scholarly journals Decoupling a tandem-repeat protein: Impact of multiple loop insertions on a modular scaffold

2019 ◽  
Vol 9 (1) ◽  
Author(s):  
Albert Perez-Riba ◽  
Elizabeth Komives ◽  
Ewan R. G. Main ◽  
Laura S. Itzhaki
Keyword(s):  
Tandem Repeat ◽  
Modular Architecture ◽  
Tetratricopeptide Repeats ◽  
Repeat Protein ◽  
Repeat Array ◽  
Functional Capabilities ◽  
Repeat Proteins ◽  
Weakly Coupled ◽  
Tandem Repeat Proteins ◽  
Modular Platform

Abstract The simple topology and modular architecture of tandem-repeat proteins such as tetratricopeptide repeats (TPRs) and ankyrin repeats makes them straightforward to dissect and redesign. Repeat-protein stability can be manipulated in a predictable way using site-specific mutations. Here we explore a different type of modification - loop insertion - that will enable a simple route to functionalisation of this versatile scaffold. We previously showed that a single loop insertion has a dramatically different effect on stability depending on its location in the repeat array. Here we dissect this effect by a combination of multiple and alternated loop insertions to understand the origins of the context-dependent loss in stability. We find that the scaffold is remarkably robust in that its overall structure is maintained. However, adjacent repeats are now only weakly coupled, and consequently the increase in solvent protection, and thus stability, with increasing repeat number that defines the tandem-repeat protein class is lost. Our results also provide us with a rulebook with which we can apply these principles to the design of artificial repeat proteins with precisely tuned folding landscapes and functional capabilities, thereby paving the way for their exploitation as a versatile and truly modular platform in synthetic biology.

scholarly journals Folding cooperativity and allosteric function in the tandem-repeat protein class

2018 ◽  
Vol 373 (1749) ◽  
pp. 20170188 ◽  
Author(s):  
Albert Perez-Riba ◽  
Marie Synakewicz ◽  
Laura S. Itzhaki
Keyword(s):  
Binding Site ◽  
Tandem Repeat ◽  
Structural Changes ◽  
Tetratricopeptide Repeats ◽  
Repeat Protein ◽  
Repeat Array ◽  
Repeat Proteins ◽  
Bacterial Quorum Sensing ◽  
Tandem Repeat Proteins ◽  
Bacterial Quorum

The term allostery was originally developed to describe structural changes in one binding site induced by the interaction of a partner molecule with a distant binding site, and it has been studied in depth in the field of enzymology. Here, we discuss the concept of action at a distance in relation to the folding and function of the solenoid class of tandem-repeat proteins such as tetratricopeptide repeats (TPRs) and ankyrin repeats. Distantly located repeats fold cooperatively, even though only nearest-neighbour interactions exist in these proteins. A number of repeat-protein scaffolds have been reported to display allosteric effects, transferred through the repeat array, that enable them to direct the activity of the multi-subunit enzymes within which they reside. We also highlight a recently identified group of tandem-repeat proteins, the RRPNN subclass of TPRs, recent crystal structures of which indicate that they function as allosteric switches to modulate multiple bacterial quorum-sensing mechanisms. We believe that the folding cooperativity of tandem-repeat proteins and the biophysical mechanisms that transform them into allosteric switches are intimately intertwined. This opinion piece aims to combine our understanding of the two areas and develop ideas on their common underlying principles. This article is part of a discussion meeting issue ‘Allostery and molecular machines’.

scholarly journals Identification of new silk-like protein from B. magister and development of functional materials based on it

2021 ◽  
Vol 2086 (1) ◽  
pp. 012123
Author(s):  
A A Vronskaia ◽  
A D Mikushina ◽  
I E Eliseev
Keyword(s):  
Thin Films ◽  
Drug Delivery ◽  
Tandem Repeat ◽  
Composite Structure ◽  
Textile Industry ◽  
Functional Materials ◽  
Repeat Proteins ◽  
Tandem Repeat Proteins ◽  
New Protein

Abstract Tandem repeat proteins have composite structure and unique properties, which allow them to be used in multiple fields, such as soft photonics, drug delivery and textile industry. The recent discovery of squid ring teeth (SRT) proteins have expanded the existing repertoire of repetitive polypeptides. We chose previously unexplored squid B. magister for our research, isolated and analyzed a new protein forming its ring teeth and hooks, and amplified the corresponding gene. Finally, we used this new isolated SRT protein to fabricate transparent thin films and microspheres.

scholarly journals Ambidextrous helical nanotubes from self-assembly of designed helical hairpin motifs

2019 ◽  
Vol 116 (29) ◽  
pp. 14456-14464 ◽  
Author(s):  
Spencer A. Hughes ◽  
Fengbin Wang ◽  
Shengyuan Wang ◽  
Mark A. B. Kreutzberger ◽  
Tomasz Osinski ◽  
...  
Keyword(s):  
Tandem Repeat ◽  
Self Assembly ◽  
Sequence Similarity ◽  
Structural Data ◽  
Consensus Sequences ◽  
Repeat Proteins ◽  
Helical Hairpin ◽  
Tandem Repeat Proteins ◽  
Helical Protein ◽  
Helical Geometry

Tandem repeat proteins exhibit native designability and represent potentially useful scaffolds for the construction of synthetic biomimetic assemblies. We have designed 2 synthetic peptides, HEAT_R1 and LRV_M3Δ1, based on the consensus sequences of single repeats of thermophilic HEAT (PBS_HEAT) and Leucine-Rich Variant (LRV) structural motifs, respectively. Self-assembly of the peptides afforded high-aspect ratio helical nanotubes. Cryo-electron microscopy with direct electron detection was employed to analyze the structures of the solvated filaments. The 3D reconstructions from the cryo-EM maps led to atomic models for the HEAT_R1 and LRV_M3Δ1 filaments at resolutions of 6.0 and 4.4 Å, respectively. Surprisingly, despite sequence similarity at the lateral packing interface, HEAT_R1 and LRV_M3Δ1 filaments adopt the opposite helical hand and differ significantly in helical geometry, while retaining a local conformation similar to previously characterized repeat proteins of the same class. The differences in the 2 filaments could be rationalized on the basis of differences in cohesive interactions at the lateral and axial interfaces. These structural data reinforce previous observations regarding the structural plasticity of helical protein assemblies and the need for high-resolution structural analysis. Despite these observations, the native designability of tandem repeat proteins offers the opportunity to engineer novel helical nanotubes. Moreover, the resultant nanotubes have independently addressable and chemically distinguishable interior and exterior surfaces that would facilitate applications in selective recognition, transport, and release.

Mechanical Properties of Tandem-Repeat Proteins Are Governed by Network Defects

2018 ◽  
Vol 4 (3) ◽  
pp. 884-891 ◽  
Author(s):  
Abdon Pena-Francesch ◽  
Huihun Jung ◽  
Mo Segad ◽  
Ralph H. Colby ◽  
Benjamin D. Allen ◽  
...  
Keyword(s):  
Mechanical Properties ◽  
Tandem Repeat ◽  
Repeat Proteins ◽  
Tandem Repeat Proteins

scholarly journals Dissecting and reprogramming the folding and assembly of tandem-repeat proteins

2015 ◽  
Vol 43 (5) ◽  
pp. 881-888 ◽  
Author(s):  
Pamela J.E. Rowling ◽  
Elin M. Sivertsson ◽  
Albert Perez-Riba ◽  
Ewan R.G. Main ◽  
Laura S. Itzhaki
Keyword(s):  
Protein Design ◽  
Tandem Repeat ◽  
Rational Design ◽  
Topological Complexity ◽  
Energy Barriers ◽  
Step Size ◽  
Repeat Proteins ◽  
Tandem Repeat Proteins ◽  
Level Of Understanding ◽  
Modular Structures

Studying protein folding and protein design in globular proteins presents significant challenges because of the two related features, topological complexity and co-operativity. In contrast, tandem-repeat proteins have regular and modular structures composed of linearly arrayed motifs. This means that the biophysics of even giant repeat proteins is highly amenable to dissection and to rational design. Here we discuss what has been learnt about the folding mechanisms of tandem-repeat proteins. The defining features that have emerged are: (i) accessibility of multiple distinct routes between denatured and native states, both at equilibrium and under kinetic conditions; (ii) different routes are favoured for folding compared with unfolding; (iii) unfolding energy barriers are broad, reflecting stepwise unravelling of an array repeat by repeat; (iv) highly co-operative unfolding at equilibrium and the potential for exceptionally high thermodynamic stabilities by introducing consensus residues; (v) under force, helical-repeat structures are very weak with non-co-operative unfolding leading to elasticity and buffering effects. This level of understanding should enable us to create repeat proteins with made-to-measure folding mechanisms, in which one can dial into the sequence the order of repeat folding, number of pathways taken, step size (co-operativity) and fine-structure of the kinetic energy barriers.

scholarly journals DeepSymmetry: using 3D convolutional networks for identification of tandem repeats and internal symmetries in protein structures

2019 ◽  
Vol 35 (24) ◽  
pp. 5113-5120 ◽  
Author(s):  
Guillaume Pagès ◽  
Sergei Grudinin
Keyword(s):  
Tandem Repeat ◽  
Tandem Repeats ◽  
Protein Structures ◽  
Molecular Structures ◽  
Supplementary Information ◽  
Convolutional Networks ◽  
Repeat Proteins ◽  
Density Maps ◽  
Tandem Repeat Proteins ◽  
Internal Symmetries

Abstract Motivation Thanks to the recent advances in structural biology, nowadays 3D structures of various proteins are solved on a routine basis. A large portion of these structures contain structural repetitions or internal symmetries. To understand the evolution mechanisms of these proteins and how structural repetitions affect the protein function, we need to be able to detect such proteins very robustly. As deep learning is particularly suited to deal with spatially organized data, we applied it to the detection of proteins with structural repetitions. Results We present DeepSymmetry, a versatile method based on 3D convolutional networks that detects structural repetitions in proteins and their density maps. Our method is designed to identify tandem repeat proteins, proteins with internal symmetries, symmetries in the raw density maps, their symmetry order and also the corresponding symmetry axes. Detection of symmetry axes is based on learning 6D Veronese mappings of 3D vectors, and the median angular error of axis determination is less than one degree. We demonstrate the capabilities of our method on benchmarks with tandem-repeated proteins and also with symmetrical assemblies. For example, we have discovered about 7800 putative tandem repeat proteins in the PDB. Availability and implementation The method is available at https://team.inria.fr/nano-d/software/deepsymmetry. It consists of a C++ executable that transforms molecular structures into volumetric density maps, and a Python code based on the TensorFlow framework for applying the DeepSymmetry model to these maps. Supplementary information Supplementary data are available at Bioinformatics online.

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