Neighboring Residue Effects in Terminally Blocked Dipeptides: Implications for Residual Secondary Structures in Intrinsically Unfolded/Disordered Proteins

Chirality ◽  
2014 ◽  
Vol 26 (9) ◽  
pp. 443-452 ◽  
Author(s):  
Young-Sang Jung ◽  
Kwang-Im Oh ◽  
Geum-Sook Hwang ◽  
Minhaeng Cho
Keyword(s):  
Secondary Structures ◽  
Disordered Proteins ◽  
Neighboring Residue

scholarly journals Transient Secondary Structures as General Target-Binding Motifs in Intrinsically Disordered Proteins

2018 ◽  
Vol 19 (11) ◽  
pp. 3614 ◽  
Author(s):  
Do-Hyoung Kim ◽  
Kyou-Hoon Han
Keyword(s):  
Intrinsically Disordered Proteins ◽  
Three Dimensional ◽  
Secondary Structures ◽  
Disordered Proteins ◽  
Ample Evidence ◽  
Binding Motifs ◽  
Intrinsically Disordered ◽  
Long Time ◽  
Science Community ◽  
Target Binding

Intrinsically disordered proteins (IDPs) are unorthodox proteins that do not form three-dimensional structures under non-denaturing conditions, but perform important biological functions. In addition, IDPs are associated with many critical diseases including cancers, neurodegenerative diseases, and viral diseases. Due to the generic name of “unstructured” proteins used for IDPs in the early days, the notion that IDPs would be completely unstructured down to the level of secondary structures has prevailed for a long time. During the last two decades, ample evidence has been accumulated showing that IDPs in their target-free state are pre-populated with transient secondary structures critical for target binding. Nevertheless, such a message did not seem to have reached with sufficient clarity to the IDP or protein science community largely because similar but different expressions were used to denote the fundamentally same phenomenon of presence of such transient secondary structures, which is not surprising for a quickly evolving field. Here, we summarize the critical roles that these transient secondary structures play for diverse functions of IDPs by describing how various expressions referring to transient secondary structures have been used in different contexts.

Animal Actin Phylogeny and RNA Secondary Structure Study

2015 ◽  
Vol 5 (1) ◽  
pp. 46-61 ◽  
Author(s):  
Bibhuti Prasad Barik
Keyword(s):  
Large Scale ◽  
Secondary Structures ◽  
Structural Features ◽  
Structure Study ◽  
Disordered Proteins ◽  
Rna Secondary Structures ◽  
Large Scale Data ◽  
In Silico Study ◽  
Very High ◽  
Scale Data

Animal actin is a diverse and evolutionarily ancient protein. Actin genes and their corresponding protein sequences were used to infer phylogenetic affiliations. The study indicated that several species appear to be polyphyletic and several unrelated species appear to share the same clade. Consensus actin RNA secondary structures showed that the structural features of all forms were quite distinct and different from each other. This observation supports the phylogenetic inference in which similarly named species clustered together based on their lifestyles. Consideration of actin gene geneology and consensus RNA secondary structures could be used as a possible phylogenetic marker among diverse species of the animal kingdom for large scale data analysis. In-silico study revealed variations among the groups. The percentages of long disordered regions in proteins were found to be very high in all forms. Such findings suggest that the complexity and ability to adapt in diverse habitats by species may be due to higher percentage of disordered proteins.

scholarly journals Novel NMR Assignment Strategy Reveals Structural Heterogeneity in Solution of the nsP3 HVD Domain of Venezuelan Equine Encephalitis Virus

Molecules ◽  
2020 ◽  
Vol 25 (24) ◽  
pp. 5824
Author(s):  
Peter Agback ◽  
Andrey Shernyukov ◽  
Francisco Dominguez ◽  
Tatiana Agback ◽  
Elena I. Frolova
Keyword(s):  
Secondary Structures ◽  
Venezuelan Equine Encephalitis Virus ◽  
Encephalitis Virus ◽  
Disordered Proteins ◽  
Free Form ◽  
Venezuelan Equine Encephalitis ◽  
Complex Assembly ◽  
Replication Complex ◽  
Equine Encephalitis Virus ◽  
Intrinsically Disordered

In recent years, intrinsically disordered proteins (IDPs) and disordered domains have attracted great attention. Many of them contain linear motifs that mediate interactions with other factors during formation of multicomponent protein complexes. NMR spectrometry is a valuable tool for characterizing this type of interactions on both amino acid (aa) and atomic levels. Alphaviruses encode a nonstructural protein nsP3, which drives viral replication complex assembly. nsP3 proteins contain over 200-aa-long hypervariable domains (HVDs), which exhibits no homology between different alphavirus species, are predicted to be intrinsically disordered and appear to be critical for alphavirus adaptation to different cells. Previously, we have shown that nsP3 HVD of chikungunya virus (CHIKV) is completely disordered with low tendency to form secondary structures in free form. In this new study, we used novel NMR approaches to assign the spectra for the nsP3 HVD of Venezuelan equine encephalitis virus (VEEV). The HVDs of CHIKV and VEEV have no homology but are both involved in replication complex assembly and function. We have found that VEEV nsP3 HVD is also mostly disordered but contains a short stable α-helix in its C-terminal fragment, which mediates interaction with the members of cellular Fragile X syndrome protein family. Our NMR data also suggest that VEEV HVD has several regions with tendency to form secondary structures.

Effects of Acid and Alkali on the Light Absorption, Energy Transfer and Protein Secondary Structures of Core Antenna Subunits CP43 and CP47 of Photosystem II

2004 ◽  
Vol 79 (3) ◽  
pp. 291 ◽  
Author(s):  
Guo Shukui ◽  
Tang Chongqin ◽  
Yang Zhenle ◽  
Li Liangbi ◽  
Kuang Tingyun ◽  
...  
Keyword(s):  
Energy Transfer ◽  
Photosystem Ii ◽  
Light Absorption ◽  
Secondary Structures ◽  
Protein Secondary Structures ◽  
Absorption Energy

Sequence Specificity Despite Intrinsic Disorder: How a Disease-Associated Val/Met Polymorphism Shifts Tertiary Interactions in a Long Disordered Protein

2019 ◽  
Author(s):  
Ruchi Lohia ◽  
Reza Salari ◽  
Grace Brannigan
Keyword(s):  
Secondary Structure ◽  
Electrostatic Interactions ◽  
Intrinsically Disordered Proteins ◽  
Disordered Proteins ◽  
Sequence Specificity ◽  
Intrinsically Disordered ◽  
Specific Effects ◽  
Heterogeneous Polymer ◽  
Non Local ◽  
Dynamics Simulations

<div>The role of electrostatic interactions and mutations that change charge states in intrinsically disordered proteins (IDPs) is well-established, but many disease-associated mutations in IDPs are charge-neutral. The Val66Met single nucleotide polymorphism (SNP) encodes a hydrophobic-to-hydrophobic mutation at the midpoint of the prodomain of precursor brain-derived neurotrophic factor (BDNF), one of the earliest SNPs to be associated with neuropsychiatric disorders, for which the underlying molecular mechanism is unknown. Here we report on over 250 μs of fully-atomistic, explicit solvent, temperature replica exchange molecular dynamics simulations of the 91 residue BDNF prodomain, for both the V66 and M66 sequence.</div><div>The simulations were able to correctly reproduce the location of both local and non-local secondary changes due to the Val66Met mutation when compared with NMR spectroscopy. We find that the local structure change is mediated via entropic and sequence specific effects. We show that the highly disordered prodomain can be meaningfully divided into domains based on sequence alone. Monte Carlo simulations of a self-excluding heterogeneous polymer, with monomers representing each domain, suggest the sequence would be effectively segmented by the long, highly disordered polyampholyte near the sequence midpoint. This is qualitatively consistent with observed interdomain contacts within the BDNF prodomain, although contacts between the two segments are enriched relative to the self-excluding polymer. The Val66Met mutation increases interactions across the boundary between the two segments, due in part to a specific Met-Met interaction with a Methionine in the other segment. This effect propagates to cause the non-local change in secondary structure around the second methionine, previously observed in NMR. The effect is not mediated simply via changes in inter-domain contacts but is also dependent on secondary structure formation around residue 66, indicating a mechanism for secondary structure coupling in disordered proteins. </div>

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