1
|
Quiroz RCN, Philot EA, General IJ, Perahia D, Scott AL. Effect of phosphorylation on the structural dynamics, thermal stability of human dopamine transporter: A simulation study using normal modes, molecular dynamics and Markov State Model. J Mol Graph Model 2023; 118:108359. [PMID: 36279761 DOI: 10.1016/j.jmgm.2022.108359] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2022] [Revised: 10/04/2022] [Accepted: 10/06/2022] [Indexed: 11/06/2022]
Abstract
The Human Dopamine Transporter (hDAT) plays an essential role in modulating the Influx/Efflux of dopamine, and it is involved in the mechanism of certain neurodegenerative diseases such as Parkinson's disease. Several studies have reported important states for Dopamine transport: outward-facing open state (OFo), the outward-facing closed state (OFc), the holo-occluded state closed (holo), and the inward-facing open state (IFo). Furthermore, experimental assays have shown that different phosphorylation conditions in hDAT can affect the rate of dopamine absorption. We present a protocol using hybrid simulation methods to study the conformational dynamics and stability of states of hDAT under different phosphorylation sites. With this protocol, we explored the conformational space of hDAT, identified the states, and evaluated the free energy differences and the transition probabilities between them in each of the phosphorylation cases. We also presented the conformational changes and correlated them with those described in the literature. There is a thesis/hypothesis that the phosphorylation condition corresponding to NP-333 system (where all sites Ser/Thr from residue 2 to 62 and 254 to 613 are phosphorylated, except residue 333) would decrease the rate of dopamine transport from the extracellular medium to the intracellular medium by hDAT as previously described in the literature by Lin et al., 2003. Our results corroborated this thesis/hypothesis and the data reported. It is probably due to the affectation/changes/alteration of the conformational dynamics of this system that makes the intermediate states more likely and makes it difficult to initial states associated with the uptake of dopamine in the extracellular medium, corroborating the experimental results. Furthermore, our results showed that just single phosphorylation/dephosphorylation could alter intrinsic protein motions affecting the sampling of one or more states necessary for dopamine transport. In this sense, the modification of phosphorylation influences protein movements and conformational preferences, affecting the stability of states and the transition between them and, therefore, the transport.
Collapse
Affiliation(s)
- R C N Quiroz
- Biossistemas, Universidade Federal do ABC, CCNH, Santo André, Brazil; Centro de Matemática, Computação e Cognição. Laboratório de Biofísica e Biologia Computacional. Universidade Federal do ABC, Santo André, São Paulo, Brazil
| | - E A Philot
- Centro de Matemática, Computação e Cognição. Laboratório de Biofísica e Biologia Computacional. Universidade Federal do ABC, Santo André, São Paulo, Brazil
| | - I J General
- School of Science and Technology, Universidad Nacional de San Martin, ICIFI and CONICET, 25 de Mayo y Francia, San Martín, 1650, Buenos Aires, Argentina
| | - D Perahia
- Laboratoire de Biologie et Pharmacologie Appliquée, Ecole Normale Supérieure Paris-Saclay, UMR 8113, CNRS, 4 avenue des Sciences, 91190 Gif-sur-Yvette, France
| | - A L Scott
- UFABC - Universidade Federal Do ABC, Centro de Matemática, Computação e Cognição, Laboratório de Biofísica e Biologia Computacional, Brazil.
| |
Collapse
|
2
|
Oliveira RJD. Coordinate-Dependent Drift-Diffusion Reveals the Kinetic Intermediate Traps of Top7-Based Proteins. J Phys Chem B 2022; 126:10854-10869. [PMID: 36519977 DOI: 10.1021/acs.jpcb.2c07031] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
The computer-designed Top7 served as a scaffold to produce immunoreactive proteins by grafting of the 2F5 HIV-1 antibody epitope (Top7-2F5) followed by biotinylation (Top7-2F5-biotin). The resulting nonimmunoglobulin affinity proteins were effective in inducing and detecting the HIV-1 antibody. However, the grafted Top7-2F5 design led to protein aggregation, as opposed to the soluble biotinylated Top7-2F5-biotin. The structure-based model predicted that the thermodynamic cooperativity of Top7 increases after grafting and biotin-labeling, reducing their intermediate state populations. In this work, the folding kinetic traps that might contribute to the aggregation propensity are investigated by the diffusion theory. Since the engineered proteins have similar sequence and structural homology, they served as protein models to study the kinetic intermediate traps that were uncovered by characterizing the position-dependent drift-velocity (v(Q)) and the diffusion (D(Q)) coefficients. These coordinate-dependent coefficients were taken into account to obtain the folding and transition path times over the free energy transition states containing the intermediate kinetic traps. This analysis may be useful to predict the aggregated kinetic traps of scaffold-epitope proteins that might compose novel diagnostic and therapeutic platforms.
Collapse
Affiliation(s)
- Ronaldo Junio de Oliveira
- Laboratório de Biofísica Teórica, Departamento de Física, Instituto de Ciências Exatas, Naturais e Educação, Universidade Federal do Triângulo Mineiro, Uberaba, MG38064-200, Brazil
| |
Collapse
|
3
|
Oliveira RJD. Biotinylation Eliminates the Intermediate State of Top7 Designed with an HIV-1 Epitope. J Phys Chem B 2022; 126:7331-7342. [PMID: 36121918 DOI: 10.1021/acs.jpcb.2c04969] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Broadly neutralizing antibodies against HIV-1 are rare with the 2F5 antibody being one of the most protective. Insertion of an antibody epitope into a stable and small protein scaffold overcomes many of the obstacles found to produce antibodies. However, the design leads to grafting of epitopes that may cause protein aggregation. Here, I investigated the 2F5 epitope grafted into the Top7 as the scaffold in which the resulting immunoreactive protein precipitates along the storage time, as opposed to its completely soluble biotinylated version. Molecular dynamics showed that biotinylation eliminates the intermediate state of the scaffold-epitope Top7-2F5 by switching a noncooperative to a cooperative folding. The aggregation propensity of the Top7-designed proteins is examined in light of thermodynamic cooperativity and kinetic traps along the decreasing depth of the intermediate ensemble in the free energy landscape. This protocol may predict stable and soluble scaffold-epitopes with the purpose of composing novel therapeutic and diagnostic platforms.
Collapse
Affiliation(s)
- Ronaldo Junio de Oliveira
- Laboratório de Biofísica Teórica, Departamento de Física, Instituto de Ciências Exatas, Naturais e Educação, Universidade Federal do Triângulo Mineiro, Uberaba, MG 38064-200, Brazil
| |
Collapse
|
4
|
Freitas FC, Maldonado M, Oliveira Junior AB, Onuchic JN, Oliveira RJD. Biotin-painted proteins have thermodynamic stability switched by kinetic folding routes. J Chem Phys 2022; 156:195101. [PMID: 35597640 DOI: 10.1063/5.0083875] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023] Open
Abstract
Biotin-labeled proteins are widely used as tools to study protein-protein interactions and proximity in living cells. Proteomic methods broadly employ proximity-labeling technologies based on protein biotinylation in order to investigate the transient encounters of biomolecules in subcellular compartments. Biotinylation is a post-translation modification in which the biotin molecule is attached to lysine or tyrosine residues. So far, biotin-based technologies proved to be effective instruments as affinity and proximity tags. However, the influence of biotinylation on aspects such as folding, binding, mobility, thermodynamic stability, and kinetics needs to be investigated. Here, we selected two proteins [biotin carboxyl carrier protein (BCCP) and FKBP3] to test the influence of biotinylation on thermodynamic and kinetic properties. Apo (without biotin) and holo (biotinylated) protein structures were used separately to generate all-atom structure-based model simulations in a wide range of temperatures. Holo BCCP contains one biotinylation site, and FKBP3 was modeled with up to 23 biotinylated lysines. The two proteins had their estimated thermodynamic stability changed by altering their energy landscape. In all cases, after comparison between the apo and holo simulations, differences were observed on the free-energy profiles and folding routes. Energetic barriers were altered with the density of states clearly showing changes in the transition state. This study suggests that analysis of large-scale datasets of biotinylation-based proximity experiments might consider possible alterations in thermostability and folding mechanisms imposed by the attached biotins.
Collapse
Affiliation(s)
- Frederico Campos Freitas
- Laboratório de Biofísica Teórica, Departamento de Física, Instituto de Ciências Exatas, Naturais e Educação, Universidade Federal do Triângulo Mineiro, Uberaba, MG 38064-200, Brazil
| | - Michelli Maldonado
- Departamento de Matemática, Instituto de Ciências Exatas, Naturais e Educação, Universidade Federal do Triângulo Mineiro, Uberaba, MG 38064-200, Brazil
| | - Antonio Bento Oliveira Junior
- Center for Theoretical Biological Physics, Rice University, BioScience Research Collaborative, 6566 Main St., Houston, Texas 77030, USA
| | - José Nelson Onuchic
- Center for Theoretical Biological Physics, Rice University, BioScience Research Collaborative, 6566 Main St., Houston, Texas 77030, USA
| | - Ronaldo Junio de Oliveira
- Laboratório de Biofísica Teórica, Departamento de Física, Instituto de Ciências Exatas, Naturais e Educação, Universidade Federal do Triângulo Mineiro, Uberaba, MG 38064-200, Brazil
| |
Collapse
|
5
|
Crestini A, Santilli F, Martellucci S, Carbone E, Sorice M, Piscopo P, Mattei V. Prions and Neurodegenerative Diseases: A Focus on Alzheimer's Disease. J Alzheimers Dis 2021; 85:503-518. [PMID: 34864675 DOI: 10.3233/jad-215171] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Specific protein misfolding and aggregation are mechanisms underlying various neurodegenerative diseases such as prion disease and Alzheimer's disease (AD). The misfolded proteins are involved in prions, amyloid-β (Aβ), tau, and α-synuclein disorders; they share common structural, biological, and biochemical characteristics, as well as similar mechanisms of aggregation and self-propagation. Pathological features of AD include the appearance of plaques consisting of deposition of protein Aβ and neurofibrillary tangles formed by the hyperphosphorylated tau protein. Although it is not clear how protein aggregation leads to AD, we are learning that the cellular prion protein (PrPC) plays an important role in the pathogenesis of AD. Herein, we first examined the pathogenesis of prion and AD with a focus on the contribution of PrPC to the development of AD. We analyzed the mechanisms that lead to the formation of a high affinity bond between Aβ oligomers (AβOs) and PrPC. Also, we studied the role of PrPC as an AβO receptor that initiates an AβO-induced signal cascade involving mGluR5, Fyn, Pyk2, and eEF2K linking Aβ and tau pathologies, resulting in the death of neurons in the central nervous system. Finally, we have described how the PrPC-AβOs interaction can be used as a new potential therapeutic target for the treatment of PrPC-dependent AD.
Collapse
Affiliation(s)
- Alessio Crestini
- Department of Neuroscience, Istituto Superiore di Sanità, Rome, Italy
| | - Francesca Santilli
- Biomedicine and Advanced Technologies Rieti Center, "Sabina Universitas", Rieti, Italy.,Department of Experimental Medicine, "Sapienza" University, Rome, Italy
| | - Stefano Martellucci
- Biomedicine and Advanced Technologies Rieti Center, "Sabina Universitas", Rieti, Italy
| | - Elena Carbone
- Department of Neuroscience, Istituto Superiore di Sanità, Rome, Italy
| | - Maurizio Sorice
- Department of Experimental Medicine, "Sapienza" University, Rome, Italy
| | - Paola Piscopo
- Department of Neuroscience, Istituto Superiore di Sanità, Rome, Italy
| | - Vincenzo Mattei
- Biomedicine and Advanced Technologies Rieti Center, "Sabina Universitas", Rieti, Italy.,Department of Experimental Medicine, "Sapienza" University, Rome, Italy
| |
Collapse
|
6
|
Krieger JM, Doruker P, Scott AL, Perahia D, Bahar I. Towards gaining sight of multiscale events: utilizing network models and normal modes in hybrid methods. Curr Opin Struct Biol 2020; 64:34-41. [PMID: 32622329 DOI: 10.1016/j.sbi.2020.05.013] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2020] [Revised: 05/13/2020] [Accepted: 05/20/2020] [Indexed: 11/28/2022]
Abstract
With the explosion of normal mode analyses (NMAs) based on elastic network models (ENMs) in the last decade, and the proven precision of MD simulations for visualizing interactions at atomic scale, many hybrid methods have been proposed in recent years. These aim at exploiting the best of both worlds: the atomic precision of MD that often fall short of exploring time and length scales of biological interest, and the capability of ENM-NMA to predict the cooperative and often functional rearrangements of large structures and assemblies, albeit at low resolution. We present an overview of recent progress in the field with examples of successful applications highlighting the utility of such hybrid methods and pointing to emerging future directions guided by advances in experimental characterization of biomolecular systems structure and dynamics.
Collapse
Affiliation(s)
- James M Krieger
- 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
| | - Ana Ligia Scott
- Laboratory of Bioinformatics and Computational Biology, Federal University of ABC, Santo André, SP, Brazil
| | - David Perahia
- Laboratoire de Biologie et de Pharmacologie Appliquée, Ecole Normale Superieure Paris-Saclay, UMR 8113, CNRS, 4 Avenue des Sciences, 91190 Gif-sur-Yvette, France
| | - Ivet Bahar
- Department of Computational and Systems Biology, School of Medicine, University of Pittsburgh, 3501 Fifth Ave, Suite 3064 BST3, Pittsburgh, PA 15260, USA.
| |
Collapse
|
7
|
Prion Protein in Stem Cells: A Lipid Raft Component Involved in the Cellular Differentiation Process. Int J Mol Sci 2020; 21:ijms21114168. [PMID: 32545192 PMCID: PMC7312503 DOI: 10.3390/ijms21114168] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2020] [Revised: 06/08/2020] [Accepted: 06/09/2020] [Indexed: 12/13/2022] Open
Abstract
The prion protein (PrP) is an enigmatic molecule with a pleiotropic effect on different cell types; it is localized stably in lipid raft microdomains and it is able to recruit downstream signal transduction pathways by its interaction with various biochemical partners. Since its discovery, this lipid raft component has been involved in several functions, although most of the publications focused on the pathological role of the protein. Recent studies report a key role of cellular prion protein (PrPC) in physiological processes, including cellular differentiation. Indeed, the PrPC, whose expression is modulated according to the cell differentiation degree, appears to be part of the multimolecular signaling pathways of the neuronal differentiation process. In this review, we aim to summarize the main findings that report the link between PrPC and stem cells.
Collapse
|
8
|
Xu Z, Liu H, Wang S, Zhang Q, Yao X, Zhou S, Liu H. Unraveling the Molecular Mechanism of Prion H2 C-Terminus Misfolding by Metadynamics Simulations. ACS Chem Neurosci 2020; 11:772-782. [PMID: 32023408 DOI: 10.1021/acschemneuro.9b00679] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
Conformational transition from the normal cellular form of prion protein (PrPC) to the pathogenic "scrapie" form (PrPSc) is considered to be a key event in the occurrence of prion disease. Additionally, the H2 C-terminus is widely considered to be a vital site for PrP conformational transition, which can be used as an important region to explore the potential mechanism of PrP misfolding. Therefore, to study the misfolding mechanism of PrP, 500 ns well-tempered metadynamics simulations were performed by focusing on the H2 C-terminus of PrP. For comparison, three systems were designed in total, including PrP in neutral and acidic conditions, as well as H187R mutant. The resulting free energy surfaces (FESs) obtained from metadynamics simulations reveal that acidic conditions and H187R mutation can facilitate PrP misfolding by decreasing free energy barriers for conformational transition and forming energy stable conformational states. Further analyses aimed at H2 C-terminus show that due to the increase of positive charge on residue 187 in both acidic and H187R systems, the electrostatic repulsion of residue 187 and R136/R156 increases greatly, which disrupts the electrostatic interaction network around H2 C-terminus and exposes the hydrophobic core to the solvent. Taken together, acidic conditions and H187R mutation can accelerate PrP misfolding mainly by forming more energetically stable metastable conformations with lower free energy barriers, and electrostatic network disruption involving residue 187 drives the initial misfolding of H2 C-terminus. This study provides quantitative insight into the related function of the H2 C-terminus in the PrP misfolding process, which may guide H2 C-terminus mediated drug design in the future.
Collapse
Affiliation(s)
- Zerong Xu
- School of Pharmacy, Lanzhou University, Lanzhou 730000, China
| | - Hongli Liu
- School of Pharmacy, Lanzhou University, Lanzhou 730000, China
| | - Shuo Wang
- School of Pharmacy, Lanzhou University, Lanzhou 730000, China
| | - Qianqian Zhang
- School of Pharmacy, Lanzhou University, Lanzhou 730000, China
| | - Xiaojun Yao
- State Key Laboratory of Quality Research in Chinese Medicine, Macau Institute for Applied Research in Medicine and Health, Macau University of Science and Technology, Taipa, Macau, China
| | - Shuangyan Zhou
- Chongqing Key Laboratory of Big Data for Bio Intelligence, Chongqing University of Posts and Telecommunications, Chongqing 400065, China
| | - Huanxiang Liu
- School of Pharmacy, Lanzhou University, Lanzhou 730000, China
| |
Collapse
|
9
|
Ferreira PHB, Freitas FC, McCully ME, Slade GG, de Oliveira RJ. The Role of Electrostatics and Folding Kinetics on the Thermostability of Homologous Cold Shock Proteins. J Chem Inf Model 2020; 60:546-561. [PMID: 31910002 DOI: 10.1021/acs.jcim.9b00797] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Understanding which aspects contribute to the thermostability of proteins is a challenge that has persisted for decades, and it is of great relevance for protein engineering. Several types of interactions can influence the thermostability of a protein. Among them, the electrostatic interactions have been a target of particular attention. Aiming to explore how this type of interaction can affect protein thermostability, this paper investigated four homologous cold shock proteins from psychrophilic, mesophilic, thermophilic, and hyperthermophilic organisms using a set of theoretical methodologies. It is well-known that electrostatics as well as hydrophobicity are key-elements for the stabilization of these proteins. Therefore, both interactions were initially analyzed in the native structure of each protein. Electrostatic interactions present in the native structures were calculated with the Tanford-Kirkwood model with solvent accessibility, and the amount of hydrophobic surface area buried upon folding was estimated by measuring both folded and extended structures. On the basis of Energy Landscape Theory, the local frustration and the simplified alpha-carbon structure-based model were modeled with a Debye-Hückel potential to take into account the electrostatics and the effects of an implicit solvent. Thermodynamic data for the structure-based model simulations were collected and analyzed using the Weighted Histogram Analysis and Stochastic Diffusion methods. Kinetic quantities including folding times, transition path times, folding routes, and Φ values were also obtained. As a result, we found that the methods are able to qualitatively infer that electrostatic interactions play an important role on the stabilization of the most stable thermophilic cold shock proteins, showing agreement with the experimental data.
Collapse
Affiliation(s)
- Paulo Henrique Borges Ferreira
- Laboratório de Biofísica Teórica, Departamento de Física, Instituto de Ciências Exatas, Naturais e Educação , Universidade Federal do Triângulo Mineiro , Uberaba , Minas Gerais 38064200 , Brazil
| | - Frederico Campos Freitas
- Laboratório de Biofísica Teórica, Departamento de Física, Instituto de Ciências Exatas, Naturais e Educação , Universidade Federal do Triângulo Mineiro , Uberaba , Minas Gerais 38064200 , Brazil
| | - Michelle E McCully
- Department of Biology , Santa Clara University , Santa Clara , California 95050 , United States
| | - Gabriel Gouvêa Slade
- Laboratório de Biofísica Teórica, Departamento de Física, Instituto de Ciências Exatas, Naturais e Educação , Universidade Federal do Triângulo Mineiro , Uberaba , Minas Gerais 38064200 , Brazil
| | - Ronaldo Junio de Oliveira
- Laboratório de Biofísica Teórica, Departamento de Física, Instituto de Ciências Exatas, Naturais e Educação , Universidade Federal do Triângulo Mineiro , Uberaba , Minas Gerais 38064200 , Brazil
| |
Collapse
|
10
|
Freitas FC, Lima AN, Contessoto VDG, Whitford PC, Oliveira RJD. Drift-diffusion (DrDiff) framework determines kinetics and thermodynamics of two-state folding trajectory and tunes diffusion models. J Chem Phys 2019; 151:114106. [DOI: 10.1063/1.5113499] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Affiliation(s)
- Frederico Campos Freitas
- Laboratório de Biofísica Teórica, Departamento de Física, Instituto de Ciências Exatas, Naturais e Educação, Universidade Federal do Triângulo Mineiro, Uberaba, MG, Brazil
| | - Angelica Nakagawa Lima
- Laboratório de Biofísica Teórica, Departamento de Física, Instituto de Ciências Exatas, Naturais e Educação, Universidade Federal do Triângulo Mineiro, Uberaba, MG, Brazil
- Laboratório de Biologia Computacional e Bioinformática, Universidade Federal do ABC, Santo André, SP, Brazil
| | - Vinícius de Godoi Contessoto
- Center for Theoretical Biological Physics, Rice University, Houston, Texas 77005, USA
- Departamento de Física, Universidade Estadual Paulista, São José do Rio Preto, SP, Brazil
- Brazilian Biorenewables National Laboratory - LNBR, Brazilian Center for Research in Energy and Materials - CNPEM, Campinas, SP, Brazil
| | - Paul C. Whitford
- Department of Physics, Northeastern University, Boston, Massachusetts 02115, USA
| | - Ronaldo Junio de Oliveira
- Laboratório de Biofísica Teórica, Departamento de Física, Instituto de Ciências Exatas, Naturais e Educação, Universidade Federal do Triângulo Mineiro, Uberaba, MG, Brazil
| |
Collapse
|