD region of IKKβ contains the highest concentration of hot spot residues, the strongest of which are W739, W741 and L742 (ΔΔG = 4.3, 3.5 and 3.2 kcal/mol, respectively). The region occupied by these residues defines a potentially druggable binding site on NEMO that extends for ~16 Å to additionally include the regions that bind IKKβ L737 and F734. NBD residues D738 and S740 are also important for binding but do not make direct contact with NEMO, instead likely acting to stabilize the active conformation of surrounding residues. We additionally found two previously unknown hot spot regions centered on IKKβ residues L708/V709 and L719/I723. The computational approach successfully identified all three hot spot regions on IKKβ. Moreover, the method was able to accurately quantify the energetic importance of all hot spots residues involving direct contact with NEMO. Our results provide new information to guide the discovery of small molecule inhibitors that target the NEMO/IKKβ interaction. They additionally clarify the structural and energetic complementarity between “pocket-forming” and “pocket occupying” hot spot residues, and further validate computational fragment mapping as a method for identifying hot spots at PPI interfaces.
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DOI：
10.1074/jbc.m109.099895
发表时间：
2010-04-30
期刊：
The Journal of biological chemistry
影响因子：
--
作者：
Baima ET;Guzova JA;Mathialagan S;Nagiec EE;Hardy MM;Song LR;Bonar SL;Weinberg RA;Selness SR;Woodard SS;Chrencik J;Hood WF;Schindler JF;Kishore N;Mbalaviele G
通讯作者：
Mbalaviele G
DOI：
10.1073/pnas.062398499
发表时间：
2002-04-02
影响因子：
11.1
作者：
Dennis, S;Kortvelyesi, T;Vajda, S
通讯作者：
Vajda, S
影响因子：
14.9
作者：
Flicek P;Ahmed I;Amode MR;Barrell D;Beal K;Brent S;Carvalho-Silva D;Clapham P;Coates G;Fairley S;Fitzgerald S;Gil L;García-Girón C;Gordon L;Hourlier T;Hunt S;Juettemann T;Kähäri AK;Keenan S;Komorowska M;Kulesha E;Longden I;Maurel T;McLaren WM;Muffato M;Nag R;Overduin B;Pignatelli M;Pritchard B;Pritchard E;Riat HS;Ritchie GR;Ruffier M;Schuster M;Sheppard D;Sobral D;Taylor K;Thormann A;Trevanion S;White S;Wilder SP;Aken BL;Birney E;Cunningham F;Dunham I;Harrow J;Herrero J;Hubbard TJ;Johnson N;Kinsella R;Parker A;Spudich G;Yates A;Zadissa A;Searle SM
通讯作者：
Searle SM
影响因子：
7.3
作者：
de Kloe, Gerdien E.;Retra, Kim;de Esch, Iwan J. P.
通讯作者：
de Esch, Iwan J. P.
影响因子：
5.6
作者：
Clackson, T;Ultsch, MH;de Vos, AM
通讯作者：
de Vos, AM