1
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Guarra F, Colombo G. Conformational Dynamics, Energetics, and the Divergent Evolution of Allosteric Regulation: The Case of the Yeast MAPK Family. Chembiochem 2024:e202400175. [PMID: 38775368 DOI: 10.1002/cbic.202400175] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2024] [Revised: 04/24/2024] [Indexed: 07/06/2024]
Abstract
Allosteric mechanisms provide finely-tuned control over signalling proteins. Proteins of the same family may share high sequence identity and structural similarity but show distinct traits of allosteric control and evolutionary divergent regulation. Revealing the determinants of such properties may be important to understand the molecular bases of different regulatory pathways. Herein, we investigate whether and how evolutionarily-divergent traits of allosteric regulation in homologous proteins can be decoded in terms of internal dynamics and interaction networks that support functionally oriented conformations. In this framework, we start from the comparative analysis of the dynamics and energetics of the yeast MAP Kinases (MAPKs) Fus3 and Kss1 in their native basins. Importantly, distinctive dynamic and energetic stabilization features emerge, which can be related to the two proteins' differential ability to be phosphorylated and engage with the allosteric activator Ste5. We then expanded our study to other evolutionarily-related MAPKs. We show that the dynamical and energetical traits defining the distinct regulatory profiles of Fus3 and Kss1 can be traced along their evolutionary tree. Overall, our approach is able to reconnect (latent) allostery with the principal elements of protein structural stabilization and dynamics, showing how allosteric regulation was encrypted in MAPKs structure well before Ste5 appearance.
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Affiliation(s)
- Federica Guarra
- Department of Chemistry, University of Pavia, Via Taramelli 12, 27100, Pavia, Italia
| | - Giorgio Colombo
- Department of Chemistry, University of Pavia, Via Taramelli 12, 27100, Pavia, Italia
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2
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Castelli M, Magni A, Bonollo G, Pavoni S, Frigerio F, Oliveira ASF, Cinquini F, Serapian SA, Colombo G. Molecular mechanisms of chaperone-directed protein folding: Insights from atomistic simulations. Protein Sci 2023; 33:e4880. [PMID: 38145386 PMCID: PMC10895457 DOI: 10.1002/pro.4880] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2023] [Revised: 12/06/2023] [Accepted: 12/19/2023] [Indexed: 12/26/2023]
Abstract
Molecular chaperones, a family of proteins of which Hsp90 and Hsp70 are integral members, form an essential machinery to maintain healthy proteomes by controlling the folding and activation of a plethora of substrate client proteins. This is achieved through cycles in which Hsp90 and Hsp70, regulated by task-specific co-chaperones, process ATP and become part of a complex network that undergoes extensive compositional and conformational variations. Despite impressive advances in structural knowledge, the mechanisms that regulate the dynamics of functional assemblies, their response to nucleotides, and their relevance for client remodeling are still elusive. Here, we focus on the glucocorticoid receptor (GR):Hsp90:Hsp70:co-chaperone Hop client-loading and the GR:Hsp90:co-chaperone p23 client-maturation complexes, key assemblies in the folding cycle of glucocorticoid receptor (GR), a client strictly dependent upon Hsp90/Hsp70 for activity. Using a combination of molecular dynamics simulation approaches, we unveil with unprecedented detail the mechanisms that underpin function in these chaperone machineries. Specifically, we dissect the processes by which the nucleotide-encoded message is relayed to the client and how the distinct partners of the assemblies cooperate to (pre)organize partially folded GR during Loading and Maturation. We show how different ligand states determine distinct dynamic profiles for the functional interfaces defining the interactions in the complexes and modulate their overall flexibility to facilitate progress along the chaperone cycle. Finally, we also show that the GR regions engaged by the chaperone machinery display peculiar energetic signatures in the folded state, which enhance the probability of partial unfolding fluctuations. From these results, we propose a model where a dynamic cross-talk emerges between the chaperone dynamics states and remodeling of client-interacting regions. This factor, coupled to the highly dynamic nature of the assemblies and the conformational heterogeneity of their interactions, provides the basis for regulating the functions of distinct assemblies during the chaperoning cycle.
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Affiliation(s)
| | - Andrea Magni
- Dipartimento di Chimica, Università di Pavia, Pavia, Italy
| | | | - Silvia Pavoni
- Department of Physical Chemistry, R&D Eni SpA, San Donato Milanese, Italy
| | - Francesco Frigerio
- Department of Physical Chemistry, R&D Eni SpA, San Donato Milanese, Italy
| | - A Sofia F Oliveira
- Centre for Computational Chemistry, School of Chemistry, University of Bristol, Bristol, UK
| | - Fabrizio Cinquini
- Upstream & Technical Services - TECS/STES - Eni Spa, San Donato Milanese, Italy
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3
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Behairy MY, Eid RA, Otifi HM, Mohammed HM, Alshehri MA, Asiri A, Aldehri M, Zaki MSA, Darwish KM, Elhady SS, El-Shaer NH, Eldeen MA. Unraveling Extremely Damaging IRAK4 Variants and Their Potential Implications for IRAK4 Inhibitor Efficacy. J Pers Med 2023; 13:1648. [PMID: 38138875 PMCID: PMC10744719 DOI: 10.3390/jpm13121648] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2023] [Revised: 11/02/2023] [Accepted: 11/07/2023] [Indexed: 12/24/2023] Open
Abstract
Interleukin-1-receptor-associated kinase 4 (IRAK4) possesses a crucial function in the toll-like receptor (TLR) signaling pathway, and the dysfunction of this molecule could lead to various infectious and immune-related diseases in addition to cancers. IRAK4 genetic variants have been linked to various types of diseases. Therefore, we conducted a comprehensive analysis to recognize the missense variants with the most damaging impacts on IRAK4 with the employment of diverse bioinformatics tools to study single-nucleotide polymorphisms' effects on function, stability, secondary structures, and 3D structure. The residues' location on the protein domain and their conservation status were investigated as well. Moreover, docking tools along with structural biology were engaged in analyzing the SNPs' effects on one of the developed IRAK4 inhibitors. By analyzing IRAK4 gene SNPs, the analysis distinguished ten variants as the most detrimental missense variants. All variants were situated in highly conserved positions on an important protein domain. L318S and L318F mutations were linked to changes in IRAK4 secondary structures. Eight SNPs were revealed to have a decreasing effect on the stability of IRAK4 via both I-Mutant 2.0 and Mu-Pro tools, while Mu-Pro tool identified a decreasing effect for the G198E SNP. In addition, detrimental effects on the 3D structure of IRAK4 were also discovered for the selected variants. Molecular modeling studies highlighted the detrimental impact of these identified SNP mutant residues on the druggability of the IRAK4 ATP-binding site towards the known target inhibitor, HG-12-6, as compared to the native protein. The loss of important ligand residue-wise contacts, altered protein global flexibility, increased steric clashes, and even electronic penalties at the ligand-binding site interfaces were all suggested to be associated with SNP models for hampering the HG-12-6 affinity towards IRAK4 target protein. This given model lays the foundation for the better prediction of various disorders relevant to IRAK4 malfunction and sheds light on the impact of deleterious IRAK4 variants on IRAK4 inhibitor efficacy.
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Affiliation(s)
- Mohammed Y. Behairy
- Department of Microbiology and Immunology, Faculty of Pharmacy, University of Sadat City, Sadat City 32897, Egypt;
| | - Refaat A. Eid
- Department of Pathology, College of Medicine, King Khalid University, Abha P.O. Box 61421, Saudi Arabia; (R.A.E.); (H.M.O.)
| | - Hassan M. Otifi
- Department of Pathology, College of Medicine, King Khalid University, Abha P.O. Box 61421, Saudi Arabia; (R.A.E.); (H.M.O.)
| | - Heitham M. Mohammed
- Department of Anatomy, College of Medicine, King Khalid University, Abha P.O. Box 61421, Saudi Arabia; (H.M.M.); (M.A.); (M.S.A.Z.)
| | - Mohammed A. Alshehri
- Department of Child Health, College of Medicine, King Khalid University, Abha P.O. Box 62529, Saudi Arabia; (M.A.A.)
| | - Ashwag Asiri
- Department of Child Health, College of Medicine, King Khalid University, Abha P.O. Box 62529, Saudi Arabia; (M.A.A.)
| | - Majed Aldehri
- Department of Anatomy, College of Medicine, King Khalid University, Abha P.O. Box 61421, Saudi Arabia; (H.M.M.); (M.A.); (M.S.A.Z.)
| | - Mohamed Samir A. Zaki
- Department of Anatomy, College of Medicine, King Khalid University, Abha P.O. Box 61421, Saudi Arabia; (H.M.M.); (M.A.); (M.S.A.Z.)
| | - Khaled M. Darwish
- Department of Medicinal Chemistry, Faculty of Pharmacy, Suez Canal University, Ismailia 41522, Egypt;
| | - Sameh S. Elhady
- Department of Natural Products, Faculty of Pharmacy, King Abdulaziz University, Jeddah 21589, Saudi Arabia;
| | - Nahla H. El-Shaer
- Department of Zoology, Faculty of Science, Zagazig University, Zagazig 44511, Egypt;
| | - Muhammad Alaa Eldeen
- Department of Zoology, Faculty of Science, Zagazig University, Zagazig 44511, Egypt;
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4
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Casali E, Serapian SA, Gianquinto E, Castelli M, Bertinaria M, Spyrakis F, Colombo G. NLRP3 monomer functional dynamics: From the effects of allosteric binding to implications for drug design. Int J Biol Macromol 2023; 246:125609. [PMID: 37394218 DOI: 10.1016/j.ijbiomac.2023.125609] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2023] [Revised: 06/26/2023] [Accepted: 06/27/2023] [Indexed: 07/04/2023]
Abstract
The protein NLRP3 and its complexes are associated with an array of inflammatory pathologies, among which neurodegenerative, autoimmune, and metabolic diseases. Targeting the NLRP3 inflammasome represents a promising strategy for easing the symptoms of pathologic neuroinflammation. When the inflammasome is activated, NLRP3 undergoes a conformational change triggering the production of pro-inflammatory cytokines IL-1β and IL-18, as well as cell death by pyroptosis. NLRP3 nucleotide-binding and oligomerization (NACHT) domain plays a crucial role in this function by binding and hydrolysing ATP and is primarily responsible, together with conformational transitions involving the PYD domain, for the complex-assembly process. Allosteric ligands proved able to induce NLRP3 inhibition. Herein, we examine the origins of allosteric inhibition of NLRP3. Through the use of molecular dynamics (MD) simulations and advanced analysis methods, we provide molecular-level insights into how allosteric binding affects protein structure and dynamics, remodelling of the conformational ensembles populated by the protein, with key reverberations on how NLRP3 is preorganized for assembly and ultimately function. The data are used to develop a Machine Learning model to define the protein as Active or Inactive, only based on the analysis of its internal dynamics. We propose this model as a novel tool to select allosteric ligands.
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Affiliation(s)
- Emanuele Casali
- Department of Chemistry, University of Pavia, Viale Taramelli 12, 27100 Pavia, (Italy)
| | - Stefano A Serapian
- Department of Chemistry, University of Pavia, Viale Taramelli 12, 27100 Pavia, (Italy)
| | - Eleonora Gianquinto
- Department of Drug Science and Technology, University of Turin, Via Pietro Giuria 9, 10125 Torino, Italy
| | - Matteo Castelli
- Department of Chemistry, University of Pavia, Viale Taramelli 12, 27100 Pavia, (Italy)
| | - Massimo Bertinaria
- Department of Drug Science and Technology, University of Turin, Via Pietro Giuria 9, 10125 Torino, Italy
| | - Francesca Spyrakis
- Department of Drug Science and Technology, University of Turin, Via Pietro Giuria 9, 10125 Torino, Italy.
| | - Giorgio Colombo
- Department of Chemistry, University of Pavia, Viale Taramelli 12, 27100 Pavia, (Italy).
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5
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Triveri A, Casali E, Frasnetti E, Doria F, Frigerio F, Cinquini F, Pavoni S, Moroni E, Marchetti F, Serapian SA, Colombo G. Conformational Behavior of SARS-Cov-2 Spike Protein Variants: Evolutionary Jumps in Sequence Reverberate in Structural Dynamic Differences. J Chem Theory Comput 2023; 19:2120-2134. [PMID: 36926878 PMCID: PMC10029694 DOI: 10.1021/acs.jctc.3c00077] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/18/2023]
Abstract
SARS-CoV-2 has evolved rapidly in the first 3 years of pandemic diffusion. The initial evolution of the virus appeared to proceed through big jumps in sequence changes rather than through the stepwise accumulation of point mutations on already established variants. Here, we examine whether this nonlinear mutational process reverberates in variations of the conformational dynamics of the SARS-CoV-2 Spike protein (S-protein), the first point of contact between the virus and the human host. We run extensive microsecond-scale molecular dynamics simulations of seven distinct variants of the protein in their fully glycosylated state and set out to elucidate possible links between the mutational spectrum of the S-protein and the structural dynamics of the respective variant, at global and local levels. The results reveal that mutation-dependent structural and dynamic modulations mostly consist of increased coordinated motions in variants that acquire stability and in an increased internal flexibility in variants that are less stable. Importantly, a limited number of functionally important substructures (the receptor binding domain, in particular) share the same time of movements in all variants, indicating efficient preorganization for functional regions dedicated to host interactions. Our results support a model in which the internal dynamics of the S-proteins from different strains varies in a way that reflects the observed random and non-stepwise jumps in sequence evolution, while conserving the functionally oriented traits of conformational dynamics necessary to support productive interactions with host receptors.
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Affiliation(s)
- Alice Triveri
- Dipartimento di Chimica,
Università di Pavia, via Taramelli 12, 27100 Pavia,
Italy
| | - Emanuele Casali
- Dipartimento di Chimica,
Università di Pavia, via Taramelli 12, 27100 Pavia,
Italy
| | - Elena Frasnetti
- Dipartimento di Chimica,
Università di Pavia, via Taramelli 12, 27100 Pavia,
Italy
| | - Filippo Doria
- Dipartimento di Chimica,
Università di Pavia, via Taramelli 12, 27100 Pavia,
Italy
| | - Francesco Frigerio
- Department of Physical Chemistry, R&D
Eni SpA, via Maritano 27, 20097 San Donato Milanese (Mi),
Italy
| | - Fabrizio Cinquini
- Upstream & Technical
Services—TECS/STES—Eni Spa, via Emilia 1, 20097 San Donato
Milanese (Mi), Italy
| | - Silvia Pavoni
- Department of Physical Chemistry, R&D
Eni SpA, via Maritano 27, 20097 San Donato Milanese (Mi),
Italy
| | | | - Filippo Marchetti
- Dipartimento di Chimica,
Università di Pavia, via Taramelli 12, 27100 Pavia,
Italy
| | - Stefano A. Serapian
- Dipartimento di Chimica,
Università di Pavia, via Taramelli 12, 27100 Pavia,
Italy
| | - Giorgio Colombo
- Dipartimento di Chimica,
Università di Pavia, via Taramelli 12, 27100 Pavia,
Italy
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6
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Torielli L, Serapian SA, Mussolin L, Moroni E, Colombo G. Integrating Protein Interaction Surface Prediction with a Fragment-Based Drug Design: Automatic Design of New Leads with Fragments on Energy Surfaces. J Chem Inf Model 2023; 63:343-353. [PMID: 36574607 PMCID: PMC9832486 DOI: 10.1021/acs.jcim.2c01408] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
Protein-protein interactions (PPIs) have emerged in the past years as significant pharmacological targets in the development of new therapeutics due to their key roles in determining pathological pathways. Herein, we present fragments on energy surfaces, a simple and general design strategy that integrates the analysis of the dynamic and energetic signatures of proteins to unveil the substructures involved in PPIs, with docking, selection, and combination of drug-like fragments to generate new PPI inhibitor candidates. Specifically, structural representatives of the target protein are used as inputs for the blind physics-based prediction of potential protein interaction surfaces using the matrix of low coupling energy decomposition method. The predicted interaction surfaces are subdivided into overlapping windows that are used as templates to direct the docking and combination of fragments representative of moieties typically found in active drugs. This protocol is then applied and validated using structurally diverse, important PPI targets as test systems. We demonstrate that our approach facilitates the exploration of the molecular diversity space of potential ligands, with no requirement of prior information on the location and properties of interaction surfaces or on the structures of potential lead compounds. Importantly, the hit molecules that emerge from our ab initio design share high chemical similarity with experimentally tested active PPI inhibitors. We propose that the protocol we describe here represents a valuable means of generating initial leads against difficult targets for further development and refinement.
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Affiliation(s)
- Luca Torielli
- Department
of Chemistry, University of Pavia, Via Taramelli 12, Pavia27100, Italy
| | - Stefano A. Serapian
- Department
of Chemistry, University of Pavia, Via Taramelli 12, Pavia27100, Italy
| | - Lara Mussolin
- Department
of Woman’s and Child’s Health, Pediatric Hematology,
Oncology and Stem Cell Transplant Center, University of Padua, Via Giustiniani, 3, Padua35128, Italy,Istituto
di Ricerca Pediatrica Città della Speranza, Corso Stati Uniti, 4 F, Padova35127, Italy
| | | | - Giorgio Colombo
- Department
of Chemistry, University of Pavia, Via Taramelli 12, Pavia27100, Italy,
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7
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Triveri A, Sanchez-Martin C, Torielli L, Serapian SA, Marchetti F, D'Acerno G, Pirota V, Castelli M, Moroni E, Ferraro M, Quadrelli P, Rasola A, Colombo G. Protein allostery and ligand design: Computational design meets experiments to discover novel chemical probes. J Mol Biol 2022; 434:167468. [DOI: 10.1016/j.jmb.2022.167468] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2021] [Revised: 01/18/2022] [Accepted: 01/21/2022] [Indexed: 10/19/2022]
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8
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Serapian SA, Sanchez-Martín C, Moroni E, Rasola A, Colombo G. Targeting the mitochondrial chaperone TRAP1: strategies and therapeutic perspectives. Trends Pharmacol Sci 2021; 42:566-576. [PMID: 33992469 DOI: 10.1016/j.tips.2021.04.003] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2021] [Revised: 03/28/2021] [Accepted: 04/09/2021] [Indexed: 12/19/2022]
Abstract
TRAP1, the mitochondrial isoform of heat shock protein (Hsp)90 chaperones, is a key regulator of metabolism and organelle homeostasis in diverse pathological states. While selective TRAP1 targeting is an attractive goal, classical active-site-directed strategies have proved difficult, due to high active site conservation among Hsp90 paralogs. Here, we discuss advances in developing TRAP1-directed strategies, from lead modification with mitochondria delivery groups to the computational discovery of allosteric sites and ligands. Specifically, we address the unique opportunities that targeting TRAP1 opens up in tackling fundamental questions on its biology and in unveiling new therapeutic approaches. Finally, we show how crucial to this endeavor is our ability to predict the activities of TRAP1-selective allosteric ligands and to optimize target engagement to avoid side effects.
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Affiliation(s)
- Stefano A Serapian
- Dipartimento di Chimica, Università di Pavia. via Taramelli 12, I-27100 Pavia, Italy
| | - Carlos Sanchez-Martín
- Dipartimento di Scienze Biomediche, Università di Padova, viale G. Colombo 3, I-35131 Padova, Italy
| | | | - Andrea Rasola
- Dipartimento di Scienze Biomediche, Università di Padova, viale G. Colombo 3, I-35131 Padova, Italy.
| | - Giorgio Colombo
- Dipartimento di Chimica, Università di Pavia. via Taramelli 12, I-27100 Pavia, Italy.
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9
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Meli M, Morra G, Colombo G. Simple Model of Protein Energetics To Identify Ab Initio Folding Transitions from All-Atom MD Simulations of Proteins. J Chem Theory Comput 2020; 16:5960-5971. [PMID: 32693598 PMCID: PMC8009504 DOI: 10.1021/acs.jctc.0c00524] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
![]()
A fundamental
requirement to predict the native conformation, address
questions of sequence design and optimization, and gain insights into
the folding mechanisms of proteins lies in the definition of an unbiased
reaction coordinate that reports on the folding state without the
need to compare it to reference values, which might be unavailable
for new (designed) sequences. Here, we introduce such a reaction coordinate,
which does not depend on previous structural knowledge of the native
state but relies solely on the energy partition within the protein:
the spectral gap of the pair nonbonded energy matrix (ENergy Gap,
ENG). This quantity can be simply calculated along unbiased MD trajectories.
We show that upon folding the gap increases significantly, while its
fluctuations are reduced to a minimum. This is consistently observed
for a diverse set of systems and trajectories. Our approach allows
one to promptly identify residues that belong to the folding core
as well as residues involved in non-native contacts that need to be
disrupted to guide polypeptides to the folded state. The energy gap
and fluctuations criteria are then used to develop an automatic detection
system which allows us to extract and analyze folding transitions
from a generic MD trajectory. We speculate that our method can be
used to detect conformational ensembles in dynamic and intrinsically
disordered proteins, revealing potential preorganization for binding.
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Affiliation(s)
| | - Giulia Morra
- SCITEC-CNR, Via Mario Bianco 9, Milano 20131, Italy.,Weill-Cornell Medicine, 1300 York Avenue, New York, New York 10065, United States
| | - Giorgio Colombo
- SCITEC-CNR, Via Mario Bianco 9, Milano 20131, Italy.,University of Pavia, Department of Chemistry, Viale Taramelli 12, Pavia 27100, Italy
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10
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Verkhivker GM, Agajanian S, Hu G, Tao P. Allosteric Regulation at the Crossroads of New Technologies: Multiscale Modeling, Networks, and Machine Learning. Front Mol Biosci 2020; 7:136. [PMID: 32733918 PMCID: PMC7363947 DOI: 10.3389/fmolb.2020.00136] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2020] [Accepted: 06/08/2020] [Indexed: 12/12/2022] Open
Abstract
Allosteric regulation is a common mechanism employed by complex biomolecular systems for regulation of activity and adaptability in the cellular environment, serving as an effective molecular tool for cellular communication. As an intrinsic but elusive property, allostery is a ubiquitous phenomenon where binding or disturbing of a distal site in a protein can functionally control its activity and is considered as the "second secret of life." The fundamental biological importance and complexity of these processes require a multi-faceted platform of synergistically integrated approaches for prediction and characterization of allosteric functional states, atomistic reconstruction of allosteric regulatory mechanisms and discovery of allosteric modulators. The unifying theme and overarching goal of allosteric regulation studies in recent years have been integration between emerging experiment and computational approaches and technologies to advance quantitative characterization of allosteric mechanisms in proteins. Despite significant advances, the quantitative characterization and reliable prediction of functional allosteric states, interactions, and mechanisms continue to present highly challenging problems in the field. In this review, we discuss simulation-based multiscale approaches, experiment-informed Markovian models, and network modeling of allostery and information-theoretical approaches that can describe the thermodynamics and hierarchy allosteric states and the molecular basis of allosteric mechanisms. The wealth of structural and functional information along with diversity and complexity of allosteric mechanisms in therapeutically important protein families have provided a well-suited platform for development of data-driven research strategies. Data-centric integration of chemistry, biology and computer science using artificial intelligence technologies has gained a significant momentum and at the forefront of many cross-disciplinary efforts. We discuss new developments in the machine learning field and the emergence of deep learning and deep reinforcement learning applications in modeling of molecular mechanisms and allosteric proteins. The experiment-guided integrated approaches empowered by recent advances in multiscale modeling, network science, and machine learning can lead to more reliable prediction of allosteric regulatory mechanisms and discovery of allosteric modulators for therapeutically important protein targets.
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Affiliation(s)
- Gennady M. Verkhivker
- Graduate Program in Computational and Data Sciences, Schmid College of Science and Technology, Chapman University, Orange, CA, United States
- Department of Biomedical and Pharmaceutical Sciences, Chapman University School of Pharmacy, Irvine, CA, United States
| | - Steve Agajanian
- Graduate Program in Computational and Data Sciences, Schmid College of Science and Technology, Chapman University, Orange, CA, United States
| | - Guang Hu
- Center for Systems Biology, Department of Bioinformatics, School of Biology and Basic Medical Sciences, Soochow University, Suzhou, China
| | - Peng Tao
- Department of Chemistry, Center for Drug Discovery, Design, and Delivery (CD4), Center for Scientific Computation, Southern Methodist University, Dallas, TX, United States
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11
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Agajanian S, Oluyemi O, Verkhivker GM. Integration of Random Forest Classifiers and Deep Convolutional Neural Networks for Classification and Biomolecular Modeling of Cancer Driver Mutations. Front Mol Biosci 2019; 6:44. [PMID: 31245384 PMCID: PMC6579812 DOI: 10.3389/fmolb.2019.00044] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2019] [Accepted: 05/23/2019] [Indexed: 12/21/2022] Open
Abstract
Development of machine learning solutions for prediction of functional and clinical significance of cancer driver genes and mutations are paramount in modern biomedical research and have gained a significant momentum in a recent decade. In this work, we integrate different machine learning approaches, including tree based methods, random forest and gradient boosted tree (GBT) classifiers along with deep convolutional neural networks (CNN) for prediction of cancer driver mutations in the genomic datasets. The feasibility of CNN in using raw nucleotide sequences for classification of cancer driver mutations was initially explored by employing label encoding, one hot encoding, and embedding to preprocess the DNA information. These classifiers were benchmarked against their tree-based alternatives in order to evaluate the performance on a relative scale. We then integrated DNA-based scores generated by CNN with various categories of conservational, evolutionary and functional features into a generalized random forest classifier. The results of this study have demonstrated that CNN can learn high level features from genomic information that are complementary to the ensemble-based predictors often employed for classification of cancer mutations. By combining deep learning-generated score with only two main ensemble-based functional features, we can achieve a superior performance of various machine learning classifiers. Our findings have also suggested that synergy of nucleotide-based deep learning scores and integrated metrics derived from protein sequence conservation scores can allow for robust classification of cancer driver mutations with a limited number of highly informative features. Machine learning predictions are leveraged in molecular simulations, protein stability, and network-based analysis of cancer mutations in the protein kinase genes to obtain insights about molecular signatures of driver mutations and enhance the interpretability of cancer-specific classification models.
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Affiliation(s)
- Steve Agajanian
- Graduate Program in Computational and Data Sciences, Schmid College of Science and Technology, Chapman University, Orange, CA, United States
| | - Odeyemi Oluyemi
- Graduate Program in Computational and Data Sciences, Schmid College of Science and Technology, Chapman University, Orange, CA, United States
| | - Gennady M Verkhivker
- Graduate Program in Computational and Data Sciences, Schmid College of Science and Technology, Chapman University, Orange, CA, United States.,Department of Biomedical and Pharmaceutical Sciences, Chapman University School of Pharmacy, Irvine, CA, United States
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12
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Shao Q, Zhu W. Ligand binding effects on the activation of the EGFR extracellular domain. Phys Chem Chem Phys 2019; 21:8141-8151. [PMID: 30933195 DOI: 10.1039/c8cp07496h] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
The epidermal growth factor receptor (EGFR) is one of the most common target proteins in anti-cancer therapy. The binding of the EGF ligand to the EGFR extracellular domain (EGFR-ECD) promotes its inactive-to-active conformational transition (activation) but the relevant detailed mechanism remains elusive still. Here, the structural characterization and energetics of the EGFR-ECD conformational transition with and without the binding of the EGF are quantitatively explored using an innovative enhanced sampling MD simulation method. Intriguingly, the EGF offers hydrophobic interactions (e.g., EGF residues of Tyr44 and Leu47) and electrostatic interactions (e.g., the EGF residues of Glu5, Asp11, Asp17, and Arg41) to play a dominant role in dragging domain III to close the ligand binding domain gap. Subsequently, the correlation between domains III and II is enhanced through salt-bridges among Glu376, Arg403, and Arg405 from domain III and Glu293, Glu295, and Arg300 from domain II. Finally, the structural bending of domain II is regulated to facilitate the disengagement of domain II from domain IV. In this regard, the functional conformational transition of EGFR-ECD is a consequence of the cooperative motion of protein domains driven by the EGF ligand binding. The present study shows a detailed scenario of the EGF induced activation of EGFR-ECD and provides valuable information for drug discovery targeting the EGFR.
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Affiliation(s)
- Qiang Shao
- Drug Discovery and Design Center, CAS Key Laboratory of Receptor Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 555 Zuchongzhi Road, Shanghai, 201203, China.
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13
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Martin-Fernandez ML, Clarke DT, Roberts SK, Zanetti-Domingues LC, Gervasio FL. Structure and Dynamics of the EGF Receptor as Revealed by Experiments and Simulations and Its Relevance to Non-Small Cell Lung Cancer. Cells 2019; 8:E316. [PMID: 30959819 PMCID: PMC6523254 DOI: 10.3390/cells8040316] [Citation(s) in RCA: 33] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2019] [Revised: 03/29/2019] [Accepted: 03/30/2019] [Indexed: 12/25/2022] Open
Abstract
The epidermal growth factor receptor (EGFR) is historically the prototypical receptor tyrosine kinase, being the first cloned and the first where the importance of ligand-induced dimer activation was ascertained. However, many years of structure determination has shown that EGFR is not completely understood. One challenge is that the many structure fragments stored at the PDB only provide a partial view because full-length proteins are flexible entities and dynamics play a key role in their functionality. Another challenge is the shortage of high-resolution data on functionally important higher-order complexes. Still, the interest in the structure/function relationships of EGFR remains unabated because of the crucial role played by oncogenic EGFR mutants in driving non-small cell lung cancer (NSCLC). Despite targeted therapies against EGFR setting a milestone in the treatment of this disease, ubiquitous drug resistance inevitably emerges after one year or so of treatment. The magnitude of the challenge has inspired novel strategies. Among these, the combination of multi-disciplinary experiments and molecular dynamic (MD) simulations have been pivotal in revealing the basic nature of EGFR monomers, dimers and multimers, and the structure-function relationships that underpin the mechanisms by which EGFR dysregulation contributes to the onset of NSCLC and resistance to treatment.
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Affiliation(s)
- Marisa L Martin-Fernandez
- Central Laser Facility, Research Complex at Harwell, STFC Rutherford Appleton Laboratory, Harwell Oxford, Didcot, Oxford OX11 0QX, UK.
| | - David T Clarke
- Central Laser Facility, Research Complex at Harwell, STFC Rutherford Appleton Laboratory, Harwell Oxford, Didcot, Oxford OX11 0QX, UK.
| | - Selene K Roberts
- Central Laser Facility, Research Complex at Harwell, STFC Rutherford Appleton Laboratory, Harwell Oxford, Didcot, Oxford OX11 0QX, UK.
| | - Laura C Zanetti-Domingues
- Central Laser Facility, Research Complex at Harwell, STFC Rutherford Appleton Laboratory, Harwell Oxford, Didcot, Oxford OX11 0QX, UK.
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14
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Marchetti F, Capelli R, Rizzato F, Laio A, Colombo G. The Subtle Trade-Off between Evolutionary and Energetic Constraints in Protein-Protein Interactions. J Phys Chem Lett 2019; 10:1489-1497. [PMID: 30855965 DOI: 10.1021/acs.jpclett.9b00191] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/12/2023]
Abstract
Life machinery, although overwhelmingly complex, is rooted on a rather limited number of molecular processes. One of the most important is protein-protein interaction. Metabolic regulation, protein folding control, and cellular motility are examples of processes based on the fine-tuned interaction of several protein partners. The region on the protein surface devoted to the recognition of a specific partner is essential for the function of the protein and is, therefore, likely to be conserved during evolution. On the other hand, the physical chemistry of amino acids underlies the mechanism of interactions. Both evolutionary and energetic constraints can then be used to build scoring functions capable of recognizing interaction sites. Our working hypothesis is that residues within the interaction interface tend at the same time to be evolutionarily conserved (to preserve their function) and to provide little contribution to the internal stabilization of the structure of their cognate protein, to facilitate conformational adaptation to the partner. Here, we show that for some classes of protein partners (for example, those involved in signal transduction and in enzymes) evolutionary constraints play the key role in defining the interaction surface. In contrast, energetic constraints emerge as more important in protein partners involved in immune response, in inhibitor proteins, and in structural proteins. Our results indicate that a general-purpose scoring function for protein-protein interaction should not be agnostic of the biological function of the partners.
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Affiliation(s)
- Filippo Marchetti
- Istituto di Chimica del Riconoscimento Molecolare , CNR Via Mario Bianco 9 , 20131 Milano , Italy
- Dipartimento di Chimica , Università degli Studi di Milano , Via Venezian 21 , I-20133 Milano , Italy
| | - Riccardo Capelli
- INM-9/IAS-5 Computational Biomedicine , Forschungszentrum Jülich , Wilhelm-Johnen-Straße , D-54245 Jülich , Germany
| | - Francesca Rizzato
- SISSA, Scuola Internazionale Superiore Studi Avanzati , Via Bonomea 265 , I-34136 Trieste , Italy
| | - Alessandro Laio
- SISSA, Scuola Internazionale Superiore Studi Avanzati , Via Bonomea 265 , I-34136 Trieste , Italy
- ICTP, International Centre for Theoretical Physics , Strada Costiera 11 , I-34100 Trieste , Italy
| | - Giorgio Colombo
- Istituto di Chimica del Riconoscimento Molecolare , CNR Via Mario Bianco 9 , 20131 Milano , Italy
- Dipartimento di Chimica , Università di Pavia , V.le Taramelli 12 , 27100 Pavia , Italy
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15
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Paladino A, Civera M, Curnis F, Paolillo M, Gennari C, Piarulli U, Corti A, Belvisi L, Colombo G. The Importance of Detail: How Differences in Ligand Structures Determine Distinct Functional Responses in Integrin α
v
β
3. Chemistry 2019; 25:5959-5970. [DOI: 10.1002/chem.201900169] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2019] [Revised: 02/22/2019] [Indexed: 01/09/2023]
Affiliation(s)
- Antonella Paladino
- Istituto di Chimica del Riconoscimento Molecolare CNR via Mario Bianco 9 20131 Milan Italy
| | - Monica Civera
- Dipartimento di ChimicaUniversità degli Studi di Milano via Golgi 19 20133 Milan Italy
| | - Flavio Curnis
- IRCCS Ospedale San Raffaele Via Olgettina 60 20132 Milan Italy
| | - Mayra Paolillo
- Dipartimento di Scienze del FarmacoUniversità degli Studi di Pavia Viale Taramelli 6 27100 Pavia Italy
| | - Cesare Gennari
- Dipartimento di ChimicaUniversità degli Studi di Milano via Golgi 19 20133 Milan Italy
| | - Umberto Piarulli
- Dipartimento di Scienza e Alta TecnologiaUniversità degli Studi dell'Insubria Via Valleggio 11 22100 Como Italy
| | - Angelo Corti
- IRCCS Ospedale San Raffaele Via Olgettina 60 20132 Milan Italy
| | - Laura Belvisi
- Dipartimento di ChimicaUniversità degli Studi di Milano via Golgi 19 20133 Milan Italy
| | - Giorgio Colombo
- Dipartimento di ChimicaUniversità degli Studi di Pavia Viale Taramelli 12 27100 Pavia Italy
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16
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Creixell P, Pandey JP, Palmeri A, Bhattacharyya M, Creixell M, Ranganathan R, Pincus D, Yaffe MB. Hierarchical Organization Endows the Kinase Domain with Regulatory Plasticity. Cell Syst 2018; 7:371-383.e4. [PMID: 30243563 DOI: 10.1016/j.cels.2018.08.008] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2018] [Revised: 06/24/2018] [Accepted: 08/13/2018] [Indexed: 02/08/2023]
Abstract
The functional diversity of kinases enables specificity in cellular signal transduction. Yet how more than 500 members of the human kinome specifically receive regulatory inputs and convey information to appropriate substrates-all while using the common signaling output of phosphorylation-remains enigmatic. Here, we perform statistical co-evolution analysis, mutational scanning, and quantitative live-cell assays to reveal a hierarchical organization of the kinase domain that facilitates the orthogonal evolution of regulatory inputs and substrate outputs while maintaining catalytic function. We find that three quasi-independent "sectors"-groups of evolutionarily coupled residues-represent functional units in the kinase domain that encode for catalytic activity, substrate specificity, and regulation. Sector positions impact both disease and pharmacology: the catalytic sector is significantly enriched for somatic cancer mutations, and residues in the regulatory sector interact with allosteric kinase inhibitors. We propose that this functional architecture endows the kinase domain with inherent regulatory plasticity.
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Affiliation(s)
- Pau Creixell
- Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA 02139, USA; Center for Precision Cancer Medicine, Massachusetts Institute of Technology, Cambridge, MA 02139, USA; Departments of Biology and Bioengineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Jai P Pandey
- Whitehead Institute for Biomedical Research, Cambridge, MA 02142, USA
| | | | - Moitrayee Bhattacharyya
- Department of Molecular and Cell Biology and California Institute for Quantitative Biosciences, University of California, Berkeley, Berkeley, CA 94720, USA
| | - Marc Creixell
- Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA 02139, USA; Center for Precision Cancer Medicine, Massachusetts Institute of Technology, Cambridge, MA 02139, USA; Departments of Biology and Bioengineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Rama Ranganathan
- Center for Physics of Evolving Systems, Department of Biochemistry and Molecular Biology, Institute for Molecular Engineering, University of Chicago, Chicago, IL 60637, USA
| | - David Pincus
- Whitehead Institute for Biomedical Research, Cambridge, MA 02142, USA.
| | - Michael B Yaffe
- Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA 02139, USA; Center for Precision Cancer Medicine, Massachusetts Institute of Technology, Cambridge, MA 02139, USA; Departments of Biology and Bioengineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA; Department of Surgery, Beth Israel Deaconess Medical Center, Divisions of Acute Care Surgery, Trauma, and Critical Care and Surgical Oncology, Harvard Medical School, Boston 02215, USA.
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17
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Stetz G, Verkhivker GM. Functional Role and Hierarchy of the Intermolecular Interactions in Binding of Protein Kinase Clients to the Hsp90–Cdc37 Chaperone: Structure-Based Network Modeling of Allosteric Regulation. J Chem Inf Model 2018; 58:405-421. [DOI: 10.1021/acs.jcim.7b00638] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Affiliation(s)
- Gabrielle Stetz
- Graduate Program
in Computational and Data Sciences, Department of Computational Sciences,
Schmid College of Science and Technology, Chapman University, One University Drive, Orange, California 92866, United States
| | - Gennady M. Verkhivker
- Graduate Program
in Computational and Data Sciences, Department of Computational Sciences,
Schmid College of Science and Technology, Chapman University, One University Drive, Orange, California 92866, United States
- Chapman University School of Pharmacy, Irvine, California 92618, United States
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18
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Paladino A, Marchetti F, Ponzoni L, Colombo G. The Interplay between Structural Stability and Plasticity Determines Mutation Profiles and Chaperone Dependence in Protein Kinases. J Chem Theory Comput 2018; 14:1059-1070. [DOI: 10.1021/acs.jctc.7b00997] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Antonella Paladino
- Istituto di Chimica del Riconoscimento Molecolare, CNR, Via Mario Bianco 9, 20131 Milano, Italy
| | - Filippo Marchetti
- Istituto di Chimica del Riconoscimento Molecolare, CNR, Via Mario Bianco 9, 20131 Milano, Italy
| | - Luca Ponzoni
- Molecular
and Statistical Biophysics, International School for Advanced Studies (SISSA), I-34136 Trieste, Italy
| | - Giorgio Colombo
- Istituto di Chimica del Riconoscimento Molecolare, CNR, Via Mario Bianco 9, 20131 Milano, Italy
- Dipartimento
di Chimica, Università di Pavia, V.le Taramelli 12, 27100 Pavia, Italy
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19
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Czemeres J, Buse K, Verkhivker GM. Atomistic simulations and network-based modeling of the Hsp90-Cdc37 chaperone binding with Cdk4 client protein: A mechanism of chaperoning kinase clients by exploiting weak spots of intrinsically dynamic kinase domains. PLoS One 2017; 12:e0190267. [PMID: 29267381 PMCID: PMC5739471 DOI: 10.1371/journal.pone.0190267] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2017] [Accepted: 11/21/2017] [Indexed: 12/31/2022] Open
Abstract
A fundamental role of the Hsp90 and Cdc37 chaperones in mediating conformational development and activation of diverse protein kinase clients is essential in signal transduction. There has been increasing evidence that the Hsp90-Cdc37 system executes its chaperoning duties by recognizing conformational instability of kinase clients and modulating their folding landscapes. The recent cryo-electron microscopy structure of the Hsp90-Cdc37-Cdk4 kinase complex has provided a framework for dissecting regulatory principles underlying differentiation and recruitment of protein kinase clients to the chaperone machinery. In this work, we have combined atomistic simulations with protein stability and network-based rigidity decomposition analyses to characterize dynamic factors underlying allosteric mechanism of the chaperone-kinase cycle and identify regulatory hotspots that control client recognition. Through comprehensive characterization of conformational dynamics and systematic identification of stabilization centers in the unbound and client- bound Hsp90 forms, we have simulated key stages of the allosteric mechanism, in which Hsp90 binding can induce instability and partial unfolding of Cdk4 client. Conformational landscapes of the Hsp90 and Cdk4 structures suggested that client binding can trigger coordinated dynamic changes and induce global rigidification of the Hsp90 inter-domain regions that is coupled with a concomitant increase in conformational flexibility of the kinase client. This process is allosteric in nature and can involve reciprocal dynamic exchanges that exert global effect on stability of the Hsp90 dimer, while promoting client instability. The network-based rigidity analysis and emulation of thermal unfolding of the Cdk4-cyclin D complex and Hsp90-Cdc37-Cdk4 complex revealed weak spots of kinase instability that are present in the native Cdk4 structure and are targeted by the chaperone during client recruitment. Our findings suggested that this mechanism may be exploited by the Hsp90-Cdc37 chaperone to recruit and protect intrinsically dynamic kinase clients from degradation. The results of this investigation are discussed and interpreted in the context of diverse experimental data, offering new insights into mechanisms of chaperone regulation and binding.
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Affiliation(s)
- Josh Czemeres
- Department of Computational and Data Sciences, Schmid College of Science and Technology, Chapman University, Orange, California, United States of America
| | - Kurt Buse
- Department of Computational and Data Sciences, Schmid College of Science and Technology, Chapman University, Orange, California, United States of America
| | - Gennady M. Verkhivker
- Department of Computational and Data Sciences, Schmid College of Science and Technology, Chapman University, Orange, California, United States of America
- Department of Biomedical and Pharmaceutical Sciences, Chapman University School of Pharmacy, Irvine, California, United States of America
- * E-mail:
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20
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Stetz G, Tse A, Verkhivker GM. Ensemble-based modeling and rigidity decomposition of allosteric interaction networks and communication pathways in cyclin-dependent kinases: Differentiating kinase clients of the Hsp90-Cdc37 chaperone. PLoS One 2017; 12:e0186089. [PMID: 29095844 PMCID: PMC5667858 DOI: 10.1371/journal.pone.0186089] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2017] [Accepted: 09/25/2017] [Indexed: 12/24/2022] Open
Abstract
The overarching goal of delineating molecular principles underlying differentiation of protein kinase clients and chaperone-based modulation of kinase activity is fundamental to understanding activity of many oncogenic kinases that require chaperoning of Hsp70 and Hsp90 systems to attain a functionally competent active form. Despite structural similarities and common activation mechanisms shared by cyclin-dependent kinase (CDK) proteins, members of this family can exhibit vastly different chaperone preferences. The molecular determinants underlying chaperone dependencies of protein kinases are not fully understood as structurally similar kinases may often elicit distinct regulatory responses to the chaperone. The regulatory divergences observed for members of CDK family are of particular interest as functional diversification among these kinases may be related to variations in chaperone dependencies and can be exploited in drug discovery of personalized therapeutic agents. In this work, we report the results of a computational investigation of several members of CDK family (CDK5, CDK6, CDK9) that represented a broad repertoire of chaperone dependencies—from nonclient CDK5, to weak client CDK6, and strong client CDK9. By using molecular simulations of multiple crystal structures we characterized conformational ensembles and collective dynamics of CDK proteins. We found that the elevated dynamics of CDK9 can trigger imbalances in cooperative collective motions and reduce stability of the active fold, thus creating a cascade of favorable conditions for chaperone intervention. The ensemble-based modeling of residue interaction networks and community analysis determined how differences in modularity of allosteric networks and topography of communication pathways can be linked with the client status of CDK proteins. This analysis unveiled depleted modularity of the allosteric network in CDK9 that alters distribution of communication pathways and leads to impaired signaling in the client kinase. According to our results, these network features may uniquely define chaperone dependencies of CDK clients. The perturbation response scanning and rigidity decomposition approaches identified regulatory hotspots that mediate differences in stability and cooperativity of allosteric interaction networks in the CDK structures. By combining these synergistic approaches, our study revealed dynamic and network signatures that can differentiate kinase clients and rationalize subtle divergences in the activation mechanisms of CDK family members. The therapeutic implications of these results are illustrated by identifying structural hotspots of pathogenic mutations that preferentially target regions of the increased flexibility to enable modulation of activation changes. Our study offers a network-based perspective on dynamic kinase mechanisms and drug design by unravelling relationships between protein kinase dynamics, allosteric communications and chaperone dependencies.
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Affiliation(s)
- Gabrielle Stetz
- Department of Computational and Data Sciences, Schmid College of Science and Technology, Chapman University, Orange, California, United States of America
| | - Amanda Tse
- Department of Computational and Data Sciences, Schmid College of Science and Technology, Chapman University, Orange, California, United States of America
| | - Gennady M. Verkhivker
- Department of Computational and Data Sciences, Schmid College of Science and Technology, Chapman University, Orange, California, United States of America
- Department of Biomedical and Pharmaceutical Sciences, Chapman University School of Pharmacy, Irvine, California, United States of America
- * E-mail:
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21
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Verkhivker GM. Network-based modelling and percolation analysis of conformational dynamics and activation in the CDK2 and CDK4 proteins: dynamic and energetic polarization of the kinase lobes may determine divergence of the regulatory mechanisms. MOLECULAR BIOSYSTEMS 2017; 13:2235-2253. [DOI: 10.1039/c7mb00355b] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Network modeling and percolation analysis of conformational dynamics and energetics of regulatory mechanisms in cyclin-dependent kinases.
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Affiliation(s)
- G. M. Verkhivker
- Graduate Program in Computational and Data Sciences
- Department of Computational Biosciences
- Schmid College of Science and Technology
- Chapman University
- Orange
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22
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Allosteric Regulation Points Control the Conformational Dynamics of the Molecular Chaperone Hsp90. J Mol Biol 2016; 428:4559-4571. [DOI: 10.1016/j.jmb.2016.09.014] [Citation(s) in RCA: 41] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2016] [Revised: 09/15/2016] [Accepted: 09/15/2016] [Indexed: 01/02/2023]
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23
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Modeling the effect of pathogenic mutations on the conformational landscape of protein kinases. Curr Opin Struct Biol 2016; 37:108-14. [DOI: 10.1016/j.sbi.2016.01.005] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2015] [Revised: 01/08/2016] [Accepted: 01/12/2016] [Indexed: 12/13/2022]
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