Folding Pathway Mediated by an Intramolecular Chaperone: Dissecting Conformational Changes Coincident with Autoprocessing and the Role of Ca2+ in Subtilisin Maturation

Spectrin is a membrane associated protein most of which properties have been tentatively elucidated. A main role of the protein has been assumed to give a supporting structure to inside of the membrane. As reported previously, however, the isolated spectrin molecule underwent self assemble to form such as fibrous, meshwork, dispersed or aggregated arrangements depending upon the buffer suspended and was suggested to play an active role in the membrane conformational changes. In this study, the role of spectrin and actin was examined in terms of the molecular arrangements on the erythrocyte membrane surface with correlation to the functional states of the ghosts.Human erythrocyte ghosts were prepared from either freshly drawn or stocked bank blood by the method of Dodge et al with a slight modification as described before. Anti-spectrin antibody was raised against rabbit by injection of purified spectrin and partially purified.

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Role of conformational heterogeneity in ligand recognition by viral RNA molecules

Physical Chemistry Chemical Physics ◽

10.1039/d1cp00679g ◽

2021 ◽

Author(s):

Lev Levintov ◽

Harish Vashisth

Keyword(s):

Conformational Changes ◽

Ribonucleic Acid ◽

Viral Rna ◽

Ligand Recognition ◽

Conformational Heterogeneity ◽

Rna Molecules ◽

Environmental Stimuli

Ribonucleic acid (RNA) molecules are known to undergo conformational changes in response to various environmental stimuli including temperature, pH, and ligands. In particular, viral RNA molecules are a key example...

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Conformational Changes of Yeast Plasma Membrane H+-ATPase during Activation by Glucose: Role of Threonine-912 in the Carboxy-Terminal Tail†

Biochemistry ◽

10.1021/bi051555f ◽

2005 ◽

Vol 44 (50) ◽

pp. 16624-16632 ◽

Cited By ~ 40

Author(s):

Silvia Lecchi ◽

Kenneth E. Allen ◽

Juan Pablo Pardo ◽

A. Brett Mason ◽

Carolyn W. Slayman

Keyword(s):

Plasma Membrane ◽

Conformational Changes ◽

Yeast Plasma Membrane ◽

Carboxy Terminal

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The Functional Role of the Conformational Changes in Arrestin Upon Activation

The Structural Basis of Arrestin Functions ◽

10.1007/978-3-319-57553-7_16 ◽

2017 ◽

pp. 219-234

Author(s):

Zhao Yang ◽

Fan Yang ◽

Anthony Nguen ◽

Chuan Liu ◽

Amy Lin ◽

...

Keyword(s):

Conformational Changes ◽

Functional Role

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Investigating the folding pathway and substrate induced conformational changes in B. malayi Guanylate kinase

International Journal of Biological Macromolecules ◽

10.1016/j.ijbiomac.2016.10.008 ◽

2017 ◽

Vol 94 ◽

pp. 621-633 ◽

Cited By ~ 9

Author(s):

Smita Gupta ◽

Sunita Yadav ◽

Venkatesan Suryanarayanan ◽

Sanjeev K. Singh ◽

Jitendra K. Saxena

Keyword(s):

Conformational Changes ◽

Folding Pathway ◽

Guanylate Kinase

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Minimal mechanistic component of proteasome activation and prevention of impairment by pathological oligomers

10.21203/rs.3.rs-900719/v1 ◽

2021 ◽

Author(s):

Janelle Chuah ◽

Tifffany Thibaudeau ◽

David Smith

Keyword(s):

Small Molecules ◽

Conformational Changes ◽

Bound State ◽

Proof Of Concept ◽

Α Subunit ◽

Gate Opening ◽

Allosteric Mechanism ◽

Dependent Mechanism ◽

Degradation Of Peptides

Abstract Impairment of proteasomal function has been implicated in neurodegenerative diseases, justifying the need to understand how the proteasome is activated for protein degradation. Here, using biochemical and structural (cryo-EM) strategies in both archaeal and mammalian proteasomes, we further determine the HbYX(-motif)-dependent mechanism of proteasomal activation used by multiple proteasome-activating complexes including the 19S Particle. We identify multiple proteasome α subunit residues involved in HbYX-dependent activation, a point mutation that activates the proteasome by partially mimicking a HbYX-bound state, and conformational changes involved in gate-opening with a 2.0A structure. Through an iterative process of peptide synthesis, we successfully design a HbYX-like dipeptide mimetic as a robust tool to elucidate how the motif autonomously activates the proteasome. The mimetic induces near complete gate-opening at saturating concentration, activating mammalian proteasomal degradation of peptides and proteins. Findings using our peptide mimetic suggest the HbYX-dependent mechanism requires cooperative binding in at least two intersubunit pockets of the α ring. Collectively, the results presented here unambiguously demonstrate the lone role of the HbYX tyrosine in the allosteric mechanism of proteasome activation and offer proof of concept for the robust potential of HbYX-like small molecules to activate the proteasome.

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Evidence that the TRPV1 S1-S4 Membrane Domain Contributes to Thermosensing

10.1101/711499 ◽

2019 ◽

Cited By ~ 1

Author(s):

Minjoo Kim ◽

Nicholas J. Sisco ◽

Jacob K. Hilton ◽

Camila M. Montano ◽

Manuel A. Castro ◽

...

Keyword(s):

Conformational Changes ◽

Solution Nmr ◽

Membrane Domain ◽

Temperature Dependent ◽

Nmr Characterization ◽

Significant Interest ◽

Pore Domain ◽

Coupling Mechanisms

AbstractSensing and responding to temperature is crucial in biology. The TRPV1 ion channel is a well-studied heat-sensing receptor that is also activated by vanilloid compounds including capsaicin. Despite significant interest, the molecular underpinnings of thermosensing have remained elusive. The TRPV1 S1-S4 membrane domain couples chemical ligand binding to the pore domain during channel gating. However, the role of the S1-S4 domain in thermosensing is unclear. Evaluation of the isolated human TRPV1 S1-S4 domain by solution NMR, Far-UV CD, and intrinsic fluorescence shows that this domain undergoes a non-denaturing temperature-dependent transition with a high thermosensitivity. Further NMR characterization of the temperature-dependent conformational changes suggests the contribution of the S1-S4 domain to thermosensing shares features with known coupling mechanisms between this domain with ligand and pH activation. Taken together, this study shows that the TRPV1 S1-S4 domain contributes to TRPV1 temperature-dependent activation.

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Surface-Exposed Adeno-Associated Virus Vp1-NLS Capsid Fusion Protein Rescues Infectivity of Noninfectious Wild-Type Vp2/Vp3 and Vp3-Only Capsids but Not That of Fivefold Pore Mutant Virions

Journal of Virology ◽

10.1128/jvi.00580-07 ◽

2007 ◽

Vol 81 (15) ◽

pp. 7833-7843 ◽

Cited By ~ 43

Author(s):

Joshua C. Grieger ◽

Jarrod S. Johnson ◽

Brittney Gurda-Whitaker ◽

Mavis Agbandje-McKenna ◽

R. Jude Samulski

Keyword(s):

Conformational Changes ◽

Structural Changes ◽

Wild Type ◽

Dot Blot ◽

Adeno Associated Virus ◽

N Terminus ◽

Localization Signal ◽

Significant Effort

ABSTRACT Over the past 2 decades, significant effort has been dedicated to the development of adeno-associated virus (AAV) as a vector for human gene therapy. However, understanding of the virus with respect to the functional domains of the capsid remains incomplete. In this study, the goal was to further examine the role of the unique Vp1 N terminus, the N terminus plus the recently identified nuclear localization signal (NLS) (J. C. Grieger, S. Snowdy, and R. J. Samulski, J. Virol 80:5199-5210, 2006), and the virion pore at the fivefold axis in infection. We generated two Vp1 fusion proteins (Vp1 and Vp1NLS) linked to the 8-kDa chemokine domain of rat fractalkine (FKN) for the purpose of surface exposure upon assembly of the virion, as previously described (K. H. Warrington, Jr., O. S. Gorbatyuk, J. K. Harrison, S. R. Opie, S. Zolotukhin, and N. Muzyczka, J. Virol 78:6595-6609, 2004). The unique Vp1 N termini were found to be exposed on the surfaces of these capsids and maintained their phospholipase A2 (PLA2) activity, as determined by native dot blot Western and PLA2 assays, respectively. Incorporation of the fusions into AAV type 2 capsids lacking a wild-type Vp1, i.e., Vp2/Vp3 and Vp3 capsid only, increased infectivity by 3- to 5-fold (Vp1FKN) and 10- to 100-fold (Vp1NLSFKN), respectively. However, the surface-exposed fusions did not restore infectivity to AAV virions containing mutations at a conserved leucine (Leu336Ala, Leu336Cys, or Leu336Trp) located at the base of the fivefold pore. EM analyses suggest that Leu336 may play a role in global structural changes to the virion directly impacting downstream conformational changes essential for infectivity and not only have local effects within the pore, as previously suggested.

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Hemagglutinin-Mediated Membrane Fusion: A Biophysical Perspective

Annual Review of Biophysics ◽

10.1146/annurev-biophys-070317-033018 ◽

2018 ◽

Vol 47 (1) ◽

pp. 153-173 ◽

Cited By ~ 14

Author(s):

Sander Boonstra ◽

Jelle S. Blijleven ◽

Wouter H. Roos ◽

Patrick R. Onck ◽

Erik van der Giessen ◽

...

Keyword(s):

Membrane Fusion ◽

Host Cell ◽

Conformational Changes ◽

Fusion Process ◽

Host Cell Membrane ◽

Activation Barriers ◽

Viral Membrane ◽

Influenza Hemagglutinin ◽

Working Together

Influenza hemagglutinin (HA) is a viral membrane protein responsible for the initial steps of the entry of influenza virus into the host cell. It mediates binding of the virus particle to the host-cell membrane and catalyzes fusion of the viral membrane with that of the host. HA is therefore a major target in the development of antiviral strategies. The fusion of two membranes involves high activation barriers and proceeds through several intermediate states. Here, we provide a biophysical description of the membrane fusion process, relating its kinetic and thermodynamic properties to the large conformational changes taking place in HA and placing these in the context of multiple HA proteins working together to mediate fusion. Furthermore, we highlight the role of novel single-particle experiments and computational approaches in understanding the fusion process and their complementarity with other biophysical approaches.

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Structural and Dynamic Characterizations Highlight the Deleterious Role of SULT1A1 R213H Polymorphism in Substrate Binding

International Journal of Molecular Sciences ◽

10.3390/ijms20246256 ◽

2019 ◽

Vol 20 (24) ◽

pp. 6256 ◽

Cited By ~ 7

Author(s):

Raju Dash ◽

Md. Chayan Ali ◽

Nayan Dash ◽

Md. Abul Kalam Azad ◽

S. M. Zahid Hosen ◽

...

Keyword(s):

Binding Energy ◽

Cancer Progression ◽

Conformational Changes ◽

Substrate Binding ◽

Dynamics Simulation ◽

Loss Of Function ◽

Functional Consequences ◽

Binding Energy Analysis ◽

Exogenous Compounds

Sulfotransferase 1A1 (SULT1A1) is responsible for catalyzing various types of endogenous and exogenous compounds. Accumulating data indicates that the polymorphism rs9282861 (R213H) is responsible for inefficient enzymatic activity and associated with cancer progression. To characterize the detailed functional consequences of this mutation behind the loss-of-function of SULT1A1, the present study deployed molecular dynamics simulation to get insights into changes in the conformation and binding energy. The dynamics scenario of SULT1A1 in both wild and mutated types as well as with and without ligand showed that R213H induced local conformational changes, especially in the substrate-binding loop rather than impairing overall stability of the protein structure. The higher conformational changes were observed in the loop3 (residues, 235–263), turning loop conformation to A-helix and B-bridge, which ultimately disrupted the plasticity of the active site. This alteration reduced the binding site volume and hydrophobicity to decrease the binding affinity of the enzyme to substrates, which was highlighted by the MM-PBSA binding energy analysis. These findings highlight the key insights of structural consequences caused by R213H mutation, which would enrich the understanding regarding the role of SULT1A1 mutation in cancer development and also xenobiotics management to individuals in the different treatment stages.

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