Structure and dynamics of UBA5-UFM1 complex formation showing new insights in the UBA5 activation mechanism

2021 ◽  
Vol 213 (4) ◽  
pp. 107796
Author(s):  
Sebastian Fuchs ◽  
Alexey G. Kikhney ◽  
Robin Schubert ◽  
Charlotte Kaiser ◽  
Eva Liebau ◽  
...  
Keyword(s):  
Complex Formation ◽  
Activation Mechanism ◽  
Structure And Dynamics

Effect of particle polydispersity on the structure and dynamics of complex formation between small particles and large polymer

RSC Advances ◽  
2014 ◽  
Vol 4 (29) ◽  
pp. 14896 ◽  
Author(s):  
Lei Ye ◽  
Xiao Chu ◽  
Zhengdong Zhang ◽  
Ying Kan ◽  
Yue Xie ◽  
...  
Keyword(s):  
Complex Formation ◽  
Small Particles ◽  
Structure And Dynamics ◽  
Particle Polydispersity

scholarly journals Characterizing the structural ensemble of γ-secretase using a multiscale molecular dynamics approach

2017 ◽  
Vol 8 (8) ◽  
pp. 5576-5584 ◽  
Author(s):  
Rodrigo Aguayo-Ortiz ◽  
Cecilia Chávez-García ◽  
John E. Straub ◽  
Laura Dominguez
Keyword(s):  
Molecular Dynamics ◽  
Multiscale Modeling ◽  
Activation Mechanism ◽  
Structure And Dynamics ◽  
Modeling Approach ◽  
Structural Ensemble

Employing a multiscale modeling approach, we characterized the structure and dynamics of the γ-secretase complex to elucidate its activation mechanism.

scholarly journals Hydroxyl radical footprinting analysis of a human haptoglobin-hemoglobin complex

2021 ◽  
Author(s):  
Dmitry S Loginov ◽  
Jan Fiala ◽  
Peter Brechlin ◽  
Gary Kruppa ◽  
Petr Novak
Keyword(s):  
Mass Spectrometry ◽  
Complex Formation ◽  
Photochemical Oxidation ◽  
Structure And Dynamics ◽  
Interaction Interface ◽  
Structural Mass Spectrometry ◽  
Hydroxyl Radical Footprinting ◽  
Structural Mass ◽  
Protein Structure And Dynamics

Methods of structural mass spectrometry have become more popular to study protein structure and dynamics. Among them, fast photochemical oxidation of proteins (FPOP) has several advantages such as irreversibility of modifications and more facile determination of the site of modification with single residue resolution. In the present study, FPOP analysis was applied to study the hemoglobin (Hb) – haptoglobin (Hp) complex allowing identification of respective regions altered upon the complex formation. Oxidative modifications were precisely localized on specific residues using a timsTOF Pro mass spectrometer. The data allowed determination of amino acids directly involved in Hb – Hp interactions and those located outside of the interaction interface yet affected by the complex formation. Data are available via ProteomeXchange with identifier PXD021621.

scholarly journals Attempts to characterize the NBD heterodimer of MRP1: transient complex formation involves Gly771 of the ABC signature sequence but does not enhance the intrinsic ATPase activity

2005 ◽  
Vol 391 (3) ◽  
pp. 481-490 ◽  
Author(s):  
Odile Ramaen ◽  
Christina Sizun ◽  
Olivier Pamlard ◽  
Eric Jacquet ◽  
Jean-Yves Lallemand
Keyword(s):  
Complex Formation ◽  
Atpase Activity ◽  
Atp Hydrolysis ◽  
Chemotherapeutic Agents ◽  
Activation Mechanism ◽  
Hydrolysis Rate ◽  
Sequential Assignment ◽  
Atp Binding ◽  
Native Page ◽  
Transient Complex

MRP1 (multidrug-resistance-associated protein 1; also known as ABCC1) is a member of the human ABC (ATP-binding cassette) transporter superfamily that confers cell resistance to chemotherapeutic agents. Considering the structural and functional similarities to the other ABC proteins, the interaction between its two NBDs (nucleotide-binding domains), NBD1 (N-terminal NBD) and NBD2 (C-terminal NBD), is proposed to be essential for the regulation of the ATP-binding/ATP-hydrolysis cycle of MRP1. We were interested in the ability of recombinant NBD1 and NBD2 to interact with each other and to influence ATPase activity. We purified NBD1 (Asn642–Ser871) and NBD2 (Ser1286–Val1531) as soluble monomers under native conditions. We measured extremely low intrinsic ATPase activity of NBD1 (10−5 s−1) and NBD2 (6×10−6 s−1) and no increase in the ATP-hydrolysis rate could be detected in an NBD1+NBD2 mixture, with concentrations up to 200 μM. Despite the fact that both monomers bind ATP, no stable NBD1·NBD2 heterodimer could be isolated by gel-filtration chromatography or native-PAGE, but we observed some significant modifications of the heteronuclear single-quantum correlation NMR spectrum of 15N-NBD1 in the presence of NBD2. This apparent NBD1·NBD2 interaction only occurred in the presence of Mg2+ and ATP. Partial sequential assignment of the NBD1 backbone resonances shows that residue Gly771 of the LSGGQ sequence is involved in NBD1·NBD2 complex formation. This is the first NMR observation of a direct interaction between the ABC signature and the opposite NBD. Our study also reveals that the NBD1·NBD2 heterodimer of MRP1 is a transient complex. This labile interaction is not sufficient to induce an ATPase co-operativity of the NBDs and suggests that other structures are required for the ATPase activation mechanism.

Structure and Dynamics of the Polyelectrolyte Complex Formation†

1997 ◽  
Vol 30 (17) ◽  
pp. 4897-4904 ◽  
Author(s):  
Natalia V. Pogodina ◽  
Nickolay V. Tsvetkov
Keyword(s):  
Complex Formation ◽  
Polyelectrolyte Complex ◽  
Structure And Dynamics

The fibrinolytic activation mechanism in human plasma

1969 ◽  
Vol 173 (1032) ◽  
pp. 293-309 ◽  
Keyword(s):  
Enzyme Activity ◽  
Complex Formation ◽  
Human Plasma ◽  
Molecular Size ◽  
Aminocaproic Acid ◽  
Fibrinolytic Enzyme ◽  
Activation Mechanism ◽  
Dependent Inhibition ◽  
Proteolytic Action ◽  
Molecular Aspects

Some recent advances are presented with special reference to molecular aspects. Emphasis is given to the formation of certain inhibitor complexes involving the human α 2 -macroglobulin. As shown with streptokinase-activated human plasma (Hamberg 1966 a , b ; Hamberg & Savolainen 1967, 1968) an association with proteins occurs, which lacks the proteolytic action on fibrin while retaining esterase and plasminogen activator activity. The complex formation is further stressed by a correlation to molecular size found with various inhibitors demonstrated below, and the concentration-dependent inhibition with ε -aminocaproic acid. The significance of these effects produced by steric hindrance for the interpretations of fibrinolytic enzyme activity and the proactivator reaction are discussed.

scholarly journals Tyrosine phosphorylation–dependent activation of TRPC6 regulated by PLC-γ1 and nephrin: effect of mutations associated with focal segmental glomerulosclerosis

2011 ◽  
Vol 22 (11) ◽  
pp. 1824-1835 ◽  
Author(s):  
Shoichiro Kanda ◽  
Yutaka Harita ◽  
Yoshio Shibagaki ◽  
Takashi Sekine ◽  
Takashi Igarashi ◽  
...  
Keyword(s):  
Complex Formation ◽  
Tyrosine Phosphorylation ◽  
Focal Segmental Glomerulosclerosis ◽  
Transient Receptor Potential ◽  
Receptor Potential ◽  
Surface Expression ◽  
Activation Mechanism ◽  
Channel Activity ◽  
Segmental Glomerulosclerosis ◽  
Specific Regulation

Transient receptor potential canonicals (TRPCs) play important roles in the regulation of intracellular calcium concentration. Mutations in the TRPC6 gene are found in patients with focal segmental glomerulosclerosis (FSGS), a proteinuric disease characterized by dysregulated function of renal glomerular epithelial cells (podocytes). There is as yet no clear picture for the activation mechanism of TRPC6 at the molecular basis, however, and the association between its channel activity and pathogenesis remains unclear. We demonstrate here that tyrosine phosphorylation of TRPC6 induces a complex formation with phospholipase C (PLC)-γ1, which is prerequisite for TRPC6 surface expression. Furthermore, nephrin, an adhesion protein between the foot processes of podocytes, binds to phosphorylated TRPC6 via its cytoplasmic domain, competitively inhibiting TRPC6–PLC-γ1 complex formation, TRPC6 surface localization, and TRPC6 activation. Importantly, FSGS-associated mutations render the mutated TRPC6s insensitive to nephrin suppression, thereby promoting their surface expression and channel activation. These results delineate the mechanism of TRPC6 activation regulated by tyrosine phosphorylation, and imply the cell type–specific regulation, which correlates the FSGS mutations with deregulated TRPC6 channel activity.

Nucleosome dynamics

2006 ◽  
Vol 73 ◽  
pp. 109-119 ◽  
Author(s):  
Chris Stockdale ◽  
Michael Bruno ◽  
Helder Ferreira ◽  
Elisa Garcia-Wilson ◽  
Nicola Wiechens ◽  
...  
Keyword(s):  
High Resolution ◽  
Chromatin Structure ◽  
Current Knowledge ◽  
Dynamic Properties ◽  
Structure And Dynamics ◽  
Nucleosome Dynamics ◽  
Sharp Focus ◽  
Recent Advances ◽  
Insight Into ◽  
Chromatin Structure And Dynamics

In the 30 years since the discovery of the nucleosome, our picture of it has come into sharp focus. The recent high-resolution structures have provided a wealth of insight into the function of the nucleosome, but they are inherently static. Our current knowledge of how nucleosomes can be reconfigured dynamically is at a much earlier stage. Here, recent advances in the understanding of chromatin structure and dynamics are highlighted. The ways in which different modes of nucleosome reconfiguration are likely to influence each other are discussed, and some of the factors likely to regulate the dynamic properties of nucleosomes are considered.

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