scholarly journals Order from disorder in the sarcomere: FATZ forms a fuzzy but tight complex and phase-separated condensates with α-actinin

2021 ◽  
Vol 7 (22) ◽  
pp. eabg7653
Author(s):  
Antonio Sponga ◽  
Joan L. Arolas ◽  
Thomas C. Schwarz ◽  
Cy M. Jeffries ◽  
Ariadna Rodriguez Chamorro ◽  
...  
Keyword(s):  
Molecular Recognition ◽  
Binding Sites ◽  
Actin Filaments ◽  
Interaction Mechanism ◽  
Preferential Orientation ◽  
Integrative Model ◽  
Conformational Ensemble ◽  
Interaction Partners ◽  
Cross Links ◽  
Recognition Elements

In sarcomeres, α-actinin cross-links actin filaments and anchors them to the Z-disk. FATZ (filamin-, α-actinin-, and telethonin-binding protein of the Z-disk) proteins interact with α-actinin and other core Z-disk proteins, contributing to myofibril assembly and maintenance. Here, we report the first structure and its cellular validation of α-actinin-2 in complex with a Z-disk partner, FATZ-1, which is best described as a conformational ensemble. We show that FATZ-1 forms a tight fuzzy complex with α-actinin-2 and propose an interaction mechanism via main molecular recognition elements and secondary binding sites. The obtained integrative model reveals a polar architecture of the complex which, in combination with FATZ-1 multivalent scaffold function, might organize interaction partners and stabilize α-actinin-2 preferential orientation in Z-disk. Last, we uncover FATZ-1 ability to phase-separate and form biomolecular condensates with α-actinin-2, raising the question whether FATZ proteins can create an interaction hub for Z-disk proteins through membraneless compartmentalization during myofibrillogenesis.

Visualization of molecular binding sites at the nanoscale in the lift-up mode by amplitude-modulation atomic force microscopy

Nanoscale ◽  
2021 ◽  
Vol 13 (7) ◽  
pp. 4213-4220
Author(s):  
Tatsuhiro Maekawa ◽  
Takashi Nyu ◽  
Evan Angelo Quimada Mondarte ◽  
Hiroyuki Tahara ◽  
Kasinan Suthiwanich ◽  
...  
Keyword(s):  
Atomic Force Microscopy ◽  
Molecular Recognition ◽  
Amplitude Modulation ◽  
Binding Sites ◽  
Local Distribution ◽  
New Approach ◽  
Molecular Binding ◽  
Force Microscopy ◽  
Atomic Force ◽  
Recognition Sites

We report a new approach to visualize the local distribution of molecular recognition sites with nanoscale resolution by amplitude-modulation atomic force microscopy.

scholarly journals Molecular Recognition: Perspective and a New Approach

Sensors ◽  
2021 ◽  
Vol 21 (8) ◽  
pp. 2757
Author(s):  
W. Rudolf Seitz ◽  
Casey J. Grenier ◽  
John R. Csoros ◽  
Rongfang Yang ◽  
Tianyu Ren
Keyword(s):  
Molecular Recognition ◽  
Molecularly Imprinted Polymers ◽  
Binding Sites ◽  
Binding Kinetics ◽  
Molecularly Imprinted ◽  
New Approach ◽  
Imprinted Polymers ◽  
High Affinity ◽  
Water Blocking ◽  
High Level

This perspective presents an overview of approaches to the preparation of molecular recognition agents for chemical sensing. These approaches include chemical synthesis, using catalysts from biological systems, partitioning, aptamers, antibodies and molecularly imprinted polymers. The latter three approaches are general in that they can be applied with a large number of analytes, both proteins and smaller molecules like drugs and hormones. Aptamers and antibodies bind analytes rapidly while molecularly imprinted polymers bind much more slowly. Most molecularly imprinted polymers, formed by polymerizing in the presence of a template, contain a high level of covalent crosslinker that causes the polymer to form a separate phase. This results in a material that is rigid with low affinity for analyte and slow binding kinetics. Our approach to templating is to use predominantly or exclusively noncovalent crosslinks. This results in soluble templated polymers that bind analyte rapidly with high affinity. The biggest challenge of this approach is that the chains are tangled when the templated polymer is dissolved in water, blocking access to binding sites.

scholarly journals Determination of the alpha-actinin-binding site on actin filaments by cryoelectron microscopy and image analysis.

1994 ◽  
Vol 126 (2) ◽  
pp. 433-443 ◽  
Author(s):  
A McGough ◽  
M Way ◽  
D DeRosier
Keyword(s):  
Image Analysis ◽  
Smooth Muscle ◽  
Binding Sites ◽  
Actin Filaments ◽  
Three Dimensional ◽  
Actin Binding ◽  
Dimensional Structure ◽  
Outer Face ◽  
Actin Binding Domain

The three-dimensional structure of actin filaments decorated with the actin-binding domain of chick smooth muscle alpha-actinin (alpha A1-2) has been determined to 21-A resolution. The shape and location of alpha A1-2 was determined by subtracting maps of F-actin from the reconstruction of decorated filaments. alpha A1-2 resembles a bell that measures approximately 38 A at its base and extends 42 A from its base to its tip. In decorated filaments, the base of alpha A1-2 is centered about the outer face of subdomain 2 of actin and contacts subdomain 1 of two neighboring monomers along the long-pitch (two-start) helical strands. Using the atomic model of F-actin (Lorenz, M., D. Popp, and K. C. Holmes. 1993. J. Mol. Biol. 234:826-836.), we have been able to test directly the likelihood that specific actin residues, which have been previously identified by others, interact with alpha A1-2. Our results indicate that residues 86-117 and 350-375 comprise distinct binding sites for alpha-actinin on adjacent actin monomers.

scholarly journals Unexpected Specificity within Dynamic Transcriptional Protein-Protein Complexes

2020 ◽  
Author(s):  
Matthew J. Henley ◽  
Brian M. Linhares ◽  
Brittany S. Morgan ◽  
Tomasz Cierpicki ◽  
Carol A. Fierke ◽  
...  
Keyword(s):  
Molecular Recognition ◽  
Electrostatic Interactions ◽  
Protein Complexes ◽  
Critical Role ◽  
Gene Activation ◽  
Disordered Proteins ◽  
Conformational Ensemble ◽  
Regulation Of Transcription ◽  
Protein Protein Interaction ◽  
Eukaryotic Gene

AbstractA key functional event in eukaryotic gene activation is the formation of dynamic protein-protein interaction networks between transcriptional activators and transcriptional coactivators. Seemingly incongruent with the tight regulation of transcription, many biochemical and biophysical studies suggest that activators use nonspecific hydrophobic and/or electrostatic interactions to bind to coactivators, with few if any specific contacts. Here a mechanistic dissection of a set of representative dynamic activator•coactivator complexes, comprised of the ETV/PEA3 family of activators and the coactivator Med25, reveals a different molecular recognition model. The data demonstrate that small sequence variations within an activator family significantly redistribute the conformational ensemble of the complex while not affecting overall affinity, and distal residues within the activator—not often considered as contributing to binding—play a key role in mediating conformational redistribution. The ETV/PEA3•Med25 ensembles are directed by specific contacts between the disordered activator and the Med25 interface, which is facilitated by structural shifts of the coactivator binding surface. Taken together, these data highlight the critical role coactivator plasticity plays in recognition of disordered activators, and indicates that molecular recognition models of disordered proteins must consider the ability of the binding partners to mediate specificity.

scholarly journals Multi-modal adaptor-clathrin contacts drive coated vesicle assembly

2021 ◽  
Author(s):  
Sarah M Smith ◽  
Gabrielle Larocque ◽  
Katherine M Wood ◽  
Kyle L Morris ◽  
Alan M Roseman ◽  
...  
Keyword(s):  
Functional Analysis ◽  
Binding Sites ◽  
Potential Role ◽  
Fundamental Property ◽  
Structural Knowledge ◽  
Coated Vesicle ◽  
Functional Importance ◽  
Coated Pits ◽  
Interaction Sites ◽  
Cross Links

Clathrin-coated pits are formed by the recognition of membrane and cargo by the heterotetrameric AP2 complex and the subsequent recruitment of clathrin triskelia. A potential role for AP2 in coated-pit assembly beyond initial clathrin recruitment has not been explored. Clathrin binds the b2 subunit of AP2, and several binding sites on b2 and on the clathrin heavy chain have been identified, but our structural knowledge of these interactions is incomplete and their functional importance during endocytosis is unclear. Here, we analysed the cryo-EM structure of clathrin cages assembled in the presence of b2 hinge and appendage (b2HA) domains. We find that the b2-appendage binds in at least two positions in the cage, demonstrating that multi-modal binding is a fundamental property of clathrin-AP2 interactions. In one position, b2-appendage cross-links two adjacent terminal domains from different triskelia below the vertex. Functional analysis of b2HA-clathrin interactions reveals that endocytosis requires two clathrin interaction sites: a clathrin-box motif on the hinge and the ''sandwich site'' on the appendage, with the appendage ''platform site'' having less importance. From these studies and the work of others, we propose that b2-appendage binding to more than one clathrin triskelion is a key feature of the system and likely explains why clathrin assembly is driven by AP2.

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