1
|
Iljina M, Mazal H, Dayananda A, Zhang Z, Stan G, Riven I, Haran G. Single-molecule FRET probes allosteric effects on protein-translocating pore loops of a AAA+ machine. Biophys J 2024; 123:374-388. [PMID: 38196191 PMCID: PMC10870172 DOI: 10.1016/j.bpj.2024.01.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2023] [Revised: 11/07/2023] [Accepted: 01/02/2024] [Indexed: 01/11/2024] Open
Abstract
AAA+ proteins (ATPases associated with various cellular activities) comprise a family of powerful ring-shaped ATP-dependent translocases that carry out numerous vital substrate-remodeling functions. ClpB is a AAA+ protein disaggregation machine that forms a two-tiered hexameric ring, with flexible pore loops protruding into its center and binding to substrate proteins. It remains unknown whether these pore loops contribute only passively to substrate-protein threading or have a more active role. Recently, we have applied single-molecule FRET spectroscopy to directly measure the dynamics of substrate-binding pore loops in ClpB. We have reported that the three pore loops of ClpB (PL1-3) undergo large-scale fluctuations on the microsecond timescale that are likely to be mechanistically important for disaggregation. Here, using single-molecule FRET, we study the allosteric coupling between the pore loops and the two nucleotide-binding domains of ClpB (NBD1-2). By mutating the conserved Walker B motifs within the NBDs to abolish ATP hydrolysis, we demonstrate how the nucleotide state of each NBD tunes pore-loop dynamics. This effect is surprisingly long-ranged; in particular, PL2 and PL3 respond differentially to a Walker B mutation in either NBD1 or NBD2, as well as to mutations in both. We characterize the conformational dynamics of pore loops and the allosteric paths connecting NBDs to pore loops by molecular dynamics simulations and find that both principal motions and allosteric paths can be altered by changing the ATPase state of ClpB. Remarkably, PL3, which is highly conserved in AAA+ machines, is found to favor an upward conformation when only NBD1 undergoes ATP hydrolysis but a downward conformation when NBD2 is active. These results explicitly demonstrate a significant long-range allosteric effect of ATP hydrolysis sites on pore-loop dynamics. Pore loops are therefore established as active participants that undergo ATP-dependent conformational changes to translocate substrate proteins through the central pores of AAA+ machines.
Collapse
Affiliation(s)
- Marija Iljina
- Department of Chemical and Biological Physics, Weizmann Institute of Science, Rehovot, Israel
| | - Hisham Mazal
- Department of Chemical and Biological Physics, Weizmann Institute of Science, Rehovot, Israel
| | - Ashan Dayananda
- Department of Chemistry, University of Cincinnati, Cincinnati, Ohio
| | - Zhaocheng Zhang
- Department of Chemistry, University of Cincinnati, Cincinnati, Ohio
| | - George Stan
- Department of Chemistry, University of Cincinnati, Cincinnati, Ohio.
| | - Inbal Riven
- Department of Chemical and Biological Physics, Weizmann Institute of Science, Rehovot, Israel
| | - Gilad Haran
- Department of Chemical and Biological Physics, Weizmann Institute of Science, Rehovot, Israel.
| |
Collapse
|
2
|
Macke AC, Stump JE, Kelly MS, Rowley J, Herath V, Mullen S, Dima RI. Searching for Structure: Characterizing the Protein Conformational Landscape with Clustering-Based Algorithms. J Chem Inf Model 2024; 64:470-482. [PMID: 38173388 DOI: 10.1021/acs.jcim.3c01511] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2024]
Abstract
The identification and characterization of the main conformations from a protein population are a challenging and inherently high-dimensional problem. Here, we evaluate the performance of the Secondary sTructural Ensembles with machine LeArning (StELa) double-clustering method, which clusters protein structures based on the relationship between the φ and ψ dihedral angles in a protein backbone and the secondary structure of the protein, thus focusing on the local properties of protein structures. The classification of states as vectors composed of the clusters' indices arising naturally from the Ramachandran plot is followed by the hierarchical clustering of the vectors to allow for the identification of the main features of the corresponding free energy landscape (FEL). We compare the performance of StELa with the established root-mean-squared-deviation (RMSD)-based clustering algorithm, which focuses on global properties of protein structures and with Combinatorial Averaged Transient Structure (CATS), the combinatorial averaged transient structure clustering method based on distributions of the φ and ψ dihedral angle coordinates. Using ensembles of conformations from molecular dynamics simulations of intrinsically disordered proteins (IDPs) of various lengths (tau protein fragments) or short fragments from a globular protein, we show that StELa is the clustering method that identifies many of the minima and relevant energy states around the minima from the corresponding FELs. In contrast, the RMSD-based algorithm yields a large number of clusters that usually cover most of the FEL, thus being unable to distinguish between states, while CATS does not sample well the FELs for long IDPs and fragments from globular proteins.
Collapse
Affiliation(s)
- Amanda C Macke
- Department of Chemistry, University of Cincinnati, Cincinnati, Ohio 45221, United States
| | - Jacob E Stump
- Department of Chemistry, University of Cincinnati, Cincinnati, Ohio 45221, United States
| | - Maria S Kelly
- Department of Chemistry, University of Cincinnati, Cincinnati, Ohio 45221, United States
| | - Jamie Rowley
- Department of Chemistry, University of Cincinnati, Cincinnati, Ohio 45221, United States
| | - Vageesha Herath
- Department of Chemistry, University of Cincinnati, Cincinnati, Ohio 45221, United States
- Department of Chemistry, Emory University, Atlanta, Georgia 30322, United States
| | - Sarah Mullen
- Department of Chemistry, The College of Wooster, Wooster, Ohio 44691, United States
- Department of Chemistry, Virginia Tech, Blacksburg, Virginia 24061, United States
| | - Ruxandra I Dima
- Department of Chemistry, University of Cincinnati, Cincinnati, Ohio 45221, United States
| |
Collapse
|
3
|
Kelly MS, Macke AC, Kahawatte S, Stump JE, Miller AR, Dima RI. The quaternary question: Determining allostery in spastin through dynamics classification learning and bioinformatics. J Chem Phys 2023; 158:125102. [PMID: 37003743 DOI: 10.1063/5.0139273] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/09/2023] Open
Abstract
The nanomachine from the ATPases associated with various cellular activities superfamily, called spastin, severs microtubules during cellular processes. To characterize the functionally important allostery in spastin, we employed methods from evolutionary information, to graph-based networks, to machine learning applied to atomistic molecular dynamics simulations of spastin in its monomeric and the functional hexameric forms, in the presence or absence of ligands. Feature selection, using machine learning approaches, for transitions between spastin states recognizes all the regions that have been proposed as allosteric or functional in the literature. The analysis of the composition of the Markov State Model macrostates in the spastin monomer, and the analysis of the direction of change in the top machine learning features for the transitions, indicate that the monomer favors the binding of ATP, which primes the regions involved in the formation of the inter-protomer interfaces for binding to other protomer(s). Allosteric path analysis of graph networks, built based on the cross-correlations between residues in simulations, shows that perturbations to a hub specific for the pre-hydrolysis hexamer propagate throughout the structure by passing through two obligatory regions: the ATP binding pocket, and pore loop 3, which connects the substrate binding site to the ATP binding site. Our findings support a model where the changes in the terminal protomers due to the binding of ligands play an active role in the force generation in spastin. The secondary structures in spastin, which are found to be highly degenerative within the network paths, are also critical for feature transitions of the classification models, which can guide the design of allosteric effectors to enhance or block allosteric signaling.
Collapse
Affiliation(s)
- Maria S Kelly
- Department of Chemistry, University of Cincinnati, Cincinnati, Ohio 45221, USA
| | - Amanda C Macke
- Department of Chemistry, University of Cincinnati, Cincinnati, Ohio 45221, USA
| | - Shehani Kahawatte
- Department of Chemistry, University of Cincinnati, Cincinnati, Ohio 45221, USA
| | - Jacob E Stump
- Department of Chemistry, University of Cincinnati, Cincinnati, Ohio 45221, USA
| | - Abigail R Miller
- Department of Chemistry, University of Cincinnati, Cincinnati, Ohio 45221, USA
| | - Ruxandra I Dima
- Department of Chemistry, University of Cincinnati, Cincinnati, Ohio 45221, USA
| |
Collapse
|
4
|
González-Paz L, Lossada C, Hurtado-León ML, Fernández-Materán FV, Paz JL, Parvizi S, Cardenas Castillo RE, Romero F, Alvarado YJ. Intrinsic Dynamics of the ClpXP Proteolytic Machine Using Elastic Network Models. ACS OMEGA 2023; 8:7302-7318. [PMID: 36873006 PMCID: PMC9979342 DOI: 10.1021/acsomega.2c04347] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/09/2022] [Accepted: 10/25/2022] [Indexed: 06/18/2023]
Abstract
ClpXP complex is an ATP-dependent mitochondrial matrix protease that binds, unfolds, translocates, and subsequently degrades specific protein substrates. Its mechanisms of operation are still being debated, and several have been proposed, including the sequential translocation of two residues (SC/2R), six residues (SC/6R), and even long-pass probabilistic models. Therefore, it has been suggested to employ biophysical-computational approaches that can determine the kinetics and thermodynamics of the translocation. In this sense, and based on the apparent inconsistency between structural and functional studies, we propose to apply biophysical approaches based on elastic network models (ENM) to study the intrinsic dynamics of the theoretically most probable hydrolysis mechanism. The proposed models ENM suggest that the ClpP region is decisive for the stabilization of the ClpXP complex, contributing to the flexibility of the residues adjacent to the pore, favoring the increase in pore size and, therefore, with the energy of interaction of its residues with a larger portion of the substrate. It is predicted that the complex may undergo a stable configurational change once assembled and that the deformability of the system once assembled is oriented, to increase the rigidity of the domains of each region (ClpP and ClpX) and to gain flexibility of the pore. Our predictions could suggest under the conditions of this study the mechanism of the interaction of the system, of which the substrate passes through the unfolding of the pore in parallel with a folding of the bottleneck. The variations in the distance calculated by molecular dynamics could allow the passage of a substrate with a size equivalent to ∼3 residues. The theoretical behavior of the pore and the stability and energy of binding to the substrate based on ENM models suggest that in this system, there are thermodynamic, structural, and configurational conditions that allow a possible translocation mechanism that is not strictly sequential.
Collapse
Affiliation(s)
- Lenin González-Paz
- Facultad
Experimental de Ciencias (FEC), Departamento de Biología, Laboratorio
de Genética y Biología Molecular (LGBM), Universidad del Zulia (LUZ), 4001 Maracaibo, Zulia, República Bolivariana
de Venezuela
- Centro
de Biomedicina Molecular (CBM). Laboratorio de Biocomputación
(LB), Instituto Venezolano de Investigaciones
Científicas (IVIC), 4001 Maracaibo, Zulia, República Bolivariana de Venezuela
| | - Carla Lossada
- Centro
de Biomedicina Molecular (CBM). Laboratorio de Biocomputación
(LB), Instituto Venezolano de Investigaciones
Científicas (IVIC), 4001 Maracaibo, Zulia, República Bolivariana de Venezuela
| | - Maria Laura Hurtado-León
- Facultad
Experimental de Ciencias (FEC), Departamento de Biología, Laboratorio
de Genética y Biología Molecular (LGBM), Universidad del Zulia (LUZ), 4001 Maracaibo, Zulia, República Bolivariana
de Venezuela
| | - Francelys V. Fernández-Materán
- Centro
de Biomedicina Molecular (CBM). Laboratorio de Biocomputación
(LB), Instituto Venezolano de Investigaciones
Científicas (IVIC), 4001 Maracaibo, Zulia, República Bolivariana de Venezuela
| | - José Luis Paz
- Departamento
Académico de Química Inorgánica, Facultad de
Química e Ingeniería Química, Universidad Nacional Mayor de San Marcos, 15081 Lima, Perú
| | - Shayan Parvizi
- Pulmonary,
Critical Care and Sleep Medicine, Baylor
College of Medicine, Houston, Texas 77030, United States
| | | | - Freddy Romero
- Pulmonary,
Critical Care and Sleep Medicine, Baylor
College of Medicine, Houston, Texas 77030, United States
| | - Ysaias J. Alvarado
- Centro
de Biomedicina Molecular (CBM), Laboratorio de Química Biofísica
Teórica y Experimental (LQBTE), Instituto
Venezolano de Investigaciones Cientificas (IVIC), 4001 Maracaibo, Zulia, República Bolivariana de Venezuela
| |
Collapse
|
5
|
Macke AC, Kelly MS, Varikoti RA, Mullen S, Groves D, Forbes C, Dima RI. Microtubule Severing Enzymes Oligomerization and Allostery: A Tale of Two Domains. J Phys Chem B 2022; 126:10569-10586. [PMID: 36475672 DOI: 10.1021/acs.jpcb.2c05288] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Severing proteins are nanomachines from the AAA+ (ATPases associated with various cellular activities) superfamily whose function is to remodel the largest cellular filaments, microtubules. The standard AAA+ machines adopt hexameric ring structures for functional reasons, while being primarily monomeric in the absence of the nucleotide. Both major severing proteins, katanin and spastin, are believed to follow this trend. However, studies proposed that they populate lower-order oligomers in the presence of cofactors, which are functionally relevant. Our simulations show that the preferred oligomeric assembly is dependent on the binding partners and on the type of severing protein. Essential dynamics analysis predicts that the stability of an oligomer is dependent on the strength of the interface between the helical bundle domain (HBD) of a monomer and the convex face of the nucleotide binding domain (NBD) of a neighboring monomer. Hot spots analysis found that the region consisting of the HBD tip and the C-terminal (CT) helix is the only common element between the allosteric networks responding to nucleotide, substrate, and intermonomer binding. Clustering analysis indicates the existence of multiple pathways for the transition between the secondary structure of the HBD tip in monomers and the structure(s) it adopts in oligomers.
Collapse
Affiliation(s)
- Amanda C Macke
- Department of Chemistry, University of Cincinnati, Cincinnati, Ohio 45221, United States
| | - Maria S Kelly
- Department of Chemistry, University of Cincinnati, Cincinnati, Ohio 45221, United States
| | - Rohith Anand Varikoti
- Department of Chemistry, University of Cincinnati, Cincinnati, Ohio 45221, United States
| | - Sarah Mullen
- Department of Chemistry, The College of Wooster, Wooster, Ohio 44691, United States
- Department of Chemistry, Virginia Tech, Blacksburg, Virginia 24061, United States
| | - Daniel Groves
- Department of Chemistry, University of Cincinnati, Cincinnati, Ohio 45221, United States
| | - Clare Forbes
- Department of Chemistry, University of Cincinnati, Cincinnati, Ohio 45221, United States
| | - Ruxandra I Dima
- Department of Chemistry, University of Cincinnati, Cincinnati, Ohio 45221, United States
| |
Collapse
|
6
|
Riven I, Mazal H, Iljina M, Haran G. Fast dynamics shape the function of the
AAA
+ machine
ClpB
: lessons from single‐molecule
FRET
spectroscopy. FEBS J 2022. [DOI: 10.1111/febs.16539] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2022] [Revised: 05/04/2022] [Accepted: 05/30/2022] [Indexed: 12/01/2022]
Affiliation(s)
- Inbal Riven
- Department of Chemical and Biological Physics Weizmann Institute of Science Rehovot Israel
| | - Hisham Mazal
- Department of Chemical and Biological Physics Weizmann Institute of Science Rehovot Israel
| | - Marija Iljina
- Department of Chemical and Biological Physics Weizmann Institute of Science Rehovot Israel
| | - Gilad Haran
- Department of Chemical and Biological Physics Weizmann Institute of Science Rehovot Israel
| |
Collapse
|
7
|
Varikoti RA, Fonseka HYY, Kelly MS, Javidi A, Damre M, Mullen S, Nugent JL, Gonzales CM, Stan G, Dima RI. Exploring the Effect of Mechanical Anisotropy of Protein Structures in the Unfoldase Mechanism of AAA+ Molecular Machines. NANOMATERIALS 2022; 12:nano12111849. [PMID: 35683705 PMCID: PMC9182431 DOI: 10.3390/nano12111849] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/02/2022] [Revised: 05/25/2022] [Accepted: 05/25/2022] [Indexed: 02/06/2023]
Abstract
Essential cellular processes of microtubule disassembly and protein degradation, which span lengths from tens of μm to nm, are mediated by specialized molecular machines with similar hexameric structure and function. Our molecular simulations at atomistic and coarse-grained scales show that both the microtubule-severing protein spastin and the caseinolytic protease ClpY, accomplish spectacular unfolding of their diverse substrates, a microtubule lattice and dihydrofolate reductase (DHFR), by taking advantage of mechanical anisotropy in these proteins. Unfolding of wild-type DHFR requires disruption of mechanically strong β-sheet interfaces near each terminal, which yields branched pathways associated with unzipping along soft directions and shearing along strong directions. By contrast, unfolding of circular permutant DHFR variants involves single pathways due to softer mechanical interfaces near terminals, but translocation hindrance can arise from mechanical resistance of partially unfolded intermediates stabilized by β-sheets. For spastin, optimal severing action initiated by pulling on a tubulin subunit is achieved through specific orientation of the machine versus the substrate (microtubule lattice). Moreover, changes in the strength of the interactions between spastin and a microtubule filament, which can be driven by the tubulin code, lead to drastically different outcomes for the integrity of the hexameric structure of the machine.
Collapse
Affiliation(s)
- Rohith Anand Varikoti
- Department of Chemistry, University of Cincinnati, Cincinnati, OH 45221, USA; (R.A.V.); (H.Y.Y.F.); (M.S.K.); (M.D.); (J.L.N.IV)
| | - Hewafonsekage Yasan Y. Fonseka
- Department of Chemistry, University of Cincinnati, Cincinnati, OH 45221, USA; (R.A.V.); (H.Y.Y.F.); (M.S.K.); (M.D.); (J.L.N.IV)
| | - Maria S. Kelly
- Department of Chemistry, University of Cincinnati, Cincinnati, OH 45221, USA; (R.A.V.); (H.Y.Y.F.); (M.S.K.); (M.D.); (J.L.N.IV)
| | - Alex Javidi
- Data Sciences, Janssen Research and Development, Spring House, PA 19477, USA;
| | - Mangesh Damre
- Department of Chemistry, University of Cincinnati, Cincinnati, OH 45221, USA; (R.A.V.); (H.Y.Y.F.); (M.S.K.); (M.D.); (J.L.N.IV)
| | - Sarah Mullen
- Department of Chemistry, The College of Wooster, Wooster, OH 44691, USA;
| | - Jimmie L. Nugent
- Department of Chemistry, University of Cincinnati, Cincinnati, OH 45221, USA; (R.A.V.); (H.Y.Y.F.); (M.S.K.); (M.D.); (J.L.N.IV)
| | | | - George Stan
- Department of Chemistry, University of Cincinnati, Cincinnati, OH 45221, USA; (R.A.V.); (H.Y.Y.F.); (M.S.K.); (M.D.); (J.L.N.IV)
- Correspondence: (G.S.); (R.I.D.)
| | - Ruxandra I. Dima
- Department of Chemistry, University of Cincinnati, Cincinnati, OH 45221, USA; (R.A.V.); (H.Y.Y.F.); (M.S.K.); (M.D.); (J.L.N.IV)
- Correspondence: (G.S.); (R.I.D.)
| |
Collapse
|