Ring Separation Highlights the Protein-Folding Mechanism Used by the Phage EL-Encoded Chaperonin

Molugu, Sudheer K.; Hildenbrand, Zacariah L.; Morgan, David; Sherman, Michael B; He, Lilin; Georgopoulos, Costa; Sernova, Natalia V.; Kurochkina, Lidia P.; Mesyanzhinov, Vadim V.; Miroshnikov, Konstantin A.; Bernal, Ricardo A.

doi:10.1016/j.str.2016.02.006

Cited by 18 publications

(44 citation statements)

References 41 publications

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“…In this case, the apo form of the chaperonin is tetradecameric. However, upon nucleotide binding, the oligomer dissociates into two heptameric rings with a largely expanded cavity, able to accommodate larger substrate proteins than other known chaperonins (Molugu et al, 2016). Thus, similar to what was proposed for the mitochondrial and T. thermophilus chaperonins, phi-EL seems to incorporate a single-ringed intermediate in its reaction cycle.…”

Section: Divergent Mechanisms? Insight From Structural Studies Of Thementioning

confidence: 99%

Dynamic Complexes in the Chaperonin-Mediated Protein Folding Cycle

Weiss

Jebara

Nisemblat

et al. 2016

Front. Mol. Biosci.

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The GroEL–GroES chaperonin system is probably one of the most studied chaperone systems at the level of the molecular mechanism. Since the first reports of a bacterial gene involved in phage morphogenesis in 1972, these proteins have stimulated intensive research for over 40 years. During this time, detailed structural and functional studies have yielded constantly evolving concepts of the chaperonin mechanism of action. Despite of almost three decades of research on this oligomeric protein, certain aspects of its function remain controversial. In this review, we highlight one central aspect of its function, namely, the active intermediates of its reaction cycle, and present how research to this day continues to change our understanding of chaperonin-mediated protein folding.

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Section: Divergent Mechanisms? Insight From Structural Studies Of Thementioning

confidence: 99%

Dynamic Complexes in the Chaperonin-Mediated Protein Folding Cycle

Weiss

Jebara

Nisemblat

et al. 2016

Front. Mol. Biosci.

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“…The dilution buffer with ADP also contained 0.08 % n-octyl-β-D-glucopyranoside. 10 Subsequently the mixture was incubated at room temperature for 5 min. Holey carbon supported copper-grids (Quantifoil R2/1 300 mesh) were plasma-cleaned for 30 s (Harrick Plasma) immediately before use.…”

Section: Cryo-electron Microscopy and Single Particle Analysismentioning

confidence: 99%

“…Two crystal forms were identified that diffracted to 4.03 and 3.54 Å resolution ( Table 1). The structure was solved by molecular replacement at 6.8 Å resolution using the cryo-EM map of the ɸEL-ATP tetradecamer as a search model (EMD-6492) [10]. The seven-fold non-crystallographic symmetry was then employed to extend the phases to 3.54 Å, resulting in an electron density map of sufficient quality to build an atomic model.…”

Section: Crystal Structures Of ɸEl In Presence Of Atp•befxmentioning

confidence: 99%

“…ɸEL prevented gp188 aggregation and maintained the protein in a functional state independent of host GroES [9][10][11]. A low resolution cryo-electron microscopy (cryo-EM) structure reported a spherical heptamer for ADP-bound ɸEL, which was suggested to represent the SP-encapsulating state [10].…”

mentioning

confidence: 99%

“…This cell wall endolysin is unstable at 37 °C [9]. ɸEL prevented gp188 aggregation and maintained the protein in a functional state independent of host GroES [9][10][11]. A low resolution cryo-electron microscopy (cryo-EM) structure reported a spherical heptamer for ADP-bound ɸEL, which was suggested to represent the SP-encapsulating state [10].Here, we performed a functional and structural characterization of the chaperonin from the phage EL of P. aeruginosa to better understand the ɸEL mechanism.…”

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confidence: 99%

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Structure and conformational cycle of a bacteriophage-encoded chaperonin

Bracher

Paul

Wang

et al. 2020

Preprint

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AbstractChaperonins are ubiquitous molecular chaperones found in all domains of life. They form ring-shaped complexes that assist in the folding of substrate proteins in an ATP-dependent reaction cycle. Key to the folding cycle is the transient encapsulation of substrate proteins by the chaperonin. Here we present a structural and functional characterization of the chaperonin gp146 (ɸEL) from the phage EL of Pseudomonas aeruginosa. ɸEL, an evolutionary distant homolog of bacterial GroEL, is active in ATP hydrolysis and prevents the aggregation of denatured protein in a nucleotide-dependent manner. However, ɸEL failed to refold the encapsulation-dependent model substrate rhodanese and did not interact with E. coli GroES, the lid-shaped co-chaperone of GroEL. ɸEL forms tetradecameric double-ring complexes, which dissociate into single rings in the presence of ATP. Crystal structures of ɸEL (at 3.54 and 4.03 Å) in presence of ATP•BeFx revealed two distinct single-ring conformational states, both with open access to the ring cavity. One state showed uniform ATP-bound subunit conformations (symmetric state), whereas the second combined distinct ATP- and ADP-bound subunit conformations (asymmetric state). Cryo-electron microscopy of apo-ɸEL revealed a double-ring structure composed of rings in the asymmetric state (3.45 Å resolution). We propose that the phage chaperonin undergoes nucleotide-dependent conformational switching between double- and single rings and functions in aggregation prevention without substrate protein encapsulation. Thus, ɸEL may represent an evolutionary more ancient chaperonin prior to acquisition of the encapsulation mechanism.

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In‐depth analysis of amino acid and nucleotide sequences of Hsp60: How conserved is this protein?

et al. 2022

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Chaperonin Hsp60, as a protein found in all organisms, is of great interest in medicine, since it is present in many tissues and can be used both as a drug and as an object of targeted therapy. Hence, Hsp60 deserves a fundamental comparative analysis to assess its evolutionary characteristics. It was found that the percent identity of Hsp60 amino acid sequences both within and between phyla was not high enough to identify Hsp60s as highly conserved proteins. However, their ATP binding sites are largely conserved. The amino acid composition of Hsp60s remained relatively constant. At the same time, the analysis of the nucleotide sequences showed that GC content in the Hsp60 genes was comparable to or greater than the genomic values, which may indicate a high resistance to mutations due to tight control of the nucleotide composition by DNA repair systems. Natural selection plays a dominant role in the evolution of Hsp60 genes. The degree of mutational pressure affecting the Hsp60 genes is quite low, and its direction does not depend on taxonomy. Interestingly, for the Hsp60 genes from Chordata, Arthropoda, and Proteobacteria the exact direction of mutational pressure could not be determined. However, upon further division into classes, it was found that the direction of the mutational pressure for Hsp60 genes from Fish differs from that for other chordates. The direction of the mutational pressure affects the synonymous codon usage bias. The number of high and low represented codons increases with increasing GC content, which can improve codon usage. Special server has been created for bioinformatics analysis of Hsp60: http://oka.protres.ru:4202/.

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Ring Separation Highlights the Protein-Folding Mechanism Used by the Phage EL-Encoded Chaperonin

Cited by 18 publications

References 41 publications

Dynamic Complexes in the Chaperonin-Mediated Protein Folding Cycle

Dynamic Complexes in the Chaperonin-Mediated Protein Folding Cycle

Structure and conformational cycle of a bacteriophage-encoded chaperonin

In‐depth analysis of amino acid and nucleotide sequences of Hsp60: How conserved is this protein?

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