nanomaterials Review Chaperonins: Nanocarriers with Biotechnological Applications Sergio Pipaón 1 , Marcos Gragera 1 , M. Teresa Bueno-Carrasco 1, Juan García-Bernalt Diego 1 , Miguel Cantero 1, Jorge Cuéllar 1 , María Rosario Fernández-Fernández 1 and José María Valpuesta 1,2,* 1 Centro Nacional de Biotecnología (CNB-CSIC). Darwin, 3. 28049 Madrid, Spain; [email protected] (S.P.); [email protected] (M.G.); [email protected] (M.T.B.-C.); [email protected] (J.G.-B.D.); [email protected] (M.C.); [email protected] (J.C.); [email protected] (M.R.F.-F.) 2 Unidad Asociada de Nanobiotecnología (IMDEA Nanociencia), 28049 Madrid, Spain * Correspondence: [email protected] Abstract: Chaperonins are molecular chaperones found in all kingdoms of life, and as such they assist in the folding of other proteins. Structurally, chaperonins are cylinders composed of two back-to-back rings, each of which is an oligomer of ~60-kDa proteins. Chaperonins are found in two main conformations, one in which the cavity is open and ready to recognise and trap unfolded client proteins, and a “closed” form in which folding takes place. The conspicuous properties of this structure (a cylinder containing a cavity that allows confinement) and the potential to control its closure and aperture have inspired a number of nanotechnological applications that will be described in this review. Keywords: molecular chaperones; chaperonins; nanocarriers; nanoreactors Citation: Pipaón, S.; Gragera, M.; Bueno-Carrasco, M.T.; García-Bernalt 1. Chaperonins: Structure and Function Diego, J.; Cantero, M.; Cuéllar, J.; In the crowded environment of the cell, most proteins need assistance to acquire their Fernández-Fernández, M.R.; Valpuesta, J.M. Chaperonins: native conformation and therefore their functional activity [1]. This task is performed by a Nanocarriers with Biotechnological group of proteins termed molecular chaperones that are involved in protein homeostasis, Applications. Nanomaterials 2021, 11, which includes assistance in folding, degradation, and prevention of aggregation [2,3]. 503. https://doi.org/10.3390/nano Molecular chaperones are a large family of proteins, usually heat shock proteins (Hsps), 11020503 most of which are classified according to the molecular mass of their monomers, though in some cases, they act as oligomers. The most important families are Hsp60, Hsp70, and Academic Editor: Angelina Angelova Hsp90, and even though they are not structurally similar, they each have a dedicated Received: 15 January 2021 surface for interaction with the client protein and two main conformations: an “open” Accepted: 13 February 2021 one that recognizes the protein; and a “closed” one in which it is trapped and somehow Published: 17 February 2021 helped to find its correct folding. These chaperonins can thus be considered to be molec- ular machines, and as such their properties could be transformed for nanotechnological Publisher’s Note: MDPI stays neutral purposes [4,5]. This review will focus on the structure and function of one of these fami- with regard to jurisdictional claims in lies of chaperones, the Hsp60 or chaperonins, and will describe the efforts undertaken to published maps and institutional affil- modify their structures for use as nanotechnological devices such as nanocontainers and iations. nanocarriers. Chaperonins are found in all kingdoms of life, and also in viruses [6,7]. Structurally, the majority of chaperonins are cylinders composed of two back-to-back rings, each of which is an oligomer of ~60 kDa proteins (Figure1). Each monomer has three domains Copyright: © 2021 by the authors. (Figure1A,D) : (1) the equatorial domain, which hosts the ATP-binding site and is respon- Licensee MDPI, Basel, Switzerland. sible for all inter-ring connections and most of the intra-ring interactions; (2) the apical This article is an open access article domain, at the entrance of the ring cavity, which hosts the recognition sites for client distributed under the terms and proteins; and (3) the intermediate domain, which transduces signals from the equatorial conditions of the Creative Commons domain (resulting from ATP binding and hydrolysis) to affect the large conformational Attribution (CC BY) license (https:// changes in the apical domain corresponding to the open and closed forms. creativecommons.org/licenses/by/ 4.0/). Nanomaterials 2021, 11, 503. https://doi.org/10.3390/nano11020503 https://www.mdpi.com/journal/nanomaterials NanomaterialsNanomaterials2021 202111, 11, x FOR PEER REVIEW 3 of 14 , , 503 2 of 12 . Figure 1. Structure of the chaperonins. (A) The atomic structure of a GroEL monomer (pdb 1KP8), withFigure the 1. equatorial Structure domain of the chaperonins. (green), apical (A) domain The atomic (purple), structure and intermediateof a GroEL monomer domain (blue).(pdb 1KP8), (B,C) Twowith orthogonal the equator viewsial domain of the (green), atomic structureapical domain of a Type (purple) I chaperonin, and intermediate oligomer domain in its open (blue). (B) and(B and C) Two orthogonal views of the atomic structure of a Type I chaperonin oligomer in its open closed (C) conformations, in the latter case induced by the presence of the small oligomer GroES (red (B) and closed (C) conformations, in the latter case induced by the presence of the small oligomer and one of the monomers in orange). The atomic structures correspond to GroEL (pdb 1KP8) and the GroES (red and one of the monomers in orange). The atomic structures correspond to GroEL (pdb GroEL/GroES1KP8) and the complex GroEL/GroES (pdb 1AON), complex respectively. (pdb 1AON), The respectively. dashed lines The (red) dashed mark lines the surface(red) mark formed the bysurface the apical formed domains by the thatapical is responsibledomains that for is interactionresponsible with for interaction misfolded with proteins. misfolded (D) The proteins. atomic structure(D) The atomic of a Type structure II monomer, of a Type the II thermosome monomer, the from thermosomeMethanococcus from maripaludis Methanococcus(pdb maripaludis 3IZH). The three(pdb domains 3IZH). The are three coloured domains as in are (A ).coloured The black as in arrow (A). The indicates black thearrow helical indicates extension the helical responsible exten- forsion closure responsible of the for cavity closure see (ofF). the (E ,cavityF) Two (see orthogonal F). (E and views F) Two of orthogonal the atomic views structure of the of atomic a Type II chaperoninstructure of oligomer a Type II (E chaperonin) in its open oligomer conformation (E) in (thermosome its open conformation from Methanococcus (thermosome maripaludis from Meth-; pdb 3IZH)anococcus and maripaludis (F) in its closed; pdb conformation 3IZH) and (F) (thermosome in its closed conformation from Thermococcus (thermosome strain KS1;from pdbThermo- 1Q3R). coccus strain KS1; pdb 1Q3R). The dashed circles (red) mark the surface formed by the apical do- The dashed circles (red) mark the surface formed by the apical domains that is responsible for part of mains that is responsible for part of the interactions with misfolded proteins. Bar = 100 Å for B, C, the interactions with misfolded proteins. Bar = 100 Å for B, C, E and F. E and F. Historically, chaperonins have been classified into two types, those of bacterial and endosymbiotic2. Chaperonins origin as (Type Nanotechnological I) and those found Devices in archaea and in the eukaryotic cytosol (TypeT II).he Type peculiar I are usually structure homo-heptameric of chaperonins, rings, with and the a best-studiedcavity entrance member of isup the to chaperonin~80 Å and GroEL volume from Escherichia large enough coli (Figure (701–A–C)130,000 [ 8]. TypeÅ 3, depending II chaperonins, on in the particular chap- those of archaeal origin (usually named thermosomes), are mostly octameric rings made up oferonin) one or two to differentaccommodate subunits. chemical Occasionally, reagents nonameric or ringsproteins have beenup found,to ~100 usually kDa, composedtogether ofwith three the different possibility subunits. of closing The most and complex opening of the their Type entrance II chaperonins through is thean eukaryotic ATP-controlled cytosolic chaperonin,mechanism termed (Figure CCT 1), or TRiC,has been which cleverly contains eightexploited different for subunitsdifferent (Figure purposes.1D–F) [ 9 – 11]. Although the two chaperonin types are structurally similar, they have two major differences which carry important consequences. Firstly, there are differences2.1. Chaperonins in how the as subunits Nanocarriers of opposite rings interact, with Type I showing a 1:2 subunit arrangement, whereas Type II has a 1:1 arrangement (compare Figure1B,D). This has a clear consequenceIn the case on of intra- Type and I chaperonins, inter-ring signalling, a non with-modified clear positive GroEL and has negative been cooperativitytested as a amongnanocarrier the subunits by loading of a ring GroEL and between with Doxorubicin rings, respectively, (Dox in), Type a hy- I chaperonins,drophobic whereasantitumor intra- drug and inter-ring[15] (Figure cooperativities 2A). In this have work, not been the unequivocally authors ob- demonstrated in Type II chaperonins [7,12]. servedThe secondhow GroEL important was difference able to between protect the Dox two chaperonin from unwanted types involves degradation the man- nerin inthe which blood the until closed the conformation chaperonin is induced. reached In the Type tumour, I, the closed where conformation GroEL in- is achievedteracts afterwith ATP plectin,