Repeat proteins challenge the concept of structural domains

2015 ◽  
Vol 43 (5) ◽  
pp. 844-849 ◽  
Author(s):  
Rocío Espada ◽  
R. Gonzalo Parra ◽  
Manfred J. Sippl ◽  
Thierry Mora ◽  
Aleksandra M. Walczak ◽  
...  
Keyword(s):  
Biological Systems ◽  
Modular Structure ◽  
Structural Domains ◽  
Repeat Array ◽  
Repeat Units ◽  
Repeat Proteins ◽  
Folding Dynamics ◽  
And Function

Structural domains are believed to be modules within proteins that can fold and function independently. Some proteins show tandem repetitions of apparent modular structure that do not fold independently, but rather co-operate in stabilizing structural forms that comprise several repeat-units. For many natural repeat-proteins, it has been shown that weak energetic links between repeats lead to the breakdown of co-operativity and the appearance of folding sub-domains within an apparently regular repeat array. The quasi-1D architecture of repeat-proteins is crucial in detailing how the local energetic balances can modulate the folding dynamics of these proteins, which can be related to the physiological behaviour of these ubiquitous biological systems.

scholarly journals Helicase-like functions in phosphate loop containing beta-alpha polypeptides

2021 ◽  
Vol 118 (16) ◽  
pp. e2016131118
Author(s):  
Pratik Vyas ◽  
Olena Trofimyuk ◽  
Liam M. Longo ◽  
Fanindra Kumar Deshmukh ◽  
Michal Sharon ◽  
...  
Keyword(s):  
Phosphoryl Transfer ◽  
Rna Helicases ◽  
Sequence Structure ◽  
Repeat Proteins ◽  
Dynamic Assembly ◽  
Essential Enzyme ◽  
Enzyme Families ◽  
And Function ◽  
Dsdna Binding ◽  
Oligomeric Forms

The P-loop Walker A motif underlies hundreds of essential enzyme families that bind nucleotide triphosphates (NTPs) and mediate phosphoryl transfer (P-loop NTPases), including the earliest DNA/RNA helicases, translocases, and recombinases. What were the primordial precursors of these enzymes? Could these large and complex proteins emerge from simple polypeptides? Previously, we showed that P-loops embedded in simple βα repeat proteins bind NTPs but also, unexpectedly so, ssDNA and RNA. Here, we extend beyond the purely biophysical function of ligand binding to demonstrate rudimentary helicase-like activities. We further constructed simple 40-residue polypeptides comprising just one β-(P-loop)-α element. Despite their simplicity, these P-loop prototypes confer functions such as strand separation and exchange. Foremost, these polypeptides unwind dsDNA, and upon addition of NTPs, or inorganic polyphosphates, release the bound ssDNA strands to allow reformation of dsDNA. Binding kinetics and low-resolution structural analyses indicate that activity is mediated by oligomeric forms spanning from dimers to high-order assemblies. The latter are reminiscent of extant P-loop recombinases such as RecA. Overall, these P-loop prototypes compose a plausible description of the sequence, structure, and function of the earliest P-loop NTPases. They also indicate that multifunctionality and dynamic assembly were key in endowing short polypeptides with elaborate, evolutionarily relevant functions.

Smotifs as structural local descriptors of supersecondary elements: classification, completeness and applications

2014 ◽  
Vol 10 (4) ◽  
Author(s):  
Jaume Bonet ◽  
Andras Fiser ◽  
Baldo Oliva ◽  
Narcis Fernandez-Fuentes
Keyword(s):  
Protein Design ◽  
Structure Prediction ◽  
Protein Structures ◽  
Regular Structure ◽  
Loop Structure ◽  
Apparent Lack ◽  
Knowledge Based ◽  
Limits Of Knowledge ◽  
Folding Dynamics ◽  
And Function

AbstractProtein structures are made up of periodic and aperiodic structural elements (i.e., α-helices, β-strands and loops). Despite the apparent lack of regular structure, loops have specific conformations and play a central role in the folding, dynamics, and function of proteins. In this article, we reviewed our previous works in the study of protein loops as local supersecondary structural motifs or Smotifs. We reexamined our works about the structural classification of loops (ArchDB) and its application to loop structure prediction (ArchPRED), including the assessment of the limits of knowledge-based loop structure prediction methods. We finalized this article by focusing on the modular nature of proteins and how the concept of Smotifs provides a convenient and practical approach to decompose proteins into strings of concatenated Smotifs and how can this be used in computational protein design and protein structure prediction.

From landing lights to mimicry: the molecular regulation of flower colouration and mechanisms for pigmentation patterning

2012 ◽  
Vol 39 (8) ◽  
pp. 619 ◽  
Author(s):  
Kevin M. Davies ◽  
Nick W. Albert ◽  
Kathy E. Schwinn
Keyword(s):  
Anthocyanin Biosynthesis ◽  
Flower Colour ◽  
Signal Pathways ◽  
Plant Signaling ◽  
Pollination Success ◽  
Repeat Proteins ◽  
Regulatory Complex ◽  
Colour Patterns ◽  
And Function ◽  
Plant Pollinator

Flower colour is a key component for plant signaling to pollinators and a staggering variety of colour variations are found in nature. Patterning of flower colour, such as pigment spots or stripes, is common and is important in promoting pollination success. Developmentally programmed pigmentation patterns are of interest with respect to the evolution of specialised plant–pollinator associations and as models for dissecting regulatory signaling in plants. This article reviews the occurrence and function of flower colour patterns, as well as the molecular genetics of anthocyanin pigmentation regulation. The transcription factors controlling anthocyanin biosynthesis have been characterised for many species and an ‘MBW’ regulatory complex of R2R3MYB, bHLH and WD-Repeat proteins is of central importance. In particular, R2R3MYBs are key determinants of pigmentation intensity and patterning in plants. Progress is now being made on how environmental or developmental signal pathways may in turn control the production of the MBW components. Furthermore, additional regulatory proteins that interact with the MBW activation complex are being identified, including a range of proteins that repress complex formation or action, either directly or indirectly. This review discusses some of the recent data on the regulatory factors and presents models of how patterns may be determined.

scholarly journals The Modular Structure and Function of the Wheat H1 Promoter with S Phase-Specific Activity

1998 ◽  
Vol 39 (3) ◽  
pp. 294-306 ◽  
Author(s):  
K.-i. Taoka ◽  
N. Ohtsubo ◽  
Y. Fujimoto ◽  
K. Mikami ◽  
T. Meshi ◽  
...  
Keyword(s):  
Specific Activity ◽  
Structure And Function ◽  
S Phase ◽  
Modular Structure ◽  
And Function

Relationships between hydrogen bonds and halogen bonds in biological systems

2017 ◽  
Vol 73 (2) ◽  
pp. 255-264 ◽  
Author(s):  
Rhianon K. Rowe ◽  
P. Shing Ho
Keyword(s):  
Biological Systems ◽  
Halogen Bonding ◽  
Structure And Function ◽  
Rational Drug Design ◽  
Biological Molecules ◽  
Halogen Bonds ◽  
Rational Drug ◽  
Complex Relationships ◽  
And Function ◽  
The Relationship

The recent recognition that halogen bonding (XB) plays important roles in the recognition and assembly of biological molecules has led to new approaches in medicinal chemistry and biomolecular engineering. When designing XBs into strategies for rational drug design or into a biomolecule to affect its structure and function, we must consider the relationship between this interaction and the more ubiquitous hydrogen bond (HB). In this review, we explore these relationships by asking whether and how XBs can replace, compete against or behave independently of HBs in various biological systems. The complex relationships between the two interactions inform us of the challenges we face in fully utilizing XBs to control the affinity and recognition of inhibitors against their therapeutic targets, and to control the structure and function of proteins, nucleic acids and other biomolecular scaffolds.

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