'The '''QTY Code''' is a design method to transform [[membrane proteins]] that are intrinsically insoluble in water into variants with [[water solubility]], while retaining their structure and function. == Similar structures of amino acids == The QTY Code is based on two key molecular structural facts: 1) all 20 natural [[amino acids]] are found in [[alpha-helices]] regardless of their [[chemical properties]], although some amino acids have a higher propensity to form an [[alpha-helix]]; and, 2) several amino acids share striking structural similarities despite their very different chemical properties. These may be paired as: [[Glutamine]] (Q) vs [[Leucine]] (L); [[Threonine]] (T) vs [[Valine]] (V) and [[Isoleucine]] (I); and [[Tyrosine]] (Y) vs [[Phenylalanine]] (F).<ref name="Biochemistry textbook">{{cite book |last1=Stryer |first1=Lubert |title=Biochemistry |date=January 1, 1981 |publisher=W.H. Freeman and Company |edition=2}}</ref><ref name="Introduction to Protein Structure">{{cite book |last1=Branden |first1=Carl Ivar |last2=Tooze |first2=John |title=Introduction to Protein Structure |date=January 1, 1999 |publisher=Garland Science |isbn=9780815323051 |edition=2}}</ref> [[File:20-amino-acids-density-map.jpg|thumb|Shapes of the 20 natural amino acids as they appear in an experimental electron density map at 1.5 angstrom resolution.]] The QTY Code systematically replaces water-insoluble amino acids (L, V, I and F) with water-soluble amino acids (Q, T and Y) in transmembrane alpha-helices.<ref name="QTY code enables">{{cite journal |last1=Zhang |first1=Shuguang |last2=Tao |first2=Fei |last3=Qing |first3=Rui |last4=Tang |first4=Hongzhi |last5=Skuhersky |first5=Michael |last6=Corin |first6=Karolina |last7=Tegler |first7=Lotta |last8=Wassie |first8=Asmamaw |last9=Wassie |first9=Brook |last10=Kwon |first10=Yongwon |last11=Suter |first11=Bernhard |last12=Entzian |first12=Clemens |last13=Schubert |first13=Thomas |last14=Yang |first14=Ge |last15=Labahn |first15=Jörg |last16=Kubicek |first16=Jan |last17=Maertens |first17=Barbara |title=QTY code enables design of detergent-free chemokine receptors that retain ligand-binding activities |journal=PNAS |date=September 11, 2018 |volume=115 |issue=37 |pages=E8652–E8659 |doi=10.1073/pnas.1811031115 |pmid=30154163 |pmc=6140526 |doi-access=free |bibcode=2018PNAS..115E8652Z }}</ref> Thus, its application to membrane proteins changes the water-insoluble form of membrane proteins into water-soluble variants.<ref name="QTY code enables" /><ref name="QTY code designed">{{cite journal |last1=Qing |first1=Rui |last2=Skuhersky |first2=Michael |last3=Chung |first3=Haeyoon |last4=Badr |first4=Myriam |last5=Schubert |first5=Thomas |last6=Zhang |first6=Shuguang |title=QTY code designed thermostable and water-soluble chimeric chemokine receptors with tunable ligand affinity |journal=PNAS |date=December 17, 2019 |volume=116 |issue=51 |pages=25668–25676 |doi=10.1073/pnas.1909026116 |pmid=31776256 |pmc=6926000 |doi-access=free |bibcode=2019PNAS..11625668Q }}</ref> The QTY Code was specifically conceived to render [[G protein-coupled receptors]] (GPCRs) into a water-soluble form. Despite substantial [[transmembrane domain]] changes, the QTY variants of GPCRs maintain stable structure and [[ligand]] binding activities.<ref name="QTY code enables" /><ref name="QTY code designed" /><ref name="QTY Code-designed">{{cite journal |last1=Hao |first1=Shilei |last2=Jin |first2=David |last3=Zhang |first3=Shuguang |last4=Qing |first4=Rui |title=QTY Code-designed Water-soluble Fc-fusion Cytokine Receptors Bind to their Respective Ligands |journal=QRB Discovery |date=9 April 2020 |volume=1 |pages=e4 |doi=10.1017/qrd.2020.4 |pmid=34192260 |pmc=7419741 }}</ref><ref name="The G protein coupled">{{cite journal |last1=Tegler |first1=Lotta |last2=Corin |first2=Karolina |last3=Pick |first3=Horst |last4=Brookes |first4=Jennifer |last5=Skuhersky |first5=Michael |last6=Vogel |first6=Horst |last7=Zhang |first7=Shuguang |title=The G protein coupled receptor CXCR4 designed by the QTY code becomes more hydrophilic and retains cell signaling activity |journal=Scientific Reports |date=7 December 2020 |volume=10 |issue=1 |page=21371 |doi=10.1038/s41598-020-77659-x |pmid=33288780 |pmc=7721705 |bibcode=2020NatSR..1021371T }}</ref><ref name="Non-full-length Water-Soluble">{{cite journal |last1=Qing |first1=Rui |last2=Tao |first2=Fei |last3=Chatterjee |first3=Pranam |last4=Yang |first4=Gaojie |last5=Han |first5=Qiuyi |last6=Chung |first6=Haeyoon |last7=Ni |first7=Jun |last8=Suter |first8=Bernhard |last9=Kubicek |first9=Jan |last10=Maertens |first10=Barbara |last11=Schubert |first11=Thomas |last12=Blackburn |first12=Camron |last13=Zhang |first13=Shuguang |title=Non-full-length Water-Soluble CXCR4QTY and CCR5QTY Chemokine Receptors: Implication for Overlooked Truncated but Functional Membrane Receptors |journal=iScience |date=18 December 2020 |volume=23 |issue=12 |page=101670 |doi=10.1016/j.isci.2020.101670 |pmid=33376963 |pmc=7756140 |bibcode=2020iSci...23j1670Q }}</ref> [[File:H-bonds of N, Q, S, T, Y.tif|thumb|Hydrogen bond interactions between water and the amino acids (Courtesy of Michael Skuhersky, MIT)]] === Hydrogen bond interactions between water and the amino acids === The side chain of [[glutamine]] (Q) can form 4 [[hydrogen bond]]s with 4 [[water]] molecules. There are 2 hydrogen donors from [[nitrogen]] and 2 hydrogen acceptors for [[oxygen]]. The –OH group of [[threonine]] (T) and [[tyrosine]] (Y) can form 3 hydrogen bonds with 3 water molecules (2 H-acceptors and 1 H-donor).<ref name="Biochemistry textbook" /> Color code: Green = carbon, red = oxygen, blue = nitrogen, gray = hydrogen, yellow disks = hydrogen bonds. [[File:QTY Code.jpg|alt=The QTY code and how it replaces L, V, I, and F with Q, T, and Y. (A) Crystallographic electronic density maps of the following amino acids: leucine (L), asparagine (N), glutamine (Q), isoleucine (I), valine (V), threonine (T), phenylalanine (F), and tyrosine (Y).|thumb|Illustration of the QTY Code.]] === Three types of alpha-helices and with nearly identical molecular structure === There are 3 types of alpha-helices and with nearly identical molecular structure, namely: a) 1.5Å per amino acid rise, b) 100˚ per amino acid turn, c) 3.6 amino acids and 360˚ per helical turn, and d) 5.4Å per helical turn. The 3 types of alpha-helices are: 1) mostly hydrophobic amino acids including [[Leucine]] (L), [[Isoleucine]] (I), [[Valine]] (V), [[Phenylalanine]] (F), [[Methionine]] (M) and [[Alanine]] (A) that are commonly found as the helical transmembrane segments in membrane proteins; 2) mostly hydrophilic amino acids including [[Aspartic acid]] (D), [[Glutamic acid]] (E), [[Glutamine]] (Q), [[Lysine]] (K), [[Arginine]] (R), [[Serine]] (S), [[Threonine]] (T), [[Tyrosine]] (Y) that are commonly found on the out layer in water-soluble [[globular proteins]]; 3) mixed hydrophobic and hydrophilic amino acids that are partitioned in 2 faces: hydrophobic face and hydrophilic face, in an analogy, like our fingers with front and back. These alpha-helices sometimes attach to surface of membrane [[lipid bilayer]], or partially buried to the hydrophobic core and partially close to the surface of water-soluble globular proteins.<ref name="Introduction to Protein Structure" /> == The QTY code == The QTY Code is likely universally applicable and also reversible, namely, Q changes to L, T changes to V and I, and Y changes to F. The QTY Code has been successful in designing many water-soluble variants of [[chemokine receptors]] and [[cytokine receptors]]. The QTY Code may likely be successfully applied to other water-insoluble aggregated proteins. The QTY Code is robust and straightforward: it is the simplest tool to carry out membrane [[protein design]] without sophisticated computer algorithms. Thus, it can be used broadly. The QTY Code has implications for designing additional GPCRs and other membrane proteins including [[cytokine receptors]] that are directly involved in [[cytokine storm syndrome]].<ref name="QTY code enables" /><ref name="QTY code designed" /><ref name="QTY Code-designed" /><ref name="The G protein coupled" /><ref name="Non-full-length Water-Soluble" /> The QTY Code has also been applied to [[cytokine receptor]] water-soluble variants with the aim of combatting the [[cytokine storm]] syndrome (also called [[cytokine release syndrome]]) suffered by [[cancer]] patients receiving [[CAR-T therapy]]. This therapeutic application may be equally applicable to severely infected [[COVID-19]] patients, for whom cytokine storms often lead to death.<ref name="Non-full-length Water-Soluble" /> In 2021, predictions of [[AlphaFold#Algorithm|AlphaFold 2]] program proved the validity of QTY Code.<ref name="AlphaFold2">{{cite journal |last1=Skuhersky |first1=Michael |last2=Tao |first2=Fei |last3=Qing |first3=Rui |last4=Smorodina |first4=Eva |last5=Jin |first5=David |last6=Zhang |first6=Shuguang |title=Comparing Native Crystal Structures and AlphaFold2 Predicted Water-S |journal=Life |date=24 November 2021 |volume=11 |issue=12 |page=1285 |doi=10.3390/life11121285 |pmid=34947816 |pmc=8704054 |doi-access=free }}</ref> AlphaFold 2 predicted QTY variants superposed well with native structures of glutamate and monoamine transporters (including transporters for serotonin, dopamine, and norepinephrine).<ref>{{Cite journal |last1=Karagöl |first1=Taner |last2=Karagöl |first2=Alper |last3=Zhang |first3=Shuguang |date=2024 |title=Structural bioinformatics studies of serotonin, dopamine and norepinephrine transporters and their AlphaFold2 predicted water-soluble QTY variants and uncovering the natural mutations of L->Q, I->T, F->Y and Q->L, T->I and Y->F |journal=PLOS ONE |volume=19 |issue=3 |pages=e0300340 |doi=10.1371/journal.pone.0300340 |doi-access=free |issn=1932-6203 |pmid=38517879|pmc=10959339 |bibcode=2024PLoSO..1900340K }}</ref><ref>{{Cite journal |last1=Karagöl |first1=Alper |last2=Karagöl |first2=Taner |last3=Smorodina |first3=Eva |last4=Zhang |first4=Shuguang |date=2024 |title=Structural bioinformatics studies of glutamate transporters and their AlphaFold2 predicted water-soluble QTY variants and uncovering the natural mutations of L->Q, I->T, F->Y and Q->L, T->I and Y->F |journal=PLOS ONE |volume=19 |issue=4 |pages=e0289644 |doi=10.1371/journal.pone.0289644 |doi-access=free |issn=1932-6203 |pmid=38598436|pmc=11006163 }}</ref> ==References== {{Reflist}} ==Further reading== * {{cite journal |doi=10.1021/acs.jpcb.1c03245|title=Protein Stability Depends Critically on the Surface Hydrogen-Bonding Network: A Case Study of Bid Protein|year=2021|last1=Hung|first1=Chien-Lun|last2=Kuo|first2=Yun-Hsuan|last3=Lee|first3=Su Wei|last4=Chiang|first4=Yun-Wei|journal=The Journal of Physical Chemistry B|volume=125|issue=30|pages=8373–8382|pmid=34314184|s2cid=236472005}} * {{cite journal |doi=10.3390/membranes11100741 |doi-access=free |title=Enhancing the Cell-Free Expression of Native Membrane Proteins by in Silico Optimization of the Coding Sequence—An Experimental Study of the Human Voltage-Dependent Anion Channel |year=2021 |last1=Zayni |first1=Sonja |last2=Damiati |first2=Samar |last3=Moreno-Flores |first3=Susana |last4=Amman |first4=Fabian |last5=Hofacker |first5=Ivo |last6=Jin |first6=David |last7=Ehmoser |first7=Eva-Kathrin |journal=Membranes |volume=11 |issue=10 |page=741 |pmid=34677509 |pmc=8540592 }} * {{cite journal |doi=10.3390/life11111217|doi-access=free|title=Co-Evolution of Opioid and Adrenergic Ligands and Receptors: Shared, Complementary Modules Explain Evolution of Functional Interactions and Suggest Novel Engineering Possibilities|year=2021|last1=Root-Bernstein|first1=Robert|last2=Churchill|first2=Beth|journal=Life|volume=11|issue=11|page=1217|pmid=34833093|pmc=8623292|bibcode=2021Life...11.1217R }} * {{cite journal |doi=10.1016/j.jmb.2021.167154|title=Principles and Methods in Computational Membrane Protein Design|year=2021|last1=Vorobieva|first1=Anastassia Andreevna|journal=Journal of Molecular Biology|volume=433|issue=20|page=167154|pmid=34271008|s2cid=236001242}} * {{cite journal |doi=10.2144/btn-2019-0030|title=Elucidating the structure of membrane proteins|year=2019|last1=Martin|first1=Joseph|last2=Sawyer|first2=Abigail|journal=BioTechniques|volume=66|issue=4|pages=167–170|pmid=30987442|s2cid=149754025|doi-access=free}} [[Category:Medicinal chemistry]] [[Category:Biochemistry]]'