title: Computational design of cyclic peptides for the customized oriented immobilization of globular proteins.
abstract: The oriented immobilization of proteins, key for the development of novel responsive biomaterials, relies on the availability of effective probes. These are generally provided by standard approaches based on in vivo maturation and in vitro selection of antibodies and/or aptamers. These techniques can suffer technical problems when a non-immunogenic epitope needs to be targeted. Here we propose a strategy to circumvent this issue by in silico design. In our method molecular binders, in the form of cyclic peptides, are computationally evolved by stochastically exploring their sequence and structure space to identify high-affinity peptides for a chosen epitope of a target globular protein: here a solvent-exposed site of β2-microglobulin (β2m). Designed sequences were screened by explicit solvent molecular dynamics simulations (MD) followed by experimental validation. Five candidates gave dose-response surface plasmon resonance signals with dissociation constants in the micromolar range. One of them was further analyzed by means of isothermal titration calorimetry, nuclear magnetic resonance, and 250 ns of MD. Atomic-force microscopy imaging showed that this peptide is able to immobilize β2m on a gold surface. In short, we have shown by a variety of experimental techniques that it is possible to capture a protein through an epitope of choice by computational design.
authors.affiliation: Department of Medical and Biological Sciences, University of Udine, Piazzale Kolbe, 4 - 33100 Udine, Italy. sara.fortuna@ung.si and SISSA, Via Bonomea 265, I-34136 Trieste, Italy.
authors.forename: Miguel A
authors.initials: MA
authors.lastname: Soler
authors.affiliation: SISSA, Via Bonomea 265, I-34136 Trieste, Italy.
authors.forename: Alex
authors.initials: A
authors.lastname: Rodriguez
authors.affiliation: Department of Medical and Biological Sciences, University of Udine, Piazzale Kolbe, 4 - 33100 Udine, Italy. sara.fortuna@ung.si.
authors.forename: Anna
authors.initials: A
authors.lastname: Russo
authors.affiliation: Department of Medical and Biological Sciences, University of Udine, Piazzale Kolbe, 4 - 33100 Udine, Italy. sara.fortuna@ung.si and PhD School of Nanotechnology, Department of Physics, University of Trieste, Via Valerio 2, 34127 Trieste, Italy.
authors.forename: Abimbola Feyisara
authors.identifier: http://orcid.org/0000-0001-8009-1755
authors.initials: AF
authors.lastname: Adedeji
authors.affiliation: Department of Medical and Biological Sciences, University of Udine, Piazzale Kolbe, 4 - 33100 Udine, Italy. sara.fortuna@ung.si.
authors.forename: Cedrix J
authors.initials: CJ
authors.lastname: Dongmo Foumthuim
authors.affiliation: Department of Medical and Biological Sciences, University of Udine, Piazzale Kolbe, 4 - 33100 Udine, Italy. sara.fortuna@ung.si.
authors.forename: Cristina
authors.initials: C
authors.lastname: Cantarutti
authors.affiliation: PhD School of Nanotechnology, Department of Physics, University of Trieste, Via Valerio 2, 34127 Trieste, Italy and Nanoinnovation Lab - Elettra-Sincrotone S.C.p.A., ss 14 km 163, 5 in AREA Science Park I-34149, Basovizza-Trieste, Italy.
authors.forename: Elena
authors.initials: E
authors.lastname: Ambrosetti
authors.affiliation: Nanoinnovation Lab - Elettra-Sincrotone S.C.p.A., ss 14 km 163, 5 in AREA Science Park I-34149, Basovizza-Trieste, Italy.
authors.forename: Loredana
authors.initials: L
authors.lastname: Casalis
authors.affiliation: Department of Medical and Biological Sciences, University of Udine, Piazzale Kolbe, 4 - 33100 Udine, Italy. sara.fortuna@ung.si.
authors.forename: Alessandra
authors.initials: A
authors.lastname: Corazza
authors.affiliation: Department of Medical and Biological Sciences, University of Udine, Piazzale Kolbe, 4 - 33100 Udine, Italy. sara.fortuna@ung.si.
authors.forename: Giacinto
authors.initials: G
authors.lastname: Scoles
authors.affiliation: Department of Pharmacy, CIRPEB: Centro Interuniversitario di Ricerca sui Peptidi Bioattivi-University of Naples "Federico II", DFM-Scarl, 80134, Naples, Italy.
authors.forename: Daniela
authors.initials: D
authors.lastname: Marasco
authors.affiliation: SISSA, Via Bonomea 265, I-34136 Trieste, Italy.
authors.forename: Alessandro
authors.initials: A
authors.lastname: Laio
authors.affiliation: Department of Medical and Biological Sciences, University of Udine, Piazzale Kolbe, 4 - 33100 Udine, Italy. sara.fortuna@ung.si.
authors.forename: Sara
authors.identifier: http://orcid.org/0000-0002-8059-6064
authors.initials: S
authors.lastname: Fortuna
mesh_terms: D002623:Chemistry Techniques, Analytical / Q000379:methods*; D003198:Computer Simulation; D000939:Epitopes / Q000737:chemistry; D008956:Models, Chemical; D056004:Molecular Dynamics Simulation; D010456:Peptides, Cyclic / Q000737:chemistry* / Q000378:metabolism; D011506:Proteins / Q000302:isolation & purification*
chemical_list: D000939:Epitopes; D010456:Peptides, Cyclic; D011506:Proteins