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 QTY code enables design of detergent-free chemokine receptors that retain ligand-binding activities

2018 ◽  
Vol 115 (37) ◽  
pp. E8652-E8659 ◽  
Author(s):  
Shuguang Zhang ◽  
Fei Tao ◽  
Rui Qing ◽  
Hongzhi Tang ◽  
Michael Skuhersky ◽  
...  
Keyword(s):  
Membrane Proteins ◽  
Ligand Binding ◽  
Chemokine Receptors ◽  
Transmembrane Domain ◽  
Water Soluble ◽  
Helical Structures ◽  
Protein Gp41 ◽  
Hydrophobic Amino Acids ◽  
And Function ◽  
G Protein Coupled

Structure and function studies of membrane proteins, particularly G protein-coupled receptors and multipass transmembrane proteins, require detergents. We have devised a simple tool, the QTY code (glutamine, threonine, and tyrosine), for designing hydrophobic domains to become water soluble without detergents. Here we report using the QTY code to systematically replace the hydrophobic amino acids leucine, valine, isoleucine, and phenylalanine in the seven transmembrane α-helices of CCR5, CXCR4, CCR10, and CXCR7. We show that QTY code-designed chemokine receptor variants retain their thermostabilities, α-helical structures, and ligand-binding activities in buffer and 50% human serum. CCR5QTY, CXCR4QTY, and CXCR7QTY also bind to HIV coat protein gp41-120. Despite substantial transmembrane domain changes, the detergent-free QTY variants maintain stable structures and retain their ligand-binding activities. We believe the QTY code will be useful for designing water-soluble variants of membrane proteins and other water-insoluble aggregated proteins.

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 QTY Code-designed Water-soluble Fc-fusion Cytokine Receptors Bind to their Respective Ligands

QRB Discovery ◽  
2020 ◽  
Vol 1 ◽  
Author(s):  
Shilei Hao ◽  
David Jin ◽  
Shuguang Zhang ◽  
Rui Qing
Keyword(s):  
Chemokine Receptors ◽  
Protein Modification ◽  
Viral Infections ◽  
Critical Role ◽  
Water Soluble ◽  
Cytokine Receptors ◽  
Interleukin Receptors ◽  
Physiological Properties ◽  
Life Threatening ◽  
Hydrophobic Amino Acids

AbstractCytokine release syndrome (CRS), or ‘cytokine storm’, is the leading side effect during chimeric antigen receptor (CAR)-T therapy that is potentially life-threatening. It also plays a critical role in viral infections such as Coronavirus Disease 2019 (COVID-19). Therefore, efficient removal of excessive cytokines is essential for treatment. We previously reported a novel protein modification tool called the QTY code, through which hydrophobic amino acids Leu, Ile, Val and Phe are replaced by Gln (Q), Thr (T) and Tyr (Y). Thus, the functional detergent-free equivalents of membrane proteins can be designed. Here, we report the application of the QTY code on six variants of cytokine receptors, including interleukin receptors IL4Rα and IL10Rα, chemokine receptors CCR9 and CXCR2, as well as interferon receptors IFNγR1 and IFNλR1. QTY-variant cytokine receptors exhibit physiological properties similar to those of native receptors without the presence of hydrophobic segments. The receptors were fused to the Fc region of immunoglobulin G (IgG) protein to form an antibody-like structure. These QTY code-designed Fc-fusion receptors were expressed in Escherichia coli and purified. The resulting water-soluble fusion receptors bind to their respective ligands with Kd values affinity similar to isolated native receptors. Our cytokine receptor–Fc-fusion proteins potentially serve as an antibody-like decoy to dampen the excessive cytokine levels associated with CRS and COVID-19 infection.

scholarly journals Role of Computational Methods in Going beyond X-ray Crystallography to Explore Protein Structure and Dynamics

2018 ◽  
Vol 19 (11) ◽  
pp. 3401 ◽  
Author(s):  
Ashutosh Srivastava ◽  
Tetsuro Nagai ◽  
Arpita Srivastava ◽  
Osamu Miyashita ◽  
Florence Tama
Keyword(s):  
Protein Dynamics ◽  
Computational Methods ◽  
Protein Structures ◽  
Three Dimensional ◽  
Dimensional Structure ◽  
X Ray ◽  
X Ray Crystallography ◽  
Insight Into

Protein structural biology came a long way since the determination of the first three-dimensional structure of myoglobin about six decades ago. Across this period, X-ray crystallography was the most important experimental method for gaining atomic-resolution insight into protein structures. However, as the role of dynamics gained importance in the function of proteins, the limitations of X-ray crystallography in not being able to capture dynamics came to the forefront. Computational methods proved to be immensely successful in understanding protein dynamics in solution, and they continue to improve in terms of both the scale and the types of systems that can be studied. In this review, we briefly discuss the limitations of X-ray crystallography in studying protein dynamics, and then provide an overview of different computational methods that are instrumental in understanding the dynamics of proteins and biomacromolecular complexes.

scholarly journals Secretion of HLA-A and -B antigens via an alternative RNA splicing pathway.

1986 ◽  
Vol 163 (5) ◽  
pp. 1173-1190 ◽  
Author(s):  
M S Krangel
Keyword(s):  
Amino Acids ◽  
Cell Line ◽  
Rna Splicing ◽  
Leukemic Cell ◽  
Integral Membrane Protein ◽  
Water Soluble ◽  
Class I ◽  
Soluble Form ◽  
Similar Process ◽  
Hydrophobic Amino Acids

Human class I major histocompatibility antigens (HLA-A, -B and -C) are integral membrane protein heterodimers, which are anchored in the membrane via a stretch of hydrophobic amino acids near the carboxyl terminus of the heavy chain. It has previously been shown that a mutagenized cell line secretes a water soluble form of the HLA-A2 antigen, due to a pattern of RNA splicing that removes exon 5 (encoding the transmembrane hydrophobic amino acids) from mature, HLA-A2--encoding transcripts. The present study was undertaken to assess whether a similar process might be operative in nonmutagenized cells. It is shown that water soluble class I molecules (primarily HLA-A24) are secreted by the T leukemic cell line HPB-ALL, and that alternative splicing removes exon 5 from a fraction of HLA-A24--encoding transcripts. It is further shown that class I molecules are secreted, possibly in an allele-specific fashion, from a variety of tumor cells and normal cells. The possible relationship between these findings and previous reports of HLA-A and -B antigens in human serum is discussed.

scholarly journals Chemokine receptor specific for IP10 and mig: structure, function, and expression in activated T-lymphocytes.

1996 ◽  
Vol 184 (3) ◽  
pp. 963-969 ◽  
Author(s):  
M Loetscher ◽  
B Gerber ◽  
P Loetscher ◽  
S A Jones ◽  
L Piali ◽  
...  
Keyword(s):  
Amino Acids ◽  
T Lymphocytes ◽  
Chemokine Receptors ◽  
Reading Frame ◽  
Transmembrane Segments ◽  
Activated T Lymphocytes ◽  
Cc Chemokines ◽  
Receptor Cdna ◽  
G Protein Coupled ◽  
Human Receptor

A human receptor that is selective for the CXC chemokines IP10 and Mig was cloned and characterized. The receptor cDNA has an open reading frame of 1104-bp encoding a protein of 368 amino acids with a molecular mass of 40,659 dalton. The sequence includes seven putative transmembrane segments characteristic of G-protein coupled receptors. It shares 40.9 and 40.3% identical amino acids with the two IL-8 receptors, and 34.2-36.9% identity with the five known CC chemokine receptors. The IP10/Mig receptor is highly expressed in IL-2-activated T lymphocytes, but is not detectable in resting T lymphocytes. B lymphocytes, monocytes and granulocytes. It mediates Ca2+ mobilization and chemotaxis in response to IP10 and Mig, but does not recognize the CXC-chemokines IL-8, GRO alpha, NAP-2, GCP-2. ENA78, PF4, the CC-chemokines MCP-1, MCP-2, MCP-3, MCP-4, MIP-1 alpha, MIP-1 beta. RANTES, 1309, eotaxin, nor lymphotactin. The exclusive expression in activated T-lymphocytes is of high interest since the receptors for chemokines which have been shown so far to attract lymphocytes, e.g., MCP-1, MCP-2, MCP-3, MIP-1 alpha, MIP-1 beta, and RANTES, are also found in monocytes and granulocytes. The present observations suggest that the IP10/Mig receptor is involved in the selective recruitment of effector T cells.

scholarly journals Different tertiary interactions create the same important 3-D features in a divergent flavivirus xrRNA

2020 ◽  
Author(s):  
Rachel A. Jones ◽  
Anna-Lena Steckelberg ◽  
Matthew J. Szucs ◽  
Benjamin M. Akiyama ◽  
Quentin Vicens ◽  
...  
Keyword(s):  
Host Cell ◽  
Untranslated Region ◽  
Viral Rna ◽  
Genomic Rna ◽  
X Ray ◽  
3 Dimensional ◽  
X Ray Crystallography ◽  
Tertiary Interactions ◽  
Viral Genomic Rna ◽  
Insight Into

ABSTRACTDuring infection by a flavivirus (FV), cells accumulate noncoding subgenomic flavivirus RNAs (sfRNAs) that interfere with several antiviral pathways. These sfRNAs are formed by structured RNA elements in the 3′ untranslated region (UTR) of the viral genomic RNA, which block the progression of host cell exoribonucleases that have targeted the viral RNA for destruction. Previous work on these exoribonuclease-resistant RNAs (xrRNAs) from mosquito-borne FVs revealed a specific 3-dimensional fold with a unique topology in which a ring-like structure protectively encircles the 5′ end of the xrRNA. Conserved nucleotides make specific tertiary interactions that support this fold. Examination of more divergent FVs reveals differences in their 3′ UTR sequences, raising the question of whether they contain xrRNAs and if so, how they fold. To answer this, we demonstrated the presence of an authentic xrRNA in the 3′ UTR of the Tamana Bat Virus (TABV) and solved its structure by x-ray crystallography. The structure reveals conserved features from previously characterized xrRNAs, but in the TABV version these features are created through a novel set of tertiary interactions not previously seen in xrRNAs. This includes two important A-C interactions, four distinct backbone kinks, several ordered Mg2+ ions, and a C+-G-C base triple. The discovery that the same overall architecture can be achieved by very different sequences and interactions in distantly related flaviviruses provides insight into the diversity of this type of RNA and will inform searches for undiscovered xrRNAs in viruses and beyond.

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.

Sign in / Sign up

Export Citation Format

Share Document