scholarly journals Distribution of disease-causing germline mutations in coiled-coils implies an important role of their N-terminal region

2020 ◽  
Vol 10 (1) ◽  
Author(s):  
Zsofia E. Kalman ◽  
Bálint Mészáros ◽  
Zoltán Gáspári ◽  
Laszlo Dobson
Keyword(s):  
Coiled Coil ◽  
Germline Mutations ◽  
Coiled Coils ◽  
Helical Structures ◽  
Diverse Range ◽  
Naturally Occurring ◽  
Human Proteins ◽  
Range Of Functions ◽  
Functional Explanations

Abstract Next-generation sequencing resulted in the identification of a huge number of naturally occurring variations in human proteins. The correct interpretation of the functional effects of these variations necessitates the understanding of how they modulate protein structure. Coiled-coils are α-helical structures responsible for a diverse range of functions, but most importantly, they facilitate the structural organization of macromolecular scaffolds via oligomerization. In this study, we analyzed a comprehensive set of disease-associated germline mutations in coiled-coil structures. Our results suggest an important role of residues near the N-terminal part of coiled-coil regions, possibly critical for superhelix assembly and folding in some cases. We also show that coiled-coils of different oligomerization states exhibit characteristically distinct patterns of disease-causing mutations. Our study provides structural and functional explanations on how disease emerges through the mutation of these structural motifs.

scholarly journals Distribution of disease-causing germline mutations in coiled-coils suggests essential role of their N-terminal region

2020 ◽  
Author(s):  
Zsofia E. Kalman ◽  
Bálint Mészáros ◽  
Zoltán Gáspári ◽  
Laszlo Dobson
Keyword(s):  
Essential Role ◽  
Coiled Coil ◽  
Germline Mutations ◽  
Coiled Coils ◽  
Helical Structures ◽  
Diverse Range ◽  
Human Proteins ◽  
Range Of Functions ◽  
Functional Explanations

AbstractNext-generation sequencing resulted in the identification of a huge number of naturally occurring variations in human proteins. The correct interpretation of the functional effects of these variations necessitates the understanding of how they modulate protein structure. Coiled-coils are α-helical structures responsible for a diverse range of functions, but most importantly, they facilitate the structural organization of macromolecular scaffolds via oligomerization. In this study, we analyzed a comprehensive set of disease-associated germline mutations in coiled-coil structures. Our results highlight the essential role of residues near the N-terminal part of coiled-coil regions, possibly critical for superhelix assembly and folding in some cases. We also show that coiled-coils of different oligomerization states exhibit characteristically distinct patterns of disease-causing mutations. Our study provides structural and functional explanations on how disease emerges through the mutation of these structural motifs.

scholarly journals ARCIMBOLDOon coiled coils

2018 ◽  
Vol 74 (3) ◽  
pp. 194-204 ◽  
Author(s):  
Iracema Caballero ◽  
Massimo Sammito ◽  
Claudia Millán ◽  
Andrey Lebedev ◽  
Nicolas Soler ◽  
...  
Keyword(s):  
Coiled Coil ◽  
Coiled Coils ◽  
Translational Symmetry ◽  
Command Line ◽  
Phase Problem ◽  
Final Solution ◽  
Resolution Limit ◽  
Helical Structures ◽  
Small Model ◽  
Test Pool

ARCIMBOLDOsolves the phase problem by combining the location of small model fragments usingPhaserwith density modification and autotracing usingSHELXE. Mainly helical structures constitute favourable cases, which can be solved using polyalanine helical fragments as search models. Nevertheless, the solution of coiled-coil structures is often complicated by their anisotropic diffraction and apparent translational noncrystallographic symmetry. Long, straight helices have internal translational symmetry and their alignment in preferential directions gives rise to systematic overlap of Patterson vectors. This situation has to be differentiated from the translational symmetry relating different monomers.ARCIMBOLDO_LITEhas been run on single workstations on a test pool of 150 coiled-coil structures with 15–635 amino acids per asymmetric unit and with diffraction data resolutions of between 0.9 and 3.0 Å. The results have been used to identify and address specific issues when solving this class of structures usingARCIMBOLDO. Features fromPhaserv.2.7 onwards are essential to correct anisotropy and produce translation solutions that will pass the packing filters. As the resolution becomes worse than 2.3 Å, the helix direction may be reversed in the placed fragments. Differentiation between true solutions and pseudo-solutions, in which helix fragments were correctly positioned but in a reverse orientation, was found to be problematic at resolutions worse than 2.3 Å. Therefore, after every new fragment-placement round, complete or sparse combinations of helices in alternative directions are generated and evaluated. The final solution is once again probed by helix reversal, refinement and extension. To conclude, density modification andSHELXEautotracing incorporating helical constraints is also exploited to extend the resolution limit in the case of coiled coils and to enhance the identification of correct solutions. This study resulted in a specialized mode withinARCIMBOLDOfor the solution of coiled-coil structures, which overrides the resolution limit and can be invoked from the command line (keyword coiled_coil) orARCIMBOLDO_LITEtask interface inCCP4i.

scholarly journals Structural and Functional Analysis of Essential pre-mRNA Splicing Factor Prp19p

2005 ◽  
Vol 25 (1) ◽  
pp. 451-460 ◽  
Author(s):  
Melanie D. Ohi ◽  
Craig W. Vander Kooi ◽  
Joshua A. Rosenberg ◽  
Liping Ren ◽  
Justin P. Hirsch ◽  
...  
Keyword(s):  
Functional Data ◽  
Coiled Coil ◽  
Single Copy ◽  
Coiled Coils ◽  
Binding Partner ◽  
Central Stalk ◽  
Interaction Surface

ABSTRACT U-box-containing Prp19p is an integral component of the Prp19p-associated complex (the nineteen complex, or NTC) that is essential for activation of the spliceosome. Prp19p makes numerous protein-protein contacts with other NTC components and is required for NTC stability. Here we show that Prp19p forms a tetramer in vitro and in vivo and we map the domain required for its oligomerization to a central tetrameric coiled-coil. Biochemical and in vivo analyses are consistent with Prp19p tetramerization providing an interaction surface for a single copy of its binding partner, Cef1p. Electron microscopy showed that the isolated Prp19p tetramer is an elongated particle consisting of four globular WD40 domains held together by a central stalk consisting of four N-terminal U-boxes and four coiled-coils. These structural and functional data provide a basis for understanding the role of Prp19p as a key architectural component of the NTC.

scholarly journals Understanding In-Silico Approaches to Design Synthetic Antifungal Peptides to Combat Fungal Infections like Mucormycosis

2021 ◽  
Vol 8 (6) ◽  
Author(s):  
Bajwa T ◽  
◽  
Sharma R ◽  
Keyword(s):  
In Silico ◽  
Fungal Pathogens ◽  
Fungal Infections ◽  
Structural Features ◽  
Antifungal Drugs ◽  
Diverse Range ◽  
Naturally Occurring ◽  
Antifungal Peptides ◽  
Range Of Functions

Antimicrobial peptides are the small sized molecule ranging in size from 2 to 9 kDa with expansive range of antimicrobial activity against bacteria, fungi, viruses etc. They are also used as first line of defense against various pathogens. With the emergence of various fungal infections in the present day and uprising antifungal resistance has made the choice of antifungal drugs very limited, the conventional drugs are slowly becoming ineffective to these fungal pathogens. Researchers have turned to these naturally occurring molecules which represent diverse range of functions and structural features but these naturally occurring peptides exhibit high toxicity, instability and low specificity towards the target which can be combatted by using various in silico and computational approaches to design and modify these AMPs in such a way that their efficiency is increased. In this article, we have specifically focused on Mucormycosis infection because of its high mortality rates and a very few synthetic AMPs have been produced against Mucorales considering the severity of this disease and the rapid surge in Mucormycosis cases emerged in the country. In this paper we will discuss about the present scenario of the disease, AMPs as antifungal therapy, role, classification of antifungal peptides, mechanism of action, advantages and limitations of natural AMPs, important physicochemical properties taken into account while designing synthetic AMPs (SAMPs) and the workflow pipeline to characterize and predict potential synthetic AMPs by using the existing web servers, databases and bioinformatics tools to develop new alternatives of conventional drugs available in the market against fungal infections.

scholarly journals Separation of coiled-coil structures in lamin A/C is required for elongation of the filament

2020 ◽  
Author(s):  
Jinsook Ahn ◽  
Soyeon Jeong ◽  
So-mi Kang ◽  
Inseong Jo ◽  
Bum-Joon Park ◽  
...  
Keyword(s):  
Structural Transition ◽  
Coiled Coil ◽  
Binding Mode ◽  
Coiled Coils ◽  
Lamin A ◽  
Structural Elements ◽  
Mutant Proteins ◽  
Biochemical Effects ◽  
Insight Into

AbstractIntermediate filaments (IFs) commonly have structural elements of a central α-helical coiled-coil domain consisting of coil 1a, coil 1b, coil 2, and their flanking linkers. Recently, crystal structure of a long lamin A/C fragment was determined and showed detailed features of a tetrameric unit. The structure further suggested a new binding mode between tetramers, designated eA22, where a parallel overlap of coil 1a and coil 2 is the key interaction. In this study, we investigated the biochemical effects of genetic mutations causing human diseases, focusing on the eA22 interaction. The mutant proteins exhibited either weakened or augmented interactions between coil 1a and coil 2. The ensuing biochemical results indicated that the interaction requires the separation of the coiled-coils in N-terminal of coil 1a and C-terminal of coil 2, coupled with the structural transition in the central α-helical rod domain. This study provides insight into the role of coil 1a as a molecular regulator in elongation of the IF proteins.

scholarly journals Combined molecular/continuum modeling reveals the role of friction during fast unfolding of coiled-coil proteins

Soft Matter ◽  
2019 ◽  
Vol 15 (24) ◽  
pp. 4961-4975 ◽  
Author(s):  
Alejandro Torres-Sánchez ◽  
Juan M. Vanegas ◽  
Prashant K. Purohit ◽  
Marino Arroyo
Keyword(s):  
Protein Unfolding ◽  
Coiled Coil ◽  
Coiled Coils ◽  
Hydrodynamic Interactions ◽  
Continuum Modeling

Coiled-coils are filamentous proteins capable of reversible unfolding. We show that hydrodynamic interactions with the solvent, usually neglected in theories of protein unfolding, are critical to understand their unfolding at high rates.

scholarly journals Renal Ca2+ and Water Handling in Response to Calcium Sensing Receptor Signaling: Physiopathological Aspects and Role of CaSR-Regulated microRNAs

2019 ◽  
Vol 20 (21) ◽  
pp. 5341 ◽  
Author(s):  
Marianna Ranieri
Keyword(s):  
Signaling Pathways ◽  
Collecting Duct ◽  
Calcium Sensing Receptor ◽  
Diverse Range ◽  
Calcium Sensing ◽  
Water Handling ◽  
Naturally Occurring ◽  
Non Coding Rnas ◽  
G Protein Coupled

Calcium (Ca2+) is a universal and vital intracellular messenger involved in a diverse range of cellular and biological processes. Changes in the concentration of extracellular Ca2+ can disrupt the normal cellular activities and the physiological function of these systems. The calcium sensing receptor (CaSR) is a unique G protein-coupled receptor (GPCR) activated by extracellular Ca2+ and by other physiological cations, aminoacids, and polyamines. CaSR is the main controller of the extracellular Ca2+ homeostatic system by regulating parathyroid hormone (PTH) secretion and, in turn, Ca2+ absorption and resorption. Recent advances highlight novel signaling pathways activated by CaSR signaling involving the regulation of microRNAs (miRNAs). miRNAs are naturally-occurring small non-coding RNAs that regulate post-transcriptional gene expression and are involved in several diseases. We previously described that high luminal Ca2+ in the renal collecting duct attenuates short-term vasopressin-induced aquaporin-2 (AQP2) trafficking through CaSR activation. Moreover, we demonstrated that CaSR signaling reduces AQP2 abundance via AQP2-targeting miRNA-137. This review summarizes the recent data related to CaSR-regulated miRNAs signaling pathways in the kidney.

scholarly journals Extending the scope of coiled-coil crystal structure solution by AMPLE through improved ab initio modelling

2020 ◽  
Vol 76 (3) ◽  
pp. 272-284 ◽  
Author(s):  
Jens M. H. Thomas ◽  
Ronan M. Keegan ◽  
Daniel J. Rigden ◽  
Owen R. Davies
Keyword(s):  
Ab Initio ◽  
Coiled Coil ◽  
Coiled Coils ◽  
Molecular Replacement ◽  
Helical Structures ◽  
Major Barrier ◽  
X Ray Crystallography ◽  
Structure Solution ◽  
Coil Structure ◽  
Experimental Phasing

The phase problem remains a major barrier to overcome in protein structure solution by X-ray crystallography. In recent years, new molecular-replacement approaches using ab initio models and ideal secondary-structure components have greatly contributed to the solution of novel structures in the absence of clear homologues in the PDB or experimental phasing information. This has been particularly successful for highly α-helical structures, and especially coiled-coils, in which the relatively rigid α-helices provide very useful molecular-replacement fragments. This has been seen within the program AMPLE, which uses clustered and truncated ensembles of numerous ab initio models in structure solution, and is already accomplished for α-helical and coiled-coil structures. Here, an expansion in the scope of coiled-coil structure solution by AMPLE is reported, which has been achieved through general improvements in the pipeline, the removal of tNCS correction in molecular replacement and two improved methods for ab initio modelling. Of the latter improvements, enforcing the modelling of elongated helices overcame the bias towards globular folds and provided a rapid method (equivalent to the time requirements of the existing modelling procedures in AMPLE) for enhanced solution. Further, the modelling of two-, three- and four-helical oligomeric coiled-coils, and the use of full/partial oligomers in molecular replacement, provided additional success in difficult and lower resolution cases. Together, these approaches have enabled the solution of a number of parallel/antiparallel dimeric, trimeric and tetrameric coiled-coils at resolutions as low as 3.3 Å, and have thus overcome previous limitations in AMPLE and provided a new functionality in coiled-coil structure solution at lower resolutions. These new approaches have been incorporated into a new release of AMPLE in which automated elongated monomer and oligomer modelling may be activated by selecting `coiled-coil' mode.

Mechanical Properties of Biopolymer Chains

1992 ◽  
Vol 292 ◽  
Author(s):  
Ruth Pachter ◽  
Peter D. Haaland ◽  
Robert L. Crane ◽  
W. Wade Adams
Keyword(s):  
Mechanical Properties ◽  
Amino Acids ◽  
Hydrogen Bonding ◽  
Molecular Hydrogen ◽  
Mechanical Response ◽  
Amide Bond ◽  
Pivotal Role ◽  
Helical Structures ◽  
Naturally Occurring

AbstractMolecular simulations that predict the molecular mechanical response of alpha-helical biopolymers with a reinforcing intra-molecular hydrogen bonding network, viz,, a ‘spring-like’ behavior, are presented in this study. Mechanical properties of extended biopolymer strands based on naturally occurring amino acids, namely poly(L-A1a) and for comparison poly(LGlu), versus synthetic PPTA containing an amide bond, are compared to those assuming alpha-helical structures. Thus, the pivotal role of such motifs in biological systems utilizing superior compressive mechanical properties can be inferred.

scholarly journals Separation of Coiled-Coil Structures in Lamin A/C Is Required for the Elongation of the Filament

Cells ◽  
2020 ◽  
Vol 10 (1) ◽  
pp. 55
Author(s):  
Jinsook Ahn ◽  
Soyeon Jeong ◽  
So-Mi Kang ◽  
Inseong Jo ◽  
Bum-Joon Park ◽  
...  
Keyword(s):  
Structural Transition ◽  
Coiled Coil ◽  
Binding Mode ◽  
Coiled Coils ◽  
Lamin A ◽  
Structural Elements ◽  
Mutant Proteins ◽  
Biochemical Effects ◽  
Insight Into

Intermediate filaments (IFs) commonly have structural elements of a central α-helical coiled-coil domain consisting of coil 1a, coil 1b, coil 2, and their flanking linkers. Recently, the crystal structure of a long lamin A/C fragment was determined and showed detailed features of a tetrameric unit. The structure further suggested a new binding mode between tetramers, designated eA22, where a parallel overlap of coil 1a and coil 2 is the critical interaction. This study investigated the biochemical effects of genetic mutations causing human diseases, focusing on the eA22 interaction. The mutant proteins exhibited either weakened or augmented interactions between coil 1a and coil 2. The ensuing biochemical results indicated that the interaction requires the separation of the coiled-coils in the N-terminal of coil 1a and the C-terminal of coil 2, coupled with the structural transition in the central α-helical rod domain. This study provides insight into the role of coil 1a as a molecular regulator in the elongation of IF proteins.

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