scholarly journals Correction for Deng et al., “Bcl2’s Flexible Loop Domain Regulates p53 Binding and Survival”

2020 ◽  
Vol 40 (21) ◽  
Author(s):  
Xingming Deng ◽  
Fengqin Gao ◽  
Tammy Flagg ◽  
Jessica Anderson ◽  
W. Stratford May
Keyword(s):  
Flexible Loop ◽  
Loop Domain

Expression and Solution NMR Study of Multi-site Phosphomimetic Mutant BCL-2 Protein

2019 ◽  
Vol 26 (6) ◽  
pp. 449-457
Author(s):  
Ting Song ◽  
Keke Cao ◽  
Yu dan Fan ◽  
Zhichao Zhang ◽  
Zong W. Guo ◽  
...  
Keyword(s):  
Structural Change ◽  
Structural Biology ◽  
Quantum Coherence ◽  
Structural Changes ◽  
Solution Nmr ◽  
Flexible Loop ◽  
Loop Region ◽  
Loop Domain ◽  
Nmr Study ◽  
Binding Groove

Background: The significance of multi-site phosphorylation of BCL-2 protein in the flexible loop domain remains controversial, in part due to the lack of structural biology studies of phosphorylated BCL-2. Objective: The purpose of the study is to explore the phosphorylation induced structural changes of BCL-2 protein. Methods: We constructed a phosphomietic mutant BCL-2(62-206) (t69e, s70e and s87e) (EEEBCL- 2-EK (62-206)), in which the BH4 domain and the part of loop region was truncated (residues 2-61) to enable a backbone resonance assignment. The phosphorylation-induced structural change was visualized by overlapping a well dispersed 15N-1H heteronuclear single quantum coherence (HSQC) NMR spectroscopy between EEE-BCL-2-EK (62-206) and BCL-2. Results: The EEE-BCL-2-EK (62-206) protein reproduced the biochemical and cellular activity of the native phosphorylated BCL-2 (pBCL-2), which was distinct from non-phosphorylated BCL-2 (npBCL-2) protein. Some residues in BH3 binding groove occurred chemical shift in the EEEBCL- 2-EK (62-206) spectrum, indicating that the phosphorylation in the loop region induces a structural change of active site. Conclusion: The phosphorylation of BCL-2 induced structural change in BH3 binding groove.

scholarly journals Anti-apoptotic BCL-2 regulation by changes in dynamics of its long unstructured loop

2020 ◽  
Vol 3 (1) ◽  
Author(s):  
Yu-Jing Lan ◽  
Pei-Shan Yeh ◽  
Te-Yu Kao ◽  
Yuan-Chao Lo ◽  
Shih-Che Sue ◽  
...  
Keyword(s):  
Selective Inhibitor ◽  
Structural Flexibility ◽  
Fluorescence Techniques ◽  
Flexible Loop ◽  
Protein Ligand Interactions ◽  
Loop Domain ◽  
Ligand Interactions ◽  
Binding Groove ◽  
Apoptotic Activity

AbstractBCL-2, a key protein in inhibiting apoptosis, has a 65-residue-long highly flexible loop domain (FLD) located on the opposite side of its ligand-binding groove. In vivo phosphorylation of the FLD enhances the affinity of BCL-2 for pro-apoptotic ligands, and consequently anti-apoptotic activity. However, it remains unknown as to how the faraway, unstructured FLD modulates the affinity. Here we investigate the protein-ligand interactions by fluorescence techniques and monitor protein dynamics by DEER and NMR spectroscopy tools. We show that phosphomimetic mutations on the FLD lead to a reduction in structural flexibility, hence promoting ligand access to the groove. The bound pro-apoptotic ligands can be displaced by the BCL-2-selective inhibitor ABT-199 efficiently, and thus released to trigger apoptosis. We show that changes in structural flexibility on an unstructured loop can activate an allosteric protein that is otherwise structurally inactive.

scholarly journals Bcl2's Flexible Loop Domain Regulates p53 Binding and Survival

2006 ◽  
Vol 26 (12) ◽  
pp. 4421-4434 ◽  
Author(s):  
Xingming Deng ◽  
Fengqin Gao ◽  
Tammy Flagg ◽  
Jessica Anderson ◽  
W. Stratford May
Keyword(s):  
Dna Damage ◽  
Apoptotic Cell ◽  
P53 Protein ◽  
Phosphorylation Site ◽  
Regulatory Region ◽  
Isolated Mitochondria ◽  
Flexible Loop ◽  
Loop Domain ◽  
Bh3 Domain

ABSTRACT p53 not only functions as a transcription factor but also has a direct, apoptogenic role at the mitochondria. We have discovered that DNA damage-induced p53-Bcl2 binding is associated with decreased Bcl2-Bax interaction and increased apoptotic cell death in a mechanism regulated by Bcl2's flexible loop regulatory domain (FLD), since purified p53 protein can disrupt the Bcl2/Bax complex by directly binding to a negative regulatory region of the FLD (amino acids [aa] 32 to 68). Deletion of the negative regulatory region (Δ32-68) abolishes Bcl2-p53 binding and enhances Bcl2's antiapoptotic function. Conversely, removal of a positive regulatory region (aa 69 to 87) of the FLD, which contains the Bcl2 phosphorylation site(s) T69, S70, and S87, enhances Bcl2-p53 binding and significantly abrogates Bcl2's survival activity. The phospho-mimetic T69E/S70E/S87E (EEE) but not the nonphosphorylatable T69A/S70A/S87A (AAA) Bcl2 mutant displays a reduced capacity to bind p53 and potently inhibits p53-induced cytochrome c release from isolated mitochondria. Furthermore, the FLD-only aa32-87 and aa32-68 peptides but not the aa69-87 peptide can directly bind p53 in vitro. p53-induced cytochrome c release occurs through a mechanism involving Bax's integral insertion into the outer mitochondrial membrane. Either DNA damage to cells or expression of p53 selectively targeted to the mitochondria results in Bcl2-p53 binding followed by exposure of Bcl2's BH3 domain in association with inactivation of Bcl2's antiapoptotic function, indicating a conformational change in Bcl2 can occur upon direct ligation of p53. Thus, Bcl2's FLD contains both positive and negative regulatory regions which functionally regulate Bcl2's antiapoptotic activity by affecting Bax or p53 binding.

scholarly journals Exploring the Conformational Space of Bcl-2 Protein Variants: Dynamic Contributions of the Flexible Loop Domain and Transmembrane Region

Molecules ◽  
2019 ◽  
Vol 24 (21) ◽  
pp. 3896
Author(s):  
Luis A. Caro-Gómez ◽  
Jorge L. Rosas-Trigueros ◽  
Edgar Mixcoha ◽  
José L. Vique-Sánchez ◽  
Humberto Gasperin-Sánchez ◽  
...  
Keyword(s):  
Transmembrane Domain ◽  
Conformational Space ◽  
Intrinsically Disordered ◽  
Flexible Loop ◽  
Loop Domain ◽  
The Family ◽  
Conformational Plasticity ◽  
Dynamics Simulations ◽  
The Individual ◽  
Structural Mechanisms

Members of the Bcl-2 protein family regulate apoptosis through interactions with several proteins. A critical intrinsically disordered region (IDR) present in some members of the Bcl-2 family is essential for their function. Also, the structural and conformational plasticity of disordered regions is essential for the regulation of the Bcl-2 protein’s activity. Further, some proteins of the family contain transmembrane-helical regions, which anchor them into organelle membranes. Bcl-2, the archetypical member of the family, is characterized by an IDR labeled as a flexible loop domain (FLD) and a transmembrane domain (TMD). Another member of this family is the Bcl-2A1 protein, containing a TMD but lacking the FLD. To our knowledge, this is the first report which characterizes the individual and simultaneous dynamical contributions of FLD and TMD in Bcl-2 and Bcl-2A1 using molecular dynamics simulations (MDS). We examined the conformational spaces of Bcl-2, Bcl-2A1, and two artificial constructs lacking the TMD (Bcl-2ΔTM and Bcl-2A1ΔTM). As the results show, FLD and TMD stabilized each protein independently when they are present. When they coincided, such as in Bcl-2, an additive stabilizing effect is observed. This information is crucial for understanding the structural mechanisms of interaction in the Bcl-2 family.

Mapping the intrinsically disordered properties of the flexible loop domain of Bcl-2: a molecular dynamics simulation study

2016 ◽  
Vol 22 (4) ◽  
Author(s):  
Ian Ilizaliturri-Flores ◽  
José Correa-Basurto ◽  
Martiniano Bello ◽  
Jorge L. Rosas-Trigueros ◽  
Beatriz Zamora-López ◽  
...  
Keyword(s):  
Molecular Dynamics ◽  
Molecular Dynamics Simulation ◽  
Simulation Study ◽  
Dynamics Simulation ◽  
Intrinsically Disordered ◽  
Flexible Loop ◽  
Loop Domain

The crystal structure of human mitochondrial 3-ketoacyl-CoA thiolase (T1): insight into the reaction mechanism of its thiolase and thioesterase activities

2014 ◽  
Vol 70 (12) ◽  
pp. 3212-3225 ◽  
Author(s):  
Tiila-Riikka Kiema ◽  
Rajesh K. Harijan ◽  
Malgorzata Strozyk ◽  
Toshiyuki Fukao ◽  
Stefan E. H. Alexson ◽  
...  
Keyword(s):  
Crystal Structure ◽  
Reaction Mechanism ◽  
Active Site ◽  
Quaternary Structure ◽  
Fatty Acyl ◽  
Physiological Importance ◽  
Loop Domain ◽  
Solution Studies ◽  
Hydrolysis Of ◽  
Insight Into

Crystal structures of human mitochondrial 3-ketoacyl-CoA thiolase (hT1) in the apo form and in complex with CoA have been determined at 2.0 Å resolution. The structures confirm the tetrameric quaternary structure of this degradative thiolase. The active site is surprisingly similar to the active site of theZoogloea ramigerabiosynthetic tetrameric thiolase (PDB entries 1dm3 and 1m1o) and different from the active site of the peroxisomal dimeric degradative thiolase (PDB entries 1afw and 2iik). A cavity analysis suggests a mode of binding for the fatty-acyl tail in a tunnel lined by the Nβ2–Nα2 loop of the adjacent subunit and the Lα1 helix of the loop domain. Soaking of the apo hT1 crystals with octanoyl-CoA resulted in a crystal structure in complex with CoA owing to the intrinsic acyl-CoA thioesterase activity of hT1. Solution studies confirm that hT1 has low acyl-CoA thioesterase activity for fatty acyl-CoA substrates. The fastest rate is observed for the hydrolysis of butyryl-CoA. It is also shown that T1 has significant biosynthetic thiolase activity, which is predicted to be of physiological importance.

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