scholarly journals A thermodynamic insight into the recognition of hydrophilic and hydrophobic amino acids in pure water by aza-scorpiand type receptors

2015 ◽  
Vol 13 (3) ◽  
pp. 843-850 ◽  
Author(s):  
Salvador Blasco ◽  
Begoña Verdejo ◽  
Carla Bazzicalupi ◽  
Antonio Bianchi ◽  
Claudia Giorgi ◽  
...  
Keyword(s):  
Amino Acids ◽  
Pure Water ◽  
Thermodynamic Studies ◽  
Hydrophobic Amino Acids ◽  
Insight Into

Thermodynamic studies about the interaction of scorpiand aza-macrocycles with amino acids in water show entropy driven stabilisations often associated with solvation/desolvation processes.

scholarly journals Comparing Native Crystal Structures and AlphaFold2 Predicted Water-Soluble G Protein-Coupled Receptor QTY Variants

Life ◽  
2021 ◽  
Vol 11 (12) ◽  
pp. 1285
Author(s):  
Michael A. Skuhersky ◽  
Fei Tao ◽  
Rui Qing ◽  
Eva Smorodina ◽  
David Jin ◽  
...  
Keyword(s):  
Amino Acids ◽  
Chemokine Receptors ◽  
Protein Structures ◽  
Water Soluble ◽  
Transmembrane Helices ◽  
3 Dimensional ◽  
X Ray Crystallography ◽  
Hydrophobic Amino Acids ◽  
G Protein Coupled ◽  
Insight Into

Accurate predictions of 3-dimensional protein structures by AlphaFold2 is a game-changer for biology, especially for structural biology. Here we present the studies of several native chemokine receptors including CCR5, CCR9, CXCR2 and CXCR4 determined by X-ray crystallography, and their water-soluble QTY counter parts predicted by AlphaFold2. In the native structures, there are hydrophobic amino acids leucine (L), isoleucine (I), valine (V) and phenylalanine (F) in the transmembrane helices. These hydrophobic amino acids are systematically replaced by hydrophilic amino acids glutamine (Q), threonine (T), and tyrosine (Y). Thus, the QTY variants become water-soluble. We also present the superimposed structures of native CCR10, CXCR5, CXCR7 and an olfactory receptor OR1D2 and their water-soluble QTY variants. Since the CryoEM structural determinations for the QTY variants of CCR10QTY and OR1D2QTY are in progress, it will be of interest to compare them when the structures become available. The superimposed structures show remarkable similarity within RMSD 1Å–2Å despite significant sequence differences (~26%–~33%). We also show the differences of hydrophobicity patches between the native GPCR and their QTY variants. Our study provides insight into the subtle differences between the hydrophobic helices and hydrophilic helices, and may further stimulate designs of water-soluble membrane proteins and other aggregated proteins.

scholarly journals Nucleocytoplasmic Shuttling of p53 Is Essential for MDM2-Mediated Cytoplasmic Degradation but Not Ubiquitination

2003 ◽  
Vol 23 (18) ◽  
pp. 6396-6405 ◽  
Author(s):  
Kevin O'Keefe ◽  
Huiping Li ◽  
Yanping Zhang
Keyword(s):  
Amino Acids ◽  
Nuclear Export ◽  
Basic Amino Acid ◽  
Nucleocytoplasmic Transport ◽  
Nuclear Pore ◽  
Nucleocytoplasmic Shuttling ◽  
Localization Signal ◽  
Hydrophobic Amino Acids ◽  
Insight Into

ABSTRACT As a shuttling protein, p53 is constantly transported through the nuclear pore complex. p53 nucleocytoplasmic transport is carried out by a bipartite nuclear localization signal (NLS) located at its C-terminal domain and two nuclear export signals (NES) located in its N- and C-terminal regions, respectively. The role of nucleocytoplasmic shuttling in p53 ubiquitination and degradation has been a subject of debate. Here we show that the two basic amino acid groups in the p53 bipartite NLS function collaboratively to import p53. Mutations disrupting individual amino acids in the NLS, although causing accumulation of p53 in the cytoplasm to various degrees, reduce but do not eliminate the NLS activity, and these mutants remain sensitive to MDM2 degradation. However, disrupting both parts of the bipartite NLS completely blocks p53 from entering the nucleus and causes p53 to become resistant to MDM2-mediated degradation. Similarly, mutations disrupting four conserved hydrophobic amino acids in the p53 C-terminal NES block p53 export and prohibit it from MDM2 degradation. We also show that colocalization of a nonshuttling p53 with MDM2 either in the nucleus or in the cytoplasm is sufficient for MDM2-induced p53 polyubiquitination but not degradation. Our data provide new insight into the mechanism and regulation of p53 nucleocytoplasmic shuttling and degradation.

13C nuclear magnetic resonance study of cyclodipeptides containing 13C enriched hydrophobic amino acids

1980 ◽  
Vol 45 (2) ◽  
pp. 482-490 ◽  
Author(s):  
Jaroslav Vičar ◽  
François Piriou ◽  
Pierre Fromageot ◽  
Karel Bláha ◽  
Serge Fermandjian
Keyword(s):  
Amino Acids ◽  
Nuclear Magnetic Resonance ◽  
Nuclear Magnetic Resonance Study ◽  
Coupling Constants ◽  
Side Chain ◽  
Amino Acid Residues ◽  
Magnetic Resonance Study ◽  
Side Chain Conformation ◽  
13C Nuclear Magnetic Resonance ◽  
Hydrophobic Amino Acids

The diastereoisomeric pairs of cyclodipeptides cis- and trans-cyclo(Ala-Ala), cyclo(Ala-Phe), cyclo(Val-Val) and cyclo(Leu-Leu) containing 85% 13C enriched amino-acid residues were synthesized and their 13C-13C coupling constants were measured. The combination of 13C-13C and 1H-1H coupling constants enabled to estimate unequivocally the side chain conformation of the valine and leucine residues.

Volatile Anesthetics Affect Nutrient Availability in Yeast

Genetics ◽  
2002 ◽  
Vol 161 (2) ◽  
pp. 563-574
Author(s):  
Laura K Palmer ◽  
Darren Wolfe ◽  
Jessica L Keeley ◽  
Ralph L Keil
Keyword(s):  
Amino Acids ◽  
Nutrient Availability ◽  
Wild Type Strain ◽  
Volatile Anesthetic ◽  
Volatile Anesthetics ◽  
Wild Type ◽  
Anesthetic Exposure ◽  
Sites Of Action ◽  
Insight Into ◽  
Lines Of Evidence

Abstract Volatile anesthetics affect all cells and tissues tested, but their mechanisms and sites of action remain unknown. To gain insight into the cellular activities of anesthetics, we have isolated genes that, when overexpressed, render Saccharomyces cerevisiae resistant to the volatile anesthetic isoflurane. One of these genes, WAK3/TAT1, encodes a permease that transports amino acids including leucine and tryptophan, for which our wild-type strain is auxotrophic. This suggests that availability of amino acids may play a key role in anesthetic response. Multiple lines of evidence support this proposal: (i) Deletion or overexpression of permeases that transport leucine and/or tryptophan alters anesthetic response; (ii) prototrophic strains are anesthetic resistant; (iii) altered concentrations of leucine and tryptophan in the medium affect anesthetic response; and (iv) uptake of leucine and tryptophan is inhibited during anesthetic exposure. Not all amino acids are critical for this response since we find that overexpression of the lysine permease does not affect anesthetic sensitivity. These findings are consistent with models in which anesthetics have a physiologically important effect on availability of specific amino acids by altering function of their permeases. In addition, we show that there is a relationship between nutrient availability and ubiquitin metabolism in this response.

scholarly journals Cryo-EM structure of amyloid fibrils formed by the entire low complexity domain of TDP-43

2021 ◽  
Vol 12 (1) ◽  
Author(s):  
Qiuye Li ◽  
W. Michael Babinchak ◽  
Witold K. Surewicz
Keyword(s):  
Amyloid Fibrils ◽  
Low Complexity ◽  
Structural Features ◽  
Protein Fragments ◽  
Hydrophobic Residues ◽  
Backbone Conformation ◽  
Hydrophobic Amino Acids ◽  
Insight Into ◽  
Lateral Sclerosis

AbstractAmyotrophic lateral sclerosis and several other neurodegenerative diseases are associated with brain deposits of amyloid-like aggregates formed by the C-terminal fragments of TDP-43 that contain the low complexity domain of the protein. Here, we report the cryo-EM structure of amyloid formed from the entire TDP-43 low complexity domain in vitro at pH 4. This structure reveals single protofilament fibrils containing a large (139-residue), tightly packed core. While the C-terminal part of this core region is largely planar and characterized by a small proportion of hydrophobic amino acids, the N-terminal region contains numerous hydrophobic residues and has a non-planar backbone conformation, resulting in rugged surfaces of fibril ends. The structural features found in these fibrils differ from those previously found for fibrils generated from short protein fragments. The present atomic model for TDP-43 LCD fibrils provides insight into potential structural perturbations caused by phosphorylation and disease-related mutations.

scholarly journals N-terminal Hydrophobic Amino Acids of Activating Transcription Factor 5 (ATF5) Protein Confer Interleukin 1β (IL-1β)-induced Stabilization

2013 ◽  
Vol 289 (7) ◽  
pp. 3888-3900 ◽  
Author(s):  
Takanori Abe ◽  
Masaki Kojima ◽  
Satoshi Akanuma ◽  
Hiromi Iwashita ◽  
Takashi Yamazaki ◽  
...  
Keyword(s):  
Amino Acids ◽  
Transcription Factor ◽  
Interleukin 1Β ◽  
Hydrophobic Amino Acids ◽  
Activating Transcription Factor

scholarly journals Water-Soluble Blue Fluorescent Nonconjugated Polymer Dots from Hyaluronic Acid and Hydrophobic Amino Acids

ACS Omega ◽  
2021 ◽  
Author(s):  
Deep S. Bhattacharya ◽  
Aishwarya Bapat ◽  
Denis Svechkarev ◽  
Aaron M. Mohs
Keyword(s):  
Amino Acids ◽  
Hyaluronic Acid ◽  
Water Soluble ◽  
Polymer Dots ◽  
Hydrophobic Amino Acids

scholarly journals Insight into anaerobic methanotrophy from 13C/12C- amino acids and 14C/12C-ANME cells in seafloor microbial ecology

2018 ◽  
Vol 8 (1) ◽  
Author(s):  
Yoshinori Takano ◽  
Yoshito Chikaraishi ◽  
Hiroyuki Imachi ◽  
Yosuke Miyairi ◽  
Nanako O. Ogawa ◽  
...  
Keyword(s):  
Amino Acids ◽  
Microbial Ecology ◽  
Insight Into

scholarly journals Deciphering the Enigma of the Histone H2A.Z-1/H2A.Z-2 Isoforms: Novel Insights and Remaining Questions

Cells ◽  
2020 ◽  
Vol 9 (5) ◽  
pp. 1167
Author(s):  
Manjinder S. Cheema ◽  
Katrina V. Good ◽  
Bohyun Kim ◽  
Heddy Soufari ◽  
Connor O’Sullivan ◽  
...  
Keyword(s):  
Gene Expression ◽  
Amino Acids ◽  
Dna Damage ◽  
Chromosome Segregation ◽  
Multiple Roles ◽  
Histone H2a ◽  
The Core ◽  
Structural Differences ◽  
Functional Involvement ◽  
Insight Into

The replication independent (RI) histone H2A.Z is one of the more extensively studied variant members of the core histone H2A family, which consists of many replication dependent (RD) members. The protein has been shown to be indispensable for survival, and involved in multiple roles from DNA damage to chromosome segregation, replication, and transcription. However, its functional involvement in gene expression is controversial. Moreover, the variant in several groups of metazoan organisms consists of two main isoforms (H2A.Z-1 and H2A.Z-2) that differ in a few (3–6) amino acids. They comprise the main topic of this review, starting from the events that led to their identification, what is currently known about them, followed by further experimental, structural, and functional insight into their roles. Despite their structural differences, a direct correlation to their functional variability remains enigmatic. As all of this is being elucidated, it appears that a strong functional involvement of isoform variability may be connected to development.

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