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Unstructured Proteins

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https://www.readbyqxmd.com/read/29234142/a-molecular-chaperone-activity-of-ccs-restores-the-maturation-of-sod1-fals-mutants
#1
Enrico Luchinat, Letizia Barbieri, Lucia Banci
Superoxide dismutase 1 (SOD1) is an important metalloprotein for cellular oxidative stress defence, that is mutated in familiar variants of Amyotrophic Lateral Sclerosis (fALS). Some mutations destabilize the apo protein, leading to the formation of misfolded, toxic species. The Copper Chaperone for SOD1 (CCS) transiently interacts with SOD1 and promotes its correct maturation by transferring copper and catalyzing disulfide bond formation. By in vitro and in-cell NMR, we investigated the role of the SOD-like domain of CCS (CCS-D2)...
December 12, 2017: Scientific Reports
https://www.readbyqxmd.com/read/29215674/bioinspired-dynamic-microcapsules
#2
N F D AlDala'een, W N K W Mohamad, N Alias, A M Ali, J Shaikh Mohammed
There is an increasing interest in bioinspired dynamic materials. Abundant illustrations of protein domains exist in nature, with remarkable ligand binding characteristics and structures that undergo conformational changes. For example, calmodulin (CaM) can have three conformational states, which are the unstructured Apo-state, Ca2+-bound ligand-exposed binding state, and compact ligand-bound state. CaM's mechanical response to biological cues is highly suitable for engineering dynamic materials. The distance between CaM globular terminals in the Ca2+-bound state is 5 nm and in the ligand-bound state is 1...
December 7, 2017: Soft Matter
https://www.readbyqxmd.com/read/29215267/new-structural-insights-into-formation-of-the-key-actin-regulating-wip-wasp-complex-determined-by-nmr-and-molecular-imaging
#3
Adi Halle-Bikovski, Sophia Fried, Eva Rozentur-Shkop, Guy Biber, Hadassa Shaked, Noah Joseph, Mira Barda-Saad, Jordan H Chill
Wiskott-Aldrich syndrome protein (WASp) is exclusively expressed in hematopoietic cells and responsible for actin-dependent processes, including cellular activation, migration, and invasiveness. The C-terminal domain of WASp-Interacting Protein (WIP) binds to WASp and regulates its activity by shielding it from degradation in a phosphorylation dependent manner as we previously demonstrated. Mutations in the WAS-encoding gene lead to the primary immunodeficiencies Wiskott-Aldrich syndrome (WAS) and X-linked thrombocytopenia (XLT)...
December 7, 2017: ACS Chemical Biology
https://www.readbyqxmd.com/read/29211802/hidden-%C3%AE-helical-propensity-segments-within-disordered-regions-of-the-transcriptional-activator-chop
#4
Ángeles Canales, Marcel Rösinger, Javier Sastre, Isabella C Felli, Jesús Jiménez-Barbero, Guillermo Giménez-Gallego, Carlos Fernández-Tornero
C/EBP-homologous protein (CHOP) is a key determinant of the apoptotic response to endoplasmic reticulum stress or DNA damage. As a member of the C/EBP family, CHOP contains a low complexity N-terminal region involved in transcriptional activation, followed by a bZIP that binds DNA after dimerization. However, in contrast to other C/EBPs, CHOP directs binding to non-canonical C/EBP sites due to unique substitutions in its DNA-binding domain. Herein, we show that the N-terminal region of CHOP is intrinsically unstructured but contains two segments presenting α-helical propensity...
2017: PloS One
https://www.readbyqxmd.com/read/29200271/the-next-frontier-quantitative-biochemistry-in-living-cells
#5
Alf Honigmann, André Nadler
Researchers striving to convert biology into an exact science foremost rely on structural biology and biochemical reconstitution approaches to obtain quantitative data. However, cell biological research is moving at an ever-accelerating speed into areas where these approaches loose much of their edge. Intrinsically unstructured proteins and biochemical interaction networks composed of interchangeable, multivalent and unspecific interactions pose unique challenges to quantitative biology, as do processes that occur in discrete cellular microenvironments...
December 4, 2017: Biochemistry
https://www.readbyqxmd.com/read/29191749/design-and-verification-of-halogen-bonding-system-at-the-complex-interface-of-human-fertilization-related-mup-pdz5-domain-with-camk-s-c-terminal-peptide
#6
Juan Wang, Yunjie Guo, Xue Zhang
Calmodulin-dependent protein kinase (CAMK) is physiologically activated in fertilized human oocytes and is involved in the Ca2+ response pathways that link the fertilization calmodulin signal to meiosis resumption and cortical granule exocytosis. The kinase has an unstructured C-terminal tail that can be recognized and bound by the PDZ5 domain of its cognate partner, the multi-PDZ domain protein (MUP). In the current study, we reported a rational biomolecular design of halogen-bonding system at the complex interface of CAMK's C-terminal peptide with MUP PDZ5 domain by using high-level computational approaches...
November 21, 2017: Computational Biology and Chemistry
https://www.readbyqxmd.com/read/29185737/parallel-tempering-of-dark-matter-from-the-ebola-virus-proteome-comparison-of-charmm36m-and-charmm22-force-fields-with-implicit-solvent
#7
Mark A Olson
Intrinsically disordered proteins are characterized by their large manifold of thermally accessible conformations and their related statistical weights making them an interesting target of simulation studies. To assess the development of a computational framework for modeling this distinct class of proteins, this work examines temperature-based replica exchange simulations to generate a conformational ensemble of a 28-residue peptide from the Ebola virus protein VP35. Starting from a prefolded helix-β-turn-helix topology observed in a crystallographic assembly, the simulation strategy tested is the recently refined CHARMM36m force field combined with a generalized Born solvent model...
November 29, 2017: Journal of Chemical Information and Modeling
https://www.readbyqxmd.com/read/29168638/homology-modeling-and-molecular-dynamics-simulation-combined-with-x-ray-solution-scattering-defining-protein-structures-of-thromboxane-and-prostacyclin-synthases
#8
Hsiao-Ching Yang, Cheng-Han Yang, Ming Yi Huang, Jyh-Feng Lu, Jinn-Shyan Wang, Yi-Qi Yeh, U-Ser Jeng
A combination of molecular dynamics (MD) simulations and X-ray scattering (SAXS) has emerged as the approach of choice for studying protein structures and dynamics in solution. This approach has potential applications for membrane proteins that neither are soluble nor form crystals easily. We explore the water-coupled dynamic structures of thromboxane synthase (TXAS) and prostacyclin synthase (PGIS) from scanning HPLC-SAXS measurements combined with MD ensemble analyses. Both proteins are heme-containing enzymes in the cytochrome P450 family, known as prostaglandin H2 (PGH2) isomerase, with counter functions in regulation of platelet aggregation...
November 23, 2017: Journal of Physical Chemistry. B
https://www.readbyqxmd.com/read/29165665/novel-structural-features-drive-dna-binding-properties-of-cmr-a-crp-family-protein-in-tb-complex-mycobacteria
#9
Sridevi Ranganathan, Jonah Cheung, Michael Cassidy, Christopher Ginter, Janice D Pata, Kathleen A McDonough
Mycobacterium tuberculosis (Mtb) encodes two CRP/FNR family transcription factors (TF) that contribute to virulence, Cmr (Rv1675c) and CRPMt (Rv3676). Prior studies identified distinct chromosomal binding profiles for each TF despite their recognizing overlapping DNA motifs. The present study shows that Cmr binding specificity is determined by discriminator nucleotides at motif positions 4 and 13. X-ray crystallography and targeted mutational analyses identified an arginine-rich loop that expands Cmr's DNA interactions beyond the classical helix-turn-helix contacts common to all CRP/FNR family members and facilitates binding to imperfect DNA sequences...
November 20, 2017: Nucleic Acids Research
https://www.readbyqxmd.com/read/29148741/controlling-association-and-separation-of-gold-nanoparticles-with-computationally-designed-zinc-coordinating-proteins
#10
Matthew J Eibling, Christopher M MacDermaid, Zhaoxia Qian, Christopher J Lanci, So-Jung Park, Jeffery G Saven
Functionalization of nanoparticles with biopolymers has yielded a wide range of structured and responsive hybrid materials. DNA provides the ability to program length and recognition using complementary oligonucleotide sequences. Nature more often leverages the versatility of proteins, however, where structure, assembly, and recognition are more subtle to engineer. Herein, a protein was computationally designed to present multiple Zn(2+) coordination sites and cooperatively self-associate to form an antiparallel helical homodimer...
November 17, 2017: Journal of the American Chemical Society
https://www.readbyqxmd.com/read/29140698/mutation-induced-deamidation-of-corneal-dystrophy-related-transforming-growth-factor-%C3%AE-induced-protein
#11
Nadia Sukusu Nielsen, Dennis Wilkens Juhl, Ebbe Toftgaard Poulsen, Marie V Lukassen, Emil Christian Poulsen, Michael W Risør, Carsten Scavenius, Jan J Enghild
Mutations in the transforming growth factor β-induced protein (TGFBIp) cause phenotypically diverse corneal dystrophies, where protein aggregation in the cornea leads to severe visual impairment. Previous studies have shown a relationship between mutant-specific corneal dystrophy phenotypes and the thermodynamic stability of TGFBIp. Using liquid chromatography-tandem mass spectrometry and nuclear magnetic resonance (NMR), we investigated correlations between the structural integrity of disease-related mutants of the fourth FAS1 domain (FAS1-4) and deamidation of TGFBIp residue Asn622...
November 22, 2017: Biochemistry
https://www.readbyqxmd.com/read/29140480/the-intrinsically-disordered-n-terminal-arm-of-the-brome-mosaic-virus-coat-protein-specifically-recognizes-the-rna-motif-that-directs-the-initiation-of-viral-rna-replication
#12
Alexander Jacobs, Haley Hoover, Edward Smith, David E Clemmer, Chul-Hyun Kim, C Cheng Kao
In the brome mosaic virus (BMV) virion, the coat protein (CP) selectively contacts the RNA motifs that regulate translation and RNA replication (Hoover et al., 2016. J. Virol. 90, 7748). We hypothesize that the unstructured N-terminal arm (NTA) of the BMV CP can specifically recognize RNA motifs. Using ion mobility spectrometry-mass spectrometry, we demonstrate that peptides containing the NTA of the CP were found to preferentially bind to an RNA hairpin motif that directs the initiation of BMV RNA synthesis...
November 11, 2017: Nucleic Acids Research
https://www.readbyqxmd.com/read/29138440/structural-basis-for-dna-recognition-of-a-single-stranded-dna-binding-protein-from-enterobacter-phage-enc34
#13
Elina Cernooka, Janis Rumnieks, Kaspars Tars, Andris Kazaks
Modern DNA sequencing capabilities have led to the discovery of a large number of new bacteriophage genomes, which are a rich source of novel proteins with an unidentified biological role. The genome of Enterobacter cancerogenus bacteriophage Enc34 contains several proteins of unknown function that are nevertheless conserved among distantly related phages. Here, we report the crystal structure of a conserved Enc34 replication protein ORF6 which contains a domain of unknown function DUF2815. Despite the low (~15%) sequence identity, the Enc34 ORF6 structurally resembles the gene 2...
November 14, 2017: Scientific Reports
https://www.readbyqxmd.com/read/29138239/expanding-the-chondroitin-glycoproteome-of-caenorhabditis-elegans
#14
Fredrik Noborn, Alejandro Gomez Toledo, Waqas Nasir, Jonas Nilsson, Tabea Dierker, Lena Kjellén, Göran Larson
Chondroitin sulfate proteoglycans (CSPGs) are important structural components of connective tissues in essentially all metazoan organisms. In vertebrates, CSPGs are involved also in more specialized processes such as neurogenesis and growth factor signaling. In invertebrates, however, knowledge of CSPGs core proteins and proteoglycan-related functions is relatively limited, even for Caenorhabditis elegans. This nematode produces large amounts of non-sulfated chondroitin in addition to low-sulfated chondroitin sulfate chains...
November 14, 2017: Journal of Biological Chemistry
https://www.readbyqxmd.com/read/29136196/analysis-of-the-natively-unstructured-rna-protein-recognition-core-in-the-escherichia-coli-rna-degradosome-and-its-interactions-with-regulatory-rna-hfq-complexes
#15
Heather A Bruce, Dijun Du, Dijana Matak-Vinkovic, Katarzyna J Bandyra, R William Broadhurst, Esther Martin, Frank Sobott, Alexander V Shkumatov, Ben F Luisi
The RNA degradosome is a multi-enzyme assembly that plays a central role in the RNA metabolism of Escherichia coli and numerous other bacterial species including pathogens. At the core of the assembly is the endoribonuclease RNase E, one of the largest E. coli proteins and also one that bears the greatest region predicted to be natively unstructured. This extensive unstructured region, situated in the C-terminal half of RNase E, is punctuated with conserved short linear motifs that recruit partner proteins, direct RNA interactions, and enable association with the cytoplasmic membrane...
November 9, 2017: Nucleic Acids Research
https://www.readbyqxmd.com/read/29127738/concerted-millisecond-timescale-dynamics-in-the-intrinsically-disordered-carboxyl-terminus-of-%C3%AE-tubulin-induced-by-mutation-of-a-conserved-tyrosine-residue
#16
Jason Harris, Maria Shadrina, Carlos Oliver, Jackie Vogel, Anthony Mittermaier
Tubulins are an ancient family of eukaryotic proteins characterized by an amino-terminal globular domain and disordered carboxyl terminus. These carboxyl termini play important roles in modulating the behavior of microtubules in living cells. However, the atomic-level basis of their function is not well understood. These regions contain multiple acidic residues and their overall charges are modulated in vivo by post-translational modifications, e.g. phosphorylation. In this study, we describe an application of NMR and computer Monte Carlo simulations to investigate how the modification of local charge alters the conformational sampling of the γ-tubulin carboxyl terminus...
November 11, 2017: Protein Science: a Publication of the Protein Society
https://www.readbyqxmd.com/read/29127198/probing-the-metastable-state-of-influenza-hemagglutinin
#17
Carolyn N Kingsley, Aleksandar Antanasijevic, Helena Palka-Hamblin, Matthew Durst, Benjamin Ramirez, Arnon Lavie, Michael Caffrey
Viral entry into host cells is mediated by membrane proteins in a metastable state that transition to a more stable state upon a stimulus. For example, in the influenza envelope protein hemagglutinin (HA), the low pH in the endosome triggers a transition from the metastable prefusion conformation to the stable fusion conformation. To identify probes that interfere with HA function, here we screened a library of H7 HA peptides for inhibition of H7 HA-mediated entry. We discovered a peptide, PEP87 (WSYNAELLVAMENQHTI), that inhibited H7 and H5 HA-mediated entry...
November 10, 2017: Journal of Biological Chemistry
https://www.readbyqxmd.com/read/29119515/the-prosecco-server-for-chemical-shift-predictions-in-ordered-and-disordered-proteins
#18
Máximo Sanz-Hernández, Alfonso De Simone
The chemical shifts measured in solution-state and solid-state nuclear magnetic resonance (NMR) are powerful probes of the structure and dynamics of protein molecules. The exploitation of chemical shifts requires methods to correlate these data with the protein structures and sequences. We present here an approach to calculate accurate chemical shifts in both ordered and disordered proteins using exclusively the information contained in their sequences. Our sequence-based approach, protein sequences and chemical shift correlations (PROSECCO), achieves the accuracy of the most advanced structure-based methods in the characterization of chemical shifts of folded proteins and improves the state of the art in the study of disordered proteins...
November 8, 2017: Journal of Biomolecular NMR
https://www.readbyqxmd.com/read/29116080/structural-basis-for-high-affinity-actin-binding-revealed-by-a-%C3%AE-iii-spectrin-sca5-missense-mutation
#19
Adam W Avery, Michael E Fealey, Fengbin Wang, Albina Orlova, Andrew R Thompson, David D Thomas, Thomas S Hays, Edward H Egelman
Spinocerebellar ataxia type 5 (SCA5) is a neurodegenerative disease caused by mutations in the cytoskeletal protein β-III-spectrin. Previously, a SCA5 mutation resulting in a leucine-to-proline substitution (L253P) in the actin-binding domain (ABD) was shown to cause a 1000-fold increase in actin-binding affinity. However, the structural basis for this increase is unknown. Here, we report a 6.9 Å cryo-EM structure of F-actin complexed with the L253P ABD. This structure, along with co-sedimentation and pulsed-EPR measurements, demonstrates that high-affinity binding caused by the CH2-localized mutation is due to opening of the two CH domains...
November 7, 2017: Nature Communications
https://www.readbyqxmd.com/read/29109287/charged-residues-in-the-h-ns-linker-drive-dna-binding-and-gene-silencing-in-single-cells
#20
Yunfeng Gao, Yong Hwee Foo, Ricksen S Winardhi, Qingnan Tang, Jie Yan, Linda J Kenney
Nucleoid-associated proteins (NAPs) facilitate chromosome organization in bacteria, but the precise mechanism remains elusive. H-NS is a NAP that also plays a major role in silencing pathogen genes. We used genetics, single-particle tracking in live cells, superresolution microscopy, atomic force microscopy, and molecular dynamics simulations to examine H-NS/DNA interactions in single cells. We discovered a role for the unstructured linker region connecting the N-terminal oligomerization and C-terminal DNA binding domains...
November 6, 2017: Proceedings of the National Academy of Sciences of the United States of America
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