Editing Protein engineering (section)

== Examples of engineered proteins ==
Computing methods have been used to design a protein with a novel fold, such as [[Top7]],<ref>{{Citation|last1=Kuhlman|first1=Brian|title=Design of a Novel Globular Protein Fold with Atomic-Level Accuracy|year=2003|last2=Dantas|last3=Ireton|last4=Varani|last5=Stoddard|last6=Baker|first2=Gautam|first3=Gregory C.|first4=Gabriele|first5=Barry L.|first6=David|journal=[[Science (journal)|Science]]|volume=302|issue=5649|pages=1364–1368|bibcode=2003Sci...302.1364K|doi=10.1126/science.1089427|pmid=14631033|s2cid=1939390 |name-list-style=amp}}</ref> and sensors for unnatural molecules.<ref>{{Citation|last1=Looger|first1=Loren L.|title=Computational design of receptor and sensor proteins with novel functions|year=2003|last2=Dwyer|last3=Smith|last4=Hellinga|first2=Mary A.|first3=James J.|first4=Homme W.|journal=[[Nature (journal)|Nature]]|volume=423|issue=6936|pages=185–190|bibcode=2003Natur.423..185L|doi=10.1038/nature01556|pmid=12736688|s2cid=4387641 |name-list-style=amp}}</ref> The engineering of [[fusion protein]]s has yielded [[rilonacept]], a pharmaceutical that has secured [[Food and Drug Administration]] (FDA) approval for treating [[cryopyrin-associated periodic syndrome]].

Another computing method, IPRO, successfully engineered the switching of cofactor specificity of ''[[Candida boidinii]]'' xylose reductase.<ref name = chin>{{Citation|title=Computational design of Candida boidinii xylose reductase for altered cofactor specificity|date=October 2009|last1=Khoury|last2=Fazelinia|last3=Chin|last4=Pantazes|last5=Cirino|last6=Maranas|first1=GA|first2=H|first3=JW|first4=RJ|first5=PC|first6=CD|journal=Protein Science|volume=18|issue=10|pages=2125–38|doi=10.1002/pro.227|pmc=2786976|pmid=19693930}}</ref>  Iterative Protein Redesign and Optimization (IPRO) redesigns proteins to increase or give specificity to native or novel [[Enzyme substrate (biology)|substrates]] and [[Cofactor (biochemistry)|cofactors]]. This is done by repeatedly randomly perturbing the structure of the proteins around specified design positions, identifying the lowest energy combination of [[Conformational isomerism|rotamers]], and determining whether the new design has a lower binding energy than prior ones. The iterative nature of this process allows IPRO to make additive mutations to a protein sequence that collectively improve the specificity toward desired substrates and/or cofactors.<ref name = chin/>

Computation-aided design has also been used to engineer complex properties of a highly ordered nano-protein assembly.<ref name="Ardejani">{{Citation|title=Stabilization of a Protein Nanocage through the Plugging of a Protein–Protein Interfacial Water Pocket|date=April 2011|last1=Ardejani|last2=Li|last3=Orner|first1=MS|first2=NX|first3=BP|journal=Biochemistry|volume=50|issue=19|pages=4029–4037|doi=10.1021/bi200207w|pmid=21488690}}</ref> A protein cage, E. coli bacterioferritin (EcBfr), which naturally shows structural instability and an incomplete self-assembly behavior by populating two oligomerization states, is the model protein in this study. Through computational analysis and comparison to its [[Protein homology|homologs]], it has been found that this protein has a smaller-than-average [[Protein dimer|dimeric interface]] on its two-fold symmetry axis due mainly to the existence of an interfacial water pocket centered on two water-bridged asparagine residues. To investigate the possibility of engineering EcBfr for modified structural stability, a semi-empirical computational method is used to virtually explore the energy differences of the 480 possible mutants at the dimeric interface relative to the [[wild type]] EcBfr.  This computational study also converges on the water-bridged [[asparagine]]s. Replacing these two asparagines with [[Hydrophobe|hydrophobic]] amino acids results in proteins that fold into [[Alpha helix|alpha-helical]] monomers and assemble into cages as evidenced by circular dichroism and transmission electron microscopy. Both thermal and chemical denaturation confirm that, all redesigned proteins, in agreement with the calculations, possess increased stability.  One of the three mutations shifts the population in favor of the higher order oligomerization state in solution as shown by both size exclusion chromatography and native gel electrophoresis.<ref name="Ardejani" />

A ''in silico'' method, PoreDesigner,<ref>{{cite journal |last1=Chowdhury |first1=Ratul |last2=Ren |first2=Tingwei |last3=Shankla |first3=Manish |last4=Decker |first4=Karl |last5=Grisewood |first5=Matthew |last6=Prabhakar |first6=Jeevan |last7=Baker |first7=Carol |last8=Golbeck |first8=John H. |last9=Aksimentiev |first9=Aleksei |last10=Kumar |first10=Manish |last11=Maranas |first11=Costas D. |title=PoreDesigner for tuning solute selectivity in a robust and highly permeable outer membrane pore |journal=Nature Communications |date=10 September 2018 |volume=9 |issue=1 |pages=3661 |doi=10.1038/s41467-018-06097-1 |pmid=30202038 |pmc=6131167 |bibcode=2018NatCo...9.3661C }}</ref> was developed to redesign bacterial channel protein (OmpF) to reduce its 1&nbsp;nm pore size to any desired sub-nm dimension. Transport experiments on the narrowest designed pores revealed complete salt rejection when assembled in biomimetic block-polymer matrices.