Molecular modeling of c-erbB2 receptor dimerization: Coiled-coil structure of wild and oncogenic transmembrane domains—Stabilization by interhelical hydrogen bonds in the oncogenic form

Biopolymers ◽  
1997 ◽  
Vol 42 (2) ◽  
pp. 157-168 ◽  
Author(s):  
Norbert Garnier ◽  
Daniel Genest ◽  
Jean Pierre Duneau ◽  
Monique Genest
Keyword(s):  
Molecular Modeling ◽  
Hydrogen Bonds ◽  
Coiled Coil ◽  
Transmembrane Domains ◽  
Receptor Dimerization ◽  
Coil Structure ◽  
Erbb2 Receptor ◽  
Oncogenic Form

TMCC3 localizes at the three-way junctions for the proper tubular network of the endoplasmic reticulum

2019 ◽  
Vol 476 (21) ◽  
pp. 3241-3260
Author(s):  
Sindhu Wisesa ◽  
Yasunori Yamamoto ◽  
Toshiaki Sakisaka
Keyword(s):  
Endoplasmic Reticulum ◽  
Membrane Proteins ◽  
Membrane Protein ◽  
Mammalian Cells ◽  
Coiled Coil ◽  
Transmembrane Domains ◽  
Domain Family ◽  
Coiled Coil Domain ◽  
U2os Cells ◽  
Er Membrane

The tubular network of the endoplasmic reticulum (ER) is formed by connecting ER tubules through three-way junctions. Two classes of the conserved ER membrane proteins, atlastins and lunapark, have been shown to reside at the three-way junctions so far and be involved in the generation and stabilization of the three-way junctions. In this study, we report TMCC3 (transmembrane and coiled-coil domain family 3), a member of the TEX28 family, as another ER membrane protein that resides at the three-way junctions in mammalian cells. When the TEX28 family members were transfected into U2OS cells, TMCC3 specifically localized at the three-way junctions in the peripheral ER. TMCC3 bound to atlastins through the C-terminal transmembrane domains. A TMCC3 mutant lacking the N-terminal coiled-coil domain abolished localization to the three-way junctions, suggesting that TMCC3 localized independently of binding to atlastins. TMCC3 knockdown caused a decrease in the number of three-way junctions and expansion of ER sheets, leading to a reduction of the tubular ER network in U2OS cells. The TMCC3 knockdown phenotype was partially rescued by the overexpression of atlastin-2, suggesting that TMCC3 knockdown would decrease the activity of atlastins. These results indicate that TMCC3 localizes at the three-way junctions for the proper tubular ER network.

The Difference of Serum Protein Transport between Echinosides and Verbascoside

2020 ◽  
Vol 42 (3) ◽  
pp. 369-369
Author(s):  
Ming Guo Ming Guo ◽  
Xiaoxue Zhao Xiaoxue Zhao ◽  
Peter E Brodelius Peter E Brodelius ◽  
Ling Fang Ling Fang ◽  
Zhihong Sun and Rui Wang Zhihong Sun and Rui Wang
Keyword(s):  
Molecular Modeling ◽  
Hydrogen Bonds ◽  
Serum Albumin ◽  
Protein Transport ◽  
Van Der Waals ◽  
Hydrolysis Product ◽  
Van Der Waals Forces ◽  
Molecular Structures ◽  
Hydrophobic Force ◽  
Binding Characteristics

Verbascoside (VER) is the enzymatic hydrolysis product of echinacoside (ECH). The molecular structures of ECH and VER have different glucosyl groups so they bind to serum albumin in different ways, resulting in different pharmacological actions. In this report, we have examined the binding characteristics between human serum albumin (HSA) and ECH/VER by molecular modeling and spectroscopic approaches. Molecular modeling revealed that VER bound to HSA mainly through hydrogen bonds, van der Waals forces and hydrophobic forces. The spectroscopic results showed that the interactions between HSA and VER/ECH involved a static binding process, and the bonding strength of the VER-HSA complex was stronger than that of the ECH-HSA complex. The value of the binding distances (r) was low, which indicated the occurrence of energy transfer. The reaction conformational pattern of HSA-VER and HSA-ECH gave a “two-state model” based on fluorescent phase diagram analysis. According to the thermodynamic model, the main forces between interaction of VER and HSA were hydrogen bonds and van der Waals forces, whereas the interaction between ECH and HSA was hydrophobic force. The fluorescence polarization analysis demonstrated that the interaction between HSA and VER or ECH generated a non-covalent complex. Compared with ECH, VER was more likely to bind with HSA because of its smaller molecular size and low polarity. The results of the spectral analysis concurred with the molecular modeling data, which provides a helpful reference for the study of the molecular reaction mechanism of VER/ECH binding to HSA.

Characterization of a coiled coil protein present in the basal body of Trypanosoma brucei

1999 ◽  
Vol 112 (24) ◽  
pp. 4687-4694 ◽  
Author(s):  
V. Dilbeck ◽  
M. Berberof ◽  
A. Van Cauwenberge ◽  
H. Alexandre ◽  
E. Pays
Keyword(s):  
Trypanosoma Brucei ◽  
Basal Body ◽  
Coiled Coil ◽  
Western Blots ◽  
Cell Extracts ◽  
Acid Protein ◽  
Coil Structure ◽  
Tubulin Antibodies ◽  
Body Component ◽  
Gamma Tubulin

TBBC (for Trypanosoma brucei basal body component) is a unique gene transcribed in a 4.8 kb mRNA encoding a 1,410 amino acid protein that consists almost entirely of a coiled coil structure. This protein appeared to localize in the basal body, with an accessory presence at the posterior end of the cell, the nucleus and over the flagellum. Since the two other known components of the trypanosome basal body are (gamma)-tubulin and an uncharacterized component termed BBA4 we performed double immunofluorescence experiments with anti-TBBC and either anti-BBA4 or anti-(gamma)-tubulin antibodies. These three components did not colocalize but were very closely associated, BBA4 being the most proximal to the kinetoplast DNA. Anti-TBBC antibodies detected a 170 kDa protein in western blots of total HeLa cell extracts. Moreover, these antibodies stained the centriole of HeLa and COS cells as well as the centriole of mouse spermatozoa, indicating that a TBBC-like centriolar component has been conserved during the evolution of eukaryotes.

scholarly journals Antigenic domains of the streptococcal Pep M5 protein. Localization of epitopes crossreactive with type 6 M protein and identification of a hypervariable region of the M molecule.

1986 ◽  
Vol 163 (1) ◽  
pp. 129-138 ◽  
Author(s):  
B N Manjula ◽  
A S Acharya ◽  
T Fairwell ◽  
V A Fischetti
Keyword(s):  
Protein Localization ◽  
Hypervariable Region ◽  
Coiled Coil ◽  
M Protein ◽  
Terminal Domain ◽  
Coil Structure ◽  
M Proteins ◽  
Group A ◽  
Antigenic Domains ◽  
Antigenic Epitopes

Pep M5, the pepsin-derived N-terminal half of the group A streptococcal type 5 M protein exhibits immunologic crossreaction with type 6 M protein, localizing some of the M6-crossreactive epitope(s) within this segment of the M5 protein. Based on the amino acid sequence of the Pep M5 protein, two structurally distinct domains have been recognized within its coiled-coil structure. We have now found that peptides derived from both the structurally distinct domains of the Pep M5 protein contain antigenic epitopes. Furthermore, only the peptides from the C-terminal domain of the Pep M5 protein crossreacted with rabbit anti-M6 sera, whereas those from the N-terminal domain did not. Consistent with this, sequence analyses of the arginyl peptides of the Pep M6 protein, the pepsin-derived N-terminal half of the M6 protein, revealed extensive homology of some of these peptides with regions within the C-terminal domain of the Pep M5 molecule. While an arginyl peptide of the Pep M6 protein exhibits 84% homology with region 150-186 of the Pep M5 protein, the C-terminal hexadecapeptide of the Pep M6 protein is virtually identical with the corresponding region of the Pep M5 protein. These results are suggestive of conformational similarities in the region around the pepsin-susceptible site within the M5 and M6 proteins. In addition, one or more epitopes of the M5 protein that are crossreactive with the M6 protein may be placed close to the pepsin-susceptible site of the M5 protein. Previous studies have suggested the N-terminal half of the M proteins to be the variable part of the molecule among the different M protein serotypes. The present results suggest that the N-terminal quarter of the M protein may represent the hypervariable domain of the M molecule.

scholarly journals Anti-S2 Peptides Modulate Myosin Coiled Coil Structure and Shift Force-PCa Curves in Human Cardiac Muscle

2019 ◽  
Vol 116 (3) ◽  
pp. 263a
Author(s):  
Bertrand C.W. Tanner ◽  
Kenneth S. Campbell ◽  
Motamed Qadan ◽  
Negar Aboonasrshiraz ◽  
Dua'a Quedan ◽  
...  
Keyword(s):  
Cardiac Muscle ◽  
Coiled Coil ◽  
Coil Structure

Structure Prediction and Nanomechanical Properties of Human Vimentin Intermediate Filament Dimers

2009 ◽  
Author(s):  
Markus J. Buehler ◽  
Zhao Qin
Keyword(s):  
Structure Prediction ◽  
Molecular Model ◽  
Experimental Studies ◽  
Coiled Coil ◽  
Beta Sheets ◽  
Dynamics Simulation ◽  
Nanomechanical Properties ◽  
Coil Structure ◽  
Equilibration Process ◽  
Vimentin Intermediate Filament

Intermediate filaments (IFs), in addition to microtubules (MTs) and microfilaments (MFs), are one of the three major components of the cytoskeleton in eukaryotic cells. As the basic building block of IFs, the properties of the IF dimmer re crucial to fully understand the molecular basis for the properties of the IF network in cells. However, the structure of IF dimers remains unknown, which has thus far prevented the elucidation of its nanomechanical properties, in particular molecular-level mechanisms of deformation. Here we present the development of a full atomistic molecular model of the vimentin dimmer, a coiled-coil structure consisting of four alpha-helixes (AHs). The structure is found to be stable in molecular dynamics simulation after an extensive equilibration process. After careful structure prediction, the behavior of the IF dimer under mechanical stress is investigated; including studies of changing the pulling velocity and a detailed analysis of the associated deformation and rupture mechanisms. Most notably, we observe a transition of AHs to beta-sheets (BSs) under mechanical deformation, as has been observed indirectly in earlier experimental studies. Our result helps to better understand the structure and fracture mechanism of this important protein filament.

Sign in / Sign up

Export Citation Format

Share Document