1
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Syed A, Zhai J, Guo B, Zhao Y, Wang JCY, Chen L. Cryo-EM structure and molecular dynamic simulations explain the enhanced stability and ATP activity of the pathological chaperonin mutant. Structure 2024; 32:575-584.e3. [PMID: 38412855 PMCID: PMC11069440 DOI: 10.1016/j.str.2024.02.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2023] [Revised: 12/18/2023] [Accepted: 02/01/2024] [Indexed: 02/29/2024]
Abstract
Chaperonins Hsp60s are required for cellular vitality by assisting protein folding in an ATP-dependent mechanism. Although conserved, the human mitochondrial mHsp60 exhibits molecular characteristics distinct from the E. coli GroEL, with different conformational assembly and higher subunit association dynamics, suggesting a different mechanism. We previously found that the pathological mutant mHsp60V72I exhibits enhanced subunit association stability and ATPase activity. To provide structural explanations for the V72I mutational effects, here we determined a cryo-EM structure of mHsp60V72I. Our structural analysis combined with molecular dynamic simulations showed mHsp60V72I with increased inter-subunit interface, binding free energy, and dissociation force, all contributing to its enhanced subunit association stability. The gate to the nucleotide-binding (NB) site in mHsp60V72I mimicked the open conformation in the nucleotide-bound state with an additional open channel leading to the NB site, both promoting the mutant's ATPase activity. Our studies highlight the importance of mHsp60's characteristics in its biological function.
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Affiliation(s)
- Aiza Syed
- Department of Molecular and Cellular Biochemistry, Indiana University Bloomington, 212 S. Hawthorne Dr., Bloomington, IN 47405, USA
| | - Jihang Zhai
- The Key Laboratory of Natural Medicine and Immuno-Engineering, Henan University, Kaifeng, Henan 475000, China
| | - Baolin Guo
- The Key Laboratory of Natural Medicine and Immuno-Engineering, Henan University, Kaifeng, Henan 475000, China
| | - Yuan Zhao
- The Key Laboratory of Natural Medicine and Immuno-Engineering, Henan University, Kaifeng, Henan 475000, China.
| | - Joseph Che-Yen Wang
- Department of Microbiology and Immunology, The Pennsylvania State University College of Medicine, 500 University Drive, Hershey, PA 17033, USA.
| | - Lingling Chen
- Department of Molecular and Cellular Biochemistry, Indiana University Bloomington, 212 S. Hawthorne Dr., Bloomington, IN 47405, USA.
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2
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Ersoy A, Altintel B, Livnat Levanon N, Ben-Tal N, Haliloglu T, Lewinson O. Computational analysis of long-range allosteric communications in CFTR. eLife 2023; 12:RP88659. [PMID: 38109179 PMCID: PMC10727502 DOI: 10.7554/elife.88659] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2023] Open
Abstract
Malfunction of the CFTR protein results in cystic fibrosis, one of the most common hereditary diseases. CFTR functions as an anion channel, the gating of which is controlled by long-range allosteric communications. Allostery also has direct bearings on CF treatment: the most effective CFTR drugs modulate its activity allosterically. Herein, we integrated Gaussian network model, transfer entropy, and anisotropic normal mode-Langevin dynamics and investigated the allosteric communications network of CFTR. The results are in remarkable agreement with experimental observations and mutational analysis and provide extensive novel insight. We identified residues that serve as pivotal allosteric sources and transducers, many of which correspond to disease-causing mutations. We find that in the ATP-free form, dynamic fluctuations of the residues that comprise the ATP-binding sites facilitate the initial binding of the nucleotide. Subsequent binding of ATP then brings to the fore and focuses on dynamic fluctuations that were present in a latent and diffuse form in the absence of ATP. We demonstrate that drugs that potentiate CFTR's conductance do so not by directly acting on the gating residues, but rather by mimicking the allosteric signal sent by the ATP-binding sites. We have also uncovered a previously undiscovered allosteric 'hotspot' located proximal to the docking site of the phosphorylated regulatory (R) domain, thereby establishing a molecular foundation for its phosphorylation-dependent excitatory role. This study unveils the molecular underpinnings of allosteric connectivity within CFTR and highlights a novel allosteric 'hotspot' that could serve as a promising target for the development of novel therapeutic interventions.
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Affiliation(s)
- Ayca Ersoy
- Department of Chemical Engineering, Bogazici UniversityIstanbulTurkey
- Polymer Research Center, Bogazici UniversityIstanbulTurkey
| | - Bengi Altintel
- Department of Chemical Engineering, Bogazici UniversityIstanbulTurkey
- Polymer Research Center, Bogazici UniversityIstanbulTurkey
| | - Nurit Livnat Levanon
- Department of Molecular Microbiology, Bruce and Ruth Rappaport Faculty of Medicine, Technion-Israel Institute of TechnologyTel AvivIsrael
| | - Nir Ben-Tal
- Department of Biochemistry and Molecular Biology, Faculty of Life Sciences, Tel-Aviv UniversityTel-AvivIsrael
| | - Turkan Haliloglu
- Department of Chemical Engineering, Bogazici UniversityIstanbulTurkey
- Polymer Research Center, Bogazici UniversityIstanbulTurkey
| | - Oded Lewinson
- Department of Molecular Microbiology, Bruce and Ruth Rappaport Faculty of Medicine, Technion-Israel Institute of TechnologyTel AvivIsrael
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3
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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.
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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
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4
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Punia R, Goel G. Computation of the Protein Conformational Transition Pathway on Ligand Binding by Linear Response-Driven Molecular Dynamics. J Chem Theory Comput 2022; 18:3268-3283. [PMID: 35484642 DOI: 10.1021/acs.jctc.1c01243] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
While extremely important for relating the protein structure to its biological function, determination of the protein conformational transition pathway upon ligand binding is made difficult due to the transient nature of intermediates, a large and rugged conformational space, and coupling between protein dynamics and ligand-protein interactions. Existing methods that rely on prior knowledge of the bound (holo) state structure are restrictive. A second concern relates to the correspondence of intermediates obtained to the metastable states on the apo → holo transition pathway. Here, we have taken the protein apo structure and ligand-binding site as only inputs and combined an elastic network model (ENM) representation of the protein Hamiltonian with linear response theory (LRT) for protein-ligand interactions to identify the set of slow normal modes of protein vibrations that have a high overlap with the direction of the protein conformational change. The structural displacement along the chosen direction was performed using excited normal modes molecular dynamics (MDeNM) simulations rather than by the direct use of LRT. Herein, the MDeNM excitation velocity was optimized on-the-fly on the basis of its coupling to protein dynamics and ligand-protein interactions. Thus, a determined set of structures was validated against crystallographic and simulation data on four protein-ligand systems, namely, adenylate kinase-di(adenosine-5')pentaphosphate, ribose binding protein-β-d-ribopyranose, DNA β-glucosyltransferase-uridine-5'-diphosphate, and G-protein α subunit-guanosine-5'-triphosphate, which present important differences in protein conformational heterogeneity, ligand binding mechanism, viz. induced-fit or conformational selection, extent, and nonlinearity in protein conformational changes upon ligand binding, and presence of allosteric effects. The obtained set of intermediates was used as an input to path metadynamics simulations to obtain the free energy profile for the apo → holo transition.
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Affiliation(s)
- Rajat Punia
- Department of Chemical Engineering, Indian Institute of Technology Delhi, Hauz Khas, Delhi 110016, India
| | - Gaurav Goel
- Department of Chemical Engineering, Indian Institute of Technology Delhi, Hauz Khas, Delhi 110016, India
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5
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Protein Fluctuations in Response to Random External Forces. APPLIED SCIENCES-BASEL 2022. [DOI: 10.3390/app12052344] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
Elastic network models (ENMs) have been widely used in the last decades to investigate protein motions and dynamics. There the intrinsic fluctuations based on the isolated structures are obtained from the normal modes of these elastic networks, and they generally show good agreement with the B-factors extracted from X-ray crystallographic experiments, which are commonly considered to be indicators of protein flexibility. In this paper, we propose a new approach to analyze protein fluctuations and flexibility, which has a more appropriate physical basis. It is based on the application of random forces to the protein ENM to simulate the effects of collisions of solvent on a protein structure. For this purpose, we consider both the Cα-atom coarse-grained anisotropic network model (ANM) and an elastic network augmented with points included for the crystallized waters. We apply random forces to these protein networks everywhere, as well as only on the protein surface alone. Despite the randomness of the directions of the applied perturbations, the computed average displacements of the protein network show a remarkably good agreement with the experimental B-factors. In particular, for our set of 919 protein structures, we find that the highest correlation with the B-factors is obtained when applying forces to the external surface of the water-augmented ANM (an overall gain of 3% in the Pearson’s coefficient for the entire dataset, with improvements up to 30% for individual proteins), rather than when evaluating the fluctuations obtained from the normal modes of a standard Cα-atom coarse-grained ANM. It follows that protein fluctuations should be considered not just as the intrinsic fluctuations of the internal dynamics, but also equally well as responses to external solvent forces, or as a combination of both.
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6
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Khade PM, Scaramozzino D, Kumar A, Lacidogna G, Carpinteri A, Jernigan RL. hdANM: a new comprehensive dynamics model for protein hinges. Biophys J 2021; 120:4955-4965. [PMID: 34687719 PMCID: PMC8633836 DOI: 10.1016/j.bpj.2021.10.017] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2021] [Revised: 09/22/2021] [Accepted: 10/18/2021] [Indexed: 01/03/2023] Open
Abstract
Hinge motions are essential for many protein functions, and their dynamics are important to understand underlying biological mechanisms. The ways that these motions are represented by various computational methods differ significantly. By focusing on a specific class of motion, we have developed a new hinge-domain anisotropic network model (hdANM) that is based on the prior identification of flexible hinges and rigid domains in the protein structure and the subsequent generation of global hinge motions. This yields a set of motions in which the relative translations and rotations of the rigid domains are modulated and controlled by the deformation of the flexible hinges, leading to a more restricted, specific view of these motions. hdANM is the first model, to our knowledge, that combines information about protein hinges and domains to model the characteristic hinge motions of a protein. The motions predicted with this new elastic network model provide important conceptual advantages for understanding the underlying biological mechanisms. As a matter of fact, the generated hinge movements are found to resemble the expected mechanisms required for the biological functions of diverse proteins. Another advantage of this model is that the domain-level coarse graining makes it significantly more computationally efficient, enabling the generation of hinge motions within even the largest molecular assemblies, such as those from cryo-electron microscopy. hdANM is also comprehensive as it can perform in the same way as the well-known protein dynamics models (anisotropic network model, rotations-translations of blocks, and nonlinear rigid block normal mode analysis), depending on the definition of flexible and rigid parts in the protein structure and on whether the motions are extrapolated in a linear or nonlinear fashion. Furthermore, our results indicate that hdANM produces more realistic motions as compared to the anisotropic network model. hdANM is an open-source software, freely available, and hosted on a user-friendly website.
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Affiliation(s)
- Pranav M Khade
- Roy J. Carver Department of Biochemistry, Biophysics, and Molecular Biology, Iowa State University, Ames, Iowa
| | - Domenico Scaramozzino
- Department of Structural, Geotechnical, and Building Engineering, Politecnico di Torino, Torino, Italy
| | - Ambuj Kumar
- Roy J. Carver Department of Biochemistry, Biophysics, and Molecular Biology, Iowa State University, Ames, Iowa
| | - Giuseppe Lacidogna
- Department of Structural, Geotechnical, and Building Engineering, Politecnico di Torino, Torino, Italy
| | - Alberto Carpinteri
- Department of Structural, Geotechnical, and Building Engineering, Politecnico di Torino, Torino, Italy
| | - Robert L Jernigan
- Roy J. Carver Department of Biochemistry, Biophysics, and Molecular Biology, Iowa State University, Ames, Iowa.
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7
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Low-Frequency Harmonic Perturbations Drive Protein Conformational Changes. Int J Mol Sci 2021; 22:ijms221910501. [PMID: 34638837 PMCID: PMC8508695 DOI: 10.3390/ijms221910501] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2021] [Revised: 09/18/2021] [Accepted: 09/26/2021] [Indexed: 02/01/2023] Open
Abstract
Protein dynamics has been investigated since almost half a century, as it is believed to constitute the fundamental connection between structure and function. Elastic network models (ENMs) have been widely used to predict protein dynamics, flexibility and the biological mechanism, from which remarkable results have been found regarding the prediction of protein conformational changes. Starting from the knowledge of the reference structure only, these conformational changes have been usually predicted either by looking at the individual mode shapes of vibrations (i.e., by considering the free vibrations of the ENM) or by applying static perturbations to the protein network (i.e., by considering a linear response theory). In this paper, we put together the two previous approaches and evaluate the complete protein response under the application of dynamic perturbations. Harmonic forces with random directions are applied to the protein ENM, which are meant to simulate the single frequency-dependent components of the collisions of the surrounding particles, and the protein response is computed by solving the dynamic equations in the underdamped regime, where mass, viscous damping and elastic stiffness contributions are explicitly taken into account. The obtained motion is investigated both in the coordinate space and in the sub-space of principal components (PCs). The results show that the application of perturbations in the low-frequency range is able to drive the protein conformational change, leading to remarkably high values of direction similarity. Eventually, this suggests that protein conformational change might be triggered by external collisions and favored by the inherent low-frequency dynamics of the protein structure.
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8
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Paul S, Venkatramani R. Estimating the Directional Flexibility of Proteins from Equilibrium Thermal Fluctuations. J Chem Theory Comput 2021; 17:3103-3118. [PMID: 33818072 DOI: 10.1021/acs.jctc.0c01070] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The directional flexibility of proteins is an equilibrium molecular property which is accessible to both experiment and computation. Single molecule force spectroscopy (SMFS) experiments report effective directional spring constants to describe the collective anisotropic response of a protein structure to mechanical pulling forces applied along selected axes. On the other hand, computational methods have thus far employed either indirect force based nonequilibrium simulations or coarse-grained elastic network models (ENM) to predict protein directional spring constants. Here, we examine the ability of equilibrium atomistic Molecular Dynamics (MD) simulations to estimate the directional flexibility and mechanical anisotropy of proteins. MD-derived effective directional spring constants are found to correlate well with SMFS spring constants (ρ2 = 0.97-0.99; Adj R2 = 0.92-0.99) and unfolding forces (ρ2 = 0.85-0.97; Adj R2 = 0.63-0.91) for five different globular proteins. Specifically, the computed spring constants reproduce the mechanical anisotropy reported by SMFS along five different directions of green fluorescence protein (GFP) and six directions of the immunoglobulin-binding B1 domain of streptococcal protein G (GB1). Further, protein dynamics as captured in MD can be translated into spring constants which can distinguish the N-C directional flexibility of ubiquitin (Ub) from two structurally homologous small ubiquitin-like modifier (SUMO1 and SUMO2) isoforms. We apply our computational framework to study the mechanical anisotropy of Ub along the seven lysine-C-term directions which are functionally relevant. We show that Ub possesses two distinct flexibility scales along these directions which roughly differ by an order of magnitude. Further, our studies reveal that the mechanical anisotropy of Ub is modified in contrasting ways by the binding of two partner proteins (UBCH5A and UEV) which attach and recognize these biomolecular tag proteins. On the basis of equilibrium MD benchmarks for flexibility along 2485 bond vectors in Ub, we propose and validate a new covariance-propagation scheme to extract spring constants from ENM normal modes. We also critically examine the ability of ENM to predict directional flexibility of proteins and suggest modifications to improve these intuitive and scalable descriptions.
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Affiliation(s)
- Sanjoy Paul
- Department of Chemical Sciences, Tata Institute of Fundamental Research, Mumbai, 400 005, India
| | - Ravindra Venkatramani
- Department of Chemical Sciences, Tata Institute of Fundamental Research, Mumbai, 400 005, India
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9
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Modal Analysis of the Lysozyme Protein Considering All-Atom and Coarse-Grained Finite Element Models. APPLIED SCIENCES-BASEL 2021. [DOI: 10.3390/app11020547] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
Proteins are the fundamental entities of several organic activities. They are essential for a broad range of tasks in a way that their shapes and folding processes are crucial to achieving proper biological functions. Low-frequency modes, generally associated with collective movements at terahertz (THz) and sub-terahertz frequencies, have been appointed as critical for the conformational processes of many proteins. Dynamic simulations, such as molecular dynamics, are vastly applied by biochemical researchers in this field. However, in the last years, proposals that define the protein as a simplified elastic macrostructure have shown appealing results when dealing with this type of problem. In this context, modal analysis based on different modelization techniques, i.e., considering both an all-atom (AA) and coarse-grained (CG) representation, is proposed to analyze the hen egg-white lysozyme. This work presents new considerations and conclusions compared to previous analyses. Experimental values for the B-factor, considering all the heavy atoms or only one representative point per amino acid, are used to evaluate the validity of the numerical solutions. In general terms, this comparison allows the assessment of the regional flexibility of the protein. Besides, the low computational requirements make this approach a quick method to extract the protein’s dynamic properties under scrutiny.
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10
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Scaramozzino D, Khade PM, Jernigan RL, Lacidogna G, Carpinteri A. Structural compliance: A new metric for protein flexibility. Proteins 2020; 88:1482-1492. [PMID: 32548853 DOI: 10.1002/prot.25968] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2020] [Revised: 04/29/2020] [Accepted: 06/06/2020] [Indexed: 12/17/2022]
Abstract
Proteins are the active players in performing essential molecular activities throughout biology, and their dynamics has been broadly demonstrated to relate to their mechanisms. The intrinsic fluctuations have often been used to represent their dynamics and then compared to the experimental B-factors. However, proteins do not move in a vacuum and their motions are modulated by solvent that can impose forces on the structure. In this paper, we introduce a new structural concept, which has been called the structural compliance, for the evaluation of the global and local deformability of the protein structure in response to intramolecular and solvent forces. Based on the application of pairwise pulling forces to a protein elastic network, this structural quantity has been computed and sometimes is even found to yield an improved correlation with the experimental B-factors, meaning that it may serve as a better metric for protein flexibility. The inverse of structural compliance, namely the structural stiffness, has also been defined, which shows a clear anticorrelation with the experimental data. Although the present applications are made to proteins, this approach can also be applied to other biomolecular structures such as RNA. This present study considers only elastic network models, but the approach could be applied further to conventional atomic molecular dynamics. Compliance is found to have a slightly better agreement with the experimental B-factors, perhaps reflecting its bias toward the effects of local perturbations, in contrast to mean square fluctuations. The code for calculating protein compliance and stiffness is freely accessible at https://jerniganlab.github.io/Software/PACKMAN/Tutorials/compliance.
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Affiliation(s)
- Domenico Scaramozzino
- Department of Structural, Geotechnical and Building Engineering, Politecnico di Torino, Corso Duca degli Abruzzi, Torino, Italy
| | - Pranav M Khade
- Bioinformatics and Computational Biology Program, Roy J. Carver Department of Biochemistry, Biophysics and Molecular Biology, Iowa State University, Ames, Iowa, USA
| | - Robert L Jernigan
- Bioinformatics and Computational Biology Program, Roy J. Carver Department of Biochemistry, Biophysics and Molecular Biology, Iowa State University, Ames, Iowa, USA
| | - Giuseppe Lacidogna
- Department of Structural, Geotechnical and Building Engineering, Politecnico di Torino, Corso Duca degli Abruzzi, Torino, Italy
| | - Alberto Carpinteri
- Department of Structural, Geotechnical and Building Engineering, Politecnico di Torino, Corso Duca degli Abruzzi, Torino, Italy
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11
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Shape-preserving elastic solid models of macromolecules. PLoS Comput Biol 2020; 16:e1007855. [PMID: 32407309 PMCID: PMC7297265 DOI: 10.1371/journal.pcbi.1007855] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2019] [Revised: 06/09/2020] [Accepted: 04/07/2020] [Indexed: 02/07/2023] Open
Abstract
Mass-spring models have been a standard approach in molecular modeling for the last few decades, such as elastic network models (ENMs) that are widely used for normal mode analysis. In this work, we present a vastly different elastic solid model (ESM) of macromolecules that shares the same simplicity and efficiency as ENMs in producing the equilibrium dynamics and moreover, offers some significant new features that may greatly benefit the research community. ESM is different from ENM in that it treats macromolecules as elastic solids. Our particular version of ESM presented in this work, named αESM, captures the shape of a given biomolecule most economically using alpha shape, a well-established technique from the computational geometry community. Consequently, it can produce most economical coarse-grained models while faithfully preserving the shape and thus makes normal mode computations and visualization of extremely large complexes more manageable. Secondly, as a solid model, ESM’s close link to finite element analysis renders it ideally suited for studying mechanical responses of macromolecules under external force. Lastly, we show that ESM can be applied also to structures without atomic coordinates such as those from cryo-electron microscopy. The complete MATLAB code of αESM is provided. Mass-spring models have been a standard approach in classical molecular modeling where atoms are modeled as spheres with a mass and their interactions modeled as springs. The models have been extremely successful. Thinking ahead, however, as molecular systems of our interest grow more quickly in size or dimension than what our computation resources can keep up with, some adjustments in methodology are timely. This work presents a vastly different elastic solid model (ESM) of macromolecules that shares the same simplicity and efficiency as mass-spring models in producing the equilibrium dynamics and moreover, offers some unique features that make it suitable for much larger systems. ESM is different from ENMs in that it treats macromolecules as elastic solids. Our particular version of ESM model presented in this work, named αESM, captures the shape of a given biomolecule most economically using alpha shape, a well-established technique from the computational geometry community. Consequently, it can produce most economical coarse-grained models while faithfully preserving the shape. ESM can be applied also to structures without atomic coordinates such as those from cryo-electron microscopy.
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12
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Role of protein-protein interactions in allosteric drug design for DNA methyltransferases. ADVANCES IN PROTEIN CHEMISTRY AND STRUCTURAL BIOLOGY 2020; 121:49-84. [PMID: 32312426 DOI: 10.1016/bs.apcsb.2019.12.005] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
DNA methyltransferases (DNMTs) not only play key roles in epigenetic gene regulation, but also serve as emerging targets for several diseases, especially for cancers. Due to the multi-domains of DNMT structures, targeting allosteric sites of protein-protein interactions (PPIs) is becoming an attractive strategy in epigenetic drug discovery. This chapter aims to review the major contemporary approaches utilized for the drug discovery based on PPIs in different dimensions, from the enumeration of allosteric mechanism to the identification of allosteric pockets. These include the construction of protein structure networks (PSNs) based on molecular dynamics (MD) simulations, performing elastic network models (ENMs) and perturbation response scanning (PRS) calculation, the sequence-based conservation and coupling analysis, and the allosteric pockets identification. Furthermore, we complement this methodology by highlighting the role of computational approaches in promising practical applications for the computer-aided drug design, with special focus on two DNMTs, namely, DNMT1 and DNMT3A.
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13
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Dima RI, Stan G. Computational Studies of Mechanical Remodeling of Substrate Proteins by AAA+ Biological Nanomachines. ACS SYMPOSIUM SERIES 2020. [DOI: 10.1021/bk-2020-1356.ch008] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Affiliation(s)
- Ruxandra I. Dima
- Department of Chemistry, University of Cincinnati, P. O. Box 210172, Cincinnati, Ohio 45221, United States
| | - George Stan
- Department of Chemistry, University of Cincinnati, P. O. Box 210172, Cincinnati, Ohio 45221, United States
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Khade PM, Kumar A, Jernigan RL. Characterizing and Predicting Protein Hinges for Mechanistic Insight. J Mol Biol 2019; 432:508-522. [PMID: 31786268 DOI: 10.1016/j.jmb.2019.11.018] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2019] [Revised: 11/01/2019] [Accepted: 11/15/2019] [Indexed: 12/21/2022]
Abstract
The functioning of proteins requires highly specific dynamics, which depend critically on the details of how amino acids are packed. Hinge motions are the most common type of large motion, typified by the opening and closing of enzymes around their substrates. The packing and geometries of residues are characterized here by graph theory. This characterization is sufficient to enable reliable hinge predictions from a single static structure, and notably, this can be from either the open or the closed form of a structure. This new method to identify hinges within protein structures is called PACKMAN. The predicted hinges are validated by using permutation tests on B-factors. Hinge prediction results are compared against lists of manually curated hinge residues, and the results suggest that PACKMAN is robust enough to reproduce the known conformational changes and is able to predict hinge regions equally well from either the open or the closed forms of a protein. A group of 167 protein pairs with open and closed structures has been investigated Examples are shown for several additional proteins, including Zika virus nonstructured (NS) proteins where there are 6 hinge regions in the NS5 protein, 5 hinge regions in the NS2B bound in the NS3 protease complex and 5 hinges in the NS3- helicase protein. Results obtained from this method can be important for generating conformational ensembles of protein targets for drug design. PACKMAN is freely accessible at (https://PACKMAN.bb.iastate.edu/).
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Affiliation(s)
- Pranav M Khade
- Bioinformatics and Computational Biology Program, Roy J. Carver Department of Biochemistry, Biophysics and Molecular Biology, Iowa State University, Ames, IA, 50011, USA
| | - Ambuj Kumar
- Bioinformatics and Computational Biology Program, Roy J. Carver Department of Biochemistry, Biophysics and Molecular Biology, Iowa State University, Ames, IA, 50011, USA
| | - Robert L Jernigan
- Bioinformatics and Computational Biology Program, Roy J. Carver Department of Biochemistry, Biophysics and Molecular Biology, Iowa State University, Ames, IA, 50011, USA.
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15
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Zhang Y, Doruker P, Kaynak B, Zhang S, Krieger J, Li H, Bahar I. Intrinsic dynamics is evolutionarily optimized to enable allosteric behavior. Curr Opin Struct Biol 2019; 62:14-21. [PMID: 31785465 DOI: 10.1016/j.sbi.2019.11.002] [Citation(s) in RCA: 57] [Impact Index Per Article: 11.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2019] [Revised: 10/31/2019] [Accepted: 11/04/2019] [Indexed: 12/13/2022]
Abstract
Allosteric behavior is central to the function of many proteins, enabling molecular machinery, metabolism, signaling and regulation. Recent years have shown that the intrinsic dynamics of allosteric proteins defined by their 3-dimensional architecture or by the topology of inter-residue contacts favors cooperative motions that bear close similarity to structural changes they undergo during their allosteric actions. These conformational motions are usually driven by energetically favorable or soft modes at the low frequency end of the mode spectrum, and they are evolutionarily conserved among orthologs. These observations brought into light evolutionary adaptation mechanisms that help maintain, optimize or regulate allosteric behavior as the evolution from bacterial to higher organisms introduces sequential heterogeneities and structural complexities.
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Affiliation(s)
- Yan Zhang
- Department of Computational and Systems Biology, School of Medicine, University of Pittsburgh, 3501 Fifth Ave, Suite 3064 BST3, Pittsburgh, PA 15260, USA
| | - Pemra Doruker
- Department of Computational and Systems Biology, School of Medicine, University of Pittsburgh, 3501 Fifth Ave, Suite 3064 BST3, Pittsburgh, PA 15260, USA
| | - Burak Kaynak
- Department of Computational and Systems Biology, School of Medicine, University of Pittsburgh, 3501 Fifth Ave, Suite 3064 BST3, Pittsburgh, PA 15260, USA
| | - She Zhang
- Department of Computational and Systems Biology, School of Medicine, University of Pittsburgh, 3501 Fifth Ave, Suite 3064 BST3, Pittsburgh, PA 15260, USA
| | - James Krieger
- Department of Computational and Systems Biology, School of Medicine, University of Pittsburgh, 3501 Fifth Ave, Suite 3064 BST3, Pittsburgh, PA 15260, USA
| | - Hongchun Li
- Department of Computational and Systems Biology, School of Medicine, University of Pittsburgh, 3501 Fifth Ave, Suite 3064 BST3, Pittsburgh, PA 15260, USA; Research Center for Computer-Aided Drug Discovery, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen 518055, China
| | - Ivet Bahar
- Department of Computational and Systems Biology, School of Medicine, University of Pittsburgh, 3501 Fifth Ave, Suite 3064 BST3, Pittsburgh, PA 15260, USA.
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16
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Abdizadeh H, Atilgan AR, Atilgan C, Dedeoglu B. Computational approaches for deciphering the equilibrium and kinetic properties of iron transport proteins. Metallomics 2018; 9:1513-1533. [PMID: 28967944 DOI: 10.1039/c7mt00216e] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Abstract
With the advances in three-dimensional structure determination techniques, high quality structures of the iron transport proteins transferrin and the bacterial ferric binding protein (FbpA) have been deposited in the past decade. These are proteins of relatively large size, and developments in hardware and software have only recently made it possible to study their dynamics using standard computational resources. We review computational techniques towards understanding the equilibrium and kinetic properties of iron transport proteins under different environmental conditions. At the level of detail that requires quantum chemical treatments, the octahedral geometry around iron has been scrutinized and it has been established that the iron coordinating tyrosines are in an unusual deprotonated state. At the atomistic level, both the N-lobe and the full bilobal structure of transferrin have been studied under varying conditions of pH, ionic strength and binding of other metal ions by molecular dynamics (MD) simulations. These studies have allowed questions to be answered, among others, on the function of second shell residues in iron release, the role of synergistic anions in preparing the active site for iron binding, and the differences between the kinetics of the N- and the C-lobe. MD simulations on FbpA have led to the detailed observation of the binding kinetics of phosphate to the apo form, and to the conformational preferences of the holo form under conditions mimicking the environmental niches provided by the periplasmic space. To study the dynamics of these proteins with their receptors, one must resort to coarse-grained methodologies, since these systems are prohibitively large for atomistic simulations. A study of the complex of human transferrin (hTf) with its pathogenic receptor by such methods has revealed a potential mechanistic explanation for the defense mechanism that arises in evolutionary warfare. Meanwhile, the motions in the transferrin receptor bound hTf have been shown to disfavor apo hTf dissociation, explaining why the two proteins remain in complex during the recycling process from the endosome to the cell surface. Open problems and possible technological applications related to metal ion binding-release in iron transport proteins that may be handled by hybrid use of quantum mechanical, MD and coarse-grained approaches are discussed.
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Affiliation(s)
- H Abdizadeh
- Faculty of Engineering and Natural Sciences, Sabancı University, Orhanlı 34956, Tuzla, Istanbul, Turkey.
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17
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Vilasi S, Bulone D, Caruso Bavisotto C, Campanella C, Marino Gammazza A, San Biagio PL, Cappello F, Conway de Macario E, Macario AJL. Chaperonin of Group I: Oligomeric Spectrum and Biochemical and Biological Implications. Front Mol Biosci 2018; 4:99. [PMID: 29423396 PMCID: PMC5788889 DOI: 10.3389/fmolb.2017.00099] [Citation(s) in RCA: 46] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2017] [Accepted: 12/28/2017] [Indexed: 01/13/2023] Open
Abstract
Chaperonins play various physiological roles and can also be pathogenic. Elucidation of their structure, e.g., oligomeric status and post-translational modifications (PTM), is necessary to understand their functions and mechanisms of action in health and disease. Group I chaperonins form tetradecamers with two stacked heptameric rings. The tetradecamer is considered the typical functional complex for folding of client polypeptides. However, other forms such as the monomer and oligomers with smaller number of subunits than the classical tetradecamer, also occur in cells. The properties and functions of the monomer and oligomers, and their roles in chaperonin-associated diseases are still incompletely understood. Chaperonin I in eukaryotes occurs in various locations, not just the mitochondrion, which is its canonical place of residence and function. Eukaryotic Chaperonin I, namely Hsp60 (designated HSP60 or HSPD1 in humans) has, indeed, been found in the cytosol; the plasma-cell membrane; on the outer surface of cells; in the intercellular space; in biological liquids such as lymph, blood, and cerebrospinal fluid; and in secretions, for instance saliva and urine. Hsp60 has also been found in cell-derived vesicles such as exosomes. The functions of Hsp60 in all these non-canonical locales are still poorly characterized and one of the questions not yet answered is in what form, i.e., monomer or oligomer, is the chaperonin present in these non-canonical locations. In view of the steady increase in interest on chaperonopathies over the last several years, we have studied human HSP60 to determine its role in various diseases, its locations in cells and tissues and migrations in the body, and its post-translational modifications that might have an impact on its location and function. We also carried out experiments to characterize the oligomeric status of extramitochondrial of HSP60 in solution. Here, we provide an overview of our results, focusing on the oligomeric equilibrium and stability of the various forms of HSP60 in comparison with GroEL. We also discuss post-translational modifications associated with anti-cancer drugs to indicate the potential of Hsp60 in Medicine, as a biomarker and etiopathogenic factor.
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Affiliation(s)
- Silvia Vilasi
- Institute of Biophysics, National Research Council, Palermo, Italy
| | - Donatella Bulone
- Institute of Biophysics, National Research Council, Palermo, Italy
| | - Celeste Caruso Bavisotto
- Section of Human Anatomy, Department of Experimental Biomedicine and Clinical Neuroscience (BIONEC), University of Palermo, Palermo, Italy.,Euro-Mediterranean Institute of Science and Technology (IEMEST), Palermo, Italy
| | - Claudia Campanella
- Section of Human Anatomy, Department of Experimental Biomedicine and Clinical Neuroscience (BIONEC), University of Palermo, Palermo, Italy.,Euro-Mediterranean Institute of Science and Technology (IEMEST), Palermo, Italy
| | - Antonella Marino Gammazza
- Section of Human Anatomy, Department of Experimental Biomedicine and Clinical Neuroscience (BIONEC), University of Palermo, Palermo, Italy.,Euro-Mediterranean Institute of Science and Technology (IEMEST), Palermo, Italy
| | | | - Francesco Cappello
- Section of Human Anatomy, Department of Experimental Biomedicine and Clinical Neuroscience (BIONEC), University of Palermo, Palermo, Italy.,Euro-Mediterranean Institute of Science and Technology (IEMEST), Palermo, Italy
| | - Everly Conway de Macario
- Department of Microbiology and Immunology, School of Medicine, University of Maryland at Baltimore, and Institute of Marine and Environmental Technology (IMET), Columbus Center, Baltimore, MD, United States
| | - Alberto J L Macario
- Euro-Mediterranean Institute of Science and Technology (IEMEST), Palermo, Italy.,Department of Microbiology and Immunology, School of Medicine, University of Maryland at Baltimore, and Institute of Marine and Environmental Technology (IMET), Columbus Center, Baltimore, MD, United States
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Computational Methods for Efficient Sampling of Protein Landscapes and Disclosing Allosteric Regions. COMPUTATIONAL MOLECULAR MODELLING IN STRUCTURAL BIOLOGY 2018; 113:33-63. [DOI: 10.1016/bs.apcsb.2018.06.001] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
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