1
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Enikeev AD, Abramov PM, Elkin DS, Komelkov AV, Beliaeva AA, Silantieva DM, Tchevkina EM. Opposite Effects of CRABP1 and CRABP2 Homologs on Proliferation of Breast Cancer Cells and Their Sensitivity to Retinoic Acid. BIOCHEMISTRY. BIOKHIMIIA 2023; 88:2107-2124. [PMID: 38462454 DOI: 10.1134/s0006297923120131] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/27/2023] [Revised: 10/23/2023] [Accepted: 10/30/2023] [Indexed: 03/12/2024]
Abstract
Resistance of tumor cells to retinoic acid (RA), a promising therapeutic agent, is the major factor limiting the use of RA in clinical practice. The mechanisms of resistance to RA are still poorly understood. Cellular Retinoic Acid Binding Proteins, CRABP1 and CRABP2, are essential mediators of RA signaling, but role of the two CRABP homologs in regulating cellular sensitivity to RA has not been well studied. In addition, the effects of CRABP1 and CRABP2 on cell proliferation have not been compared. Here, using a broad panel of breast cancer cell lines with different levels of RA sensitivity/resistance, we show for the first time that in the RA-sensitive cells, CRABP1 expression is restricted by methylation, and protein levels are highly variable. In the moderately-RA-resistant cell lines, high level of CRABP1 is observed both at the mRNA and protein levels, unchanged by inhibition of DNA methylation. The cell lines with maximum resistance to RA are characterized by complete repression of CRABP1 expression realized at transcriptional and posttranscriptional levels, and exogenous expression of each of the CRABP homologs has no effect on the studied characteristics. CRABP1 and CRABP2 proteins have opposing effects on proliferation and sensitivity to RA. In particular, CRABP1 stimulates and CRABP2 reduces proliferation and resistance to RA in the initially RA-sensitive cells, while in the more resistant cells the role of each homolog in both of these parameters is reversed. Overall, we have shown for the first time that CRABP proteins exert different effects on the growth and sensitivity to RA of breast cancer cells (stimulation, suppression, or no effect) depending on the baseline level of RA-sensitivity, with the effects of CRABP1 and CRABP2 homologs on the studied properties always being opposite.
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Affiliation(s)
- Adel D Enikeev
- Federal State Budgetary Institution "N. N. Blokhin National Medical Research Center of Oncology" of the Ministry of Health of the Russian Federation, Moscow, 115522, Russia
| | - Pavel M Abramov
- Federal State Budgetary Institution "N. N. Blokhin National Medical Research Center of Oncology" of the Ministry of Health of the Russian Federation, Moscow, 115522, Russia
| | - Danila S Elkin
- Federal State Budgetary Institution "N. N. Blokhin National Medical Research Center of Oncology" of the Ministry of Health of the Russian Federation, Moscow, 115522, Russia
| | - Andrey V Komelkov
- Federal State Budgetary Institution "N. N. Blokhin National Medical Research Center of Oncology" of the Ministry of Health of the Russian Federation, Moscow, 115522, Russia
| | - Anastasiya A Beliaeva
- Federal State Budgetary Institution "N. N. Blokhin National Medical Research Center of Oncology" of the Ministry of Health of the Russian Federation, Moscow, 115522, Russia
| | - Darya M Silantieva
- Pirogov Russian National Research Medical University, Moscow, 117997, Russia
| | - Elena M Tchevkina
- Federal State Budgetary Institution "N. N. Blokhin National Medical Research Center of Oncology" of the Ministry of Health of the Russian Federation, Moscow, 115522, Russia.
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2
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Szymoński K, Skirlińska-Nosek K, Lipiec E, Sofińska K, Czaja M, Wilkosz N, Krupa M, Wanat F, Ulatowska-Białas M, Adamek D. Combined analytical approach empowers precise spectroscopic interpretation of subcellular components of pancreatic cancer cells. Anal Bioanal Chem 2023; 415:7281-7295. [PMID: 37906289 PMCID: PMC10684650 DOI: 10.1007/s00216-023-04997-w] [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: 09/04/2023] [Revised: 09/27/2023] [Accepted: 10/09/2023] [Indexed: 11/02/2023]
Abstract
The lack of specific and sensitive early diagnostic options for pancreatic cancer (PC) results in patients being largely diagnosed with late-stage disease, thus inoperable and burdened with high mortality. Molecular spectroscopic methodologies, such as Raman or infrared spectroscopies, show promise in becoming a leader in screening for early-stage cancer diseases, including PC. However, should such technology be introduced, the identification of differentiating spectral features between various cancer types is required. This would not be possible without the precise extraction of spectra without the contamination by necrosis, inflammation, desmoplasia, or extracellular fluids such as mucous that surround tumor cells. Moreover, an efficient methodology for their interpretation has not been well defined. In this study, we compared different methods of spectral analysis to find the best for investigating the biomolecular composition of PC cells cytoplasm and nuclei separately. Sixteen PC tissue samples of main PC subtypes (ductal adenocarcinoma, intraductal papillary mucinous carcinoma, and ampulla of Vater carcinoma) were collected with Raman hyperspectral mapping, resulting in 191,355 Raman spectra and analyzed with comparative methodologies, specifically, hierarchical cluster analysis, non-negative matrix factorization, T-distributed stochastic neighbor embedding, principal components analysis (PCA), and convolutional neural networks (CNN). As a result, we propose an innovative approach to spectra classification by CNN, combined with PCA for molecular characterization. The CNN-based spectra classification achieved over 98% successful validation rate. Subsequent analyses of spectral features revealed differences among PC subtypes and between the cytoplasm and nuclei of their cells. Our study establishes an optimal methodology for cancer tissue spectral data classification and interpretation that allows precise and cognitive studies of cancer cells and their subcellular components, without mixing the results with cancer-surrounding tissue. As a proof of concept, we describe findings that add to the spectroscopic understanding of PC.
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Affiliation(s)
- Krzysztof Szymoński
- Department of Pathomorphology, Medical College, Jagiellonian University, Kraków, Poland.
- Department of Pathomorphology, University Hospital, Kraków, Poland.
| | - Katarzyna Skirlińska-Nosek
- Faculty of Physics, Astronomy and Applied Computer Science, M. Smoluchowski Institute of Physics, Jagiellonian University, Kraków, Poland
- Doctoral School of Exact and Natural Sciences, Jagiellonian University, Kraków, Poland
| | - Ewelina Lipiec
- Faculty of Physics, Astronomy and Applied Computer Science, M. Smoluchowski Institute of Physics, Jagiellonian University, Kraków, Poland
| | - Kamila Sofińska
- Faculty of Physics, Astronomy and Applied Computer Science, M. Smoluchowski Institute of Physics, Jagiellonian University, Kraków, Poland
| | - Michał Czaja
- Faculty of Physics, Astronomy and Applied Computer Science, M. Smoluchowski Institute of Physics, Jagiellonian University, Kraków, Poland
- Doctoral School of Exact and Natural Sciences, Jagiellonian University, Kraków, Poland
| | - Natalia Wilkosz
- Faculty of Physics, Astronomy and Applied Computer Science, M. Smoluchowski Institute of Physics, Jagiellonian University, Kraków, Poland
- AGH University of Krakow, Faculty of Physics and Applied Computer Science, Kraków, Poland
| | - Matylda Krupa
- Department of Pathomorphology, Medical College, Jagiellonian University, Kraków, Poland
| | - Filip Wanat
- Department of Pathomorphology, Medical College, Jagiellonian University, Kraków, Poland
| | - Magdalena Ulatowska-Białas
- Department of Pathomorphology, Medical College, Jagiellonian University, Kraków, Poland
- Department of Pathomorphology, University Hospital, Kraków, Poland
| | - Dariusz Adamek
- Department of Pathomorphology, Medical College, Jagiellonian University, Kraków, Poland
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3
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Yabut KCB, Isoherranen N. Impact of Intracellular Lipid Binding Proteins on Endogenous and Xenobiotic Ligand Metabolism and Disposition. Drug Metab Dispos 2023; 51:700-717. [PMID: 37012074 PMCID: PMC10197203 DOI: 10.1124/dmd.122.001010] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2022] [Revised: 03/16/2023] [Accepted: 02/10/2023] [Indexed: 04/05/2023] Open
Abstract
The family of intracellular lipid binding proteins (iLBPs) is comprised of 16 members of structurally related binding proteins that have ubiquitous tissue expression in humans. iLBPs collectively bind diverse essential endogenous lipids and xenobiotics. iLBPs solubilize and traffic lipophilic ligands through the aqueous milieu of the cell. Their expression is correlated with increased rates of ligand uptake into tissues and altered ligand metabolism. The importance of iLBPs in maintaining lipid homeostasis is well established. Fatty acid binding proteins (FABPs) make up the majority of iLBPs and are expressed in major organs relevant to xenobiotic absorption, distribution, and metabolism. FABPs bind a variety of xenobiotics including nonsteroidal anti-inflammatory drugs, psychoactive cannabinoids, benzodiazepines, antinociceptives, and peroxisome proliferators. FABP function is also associated with metabolic disease, making FABPs currently a target for drug development. Yet the potential contribution of FABP binding to distribution of xenobiotics into tissues and the mechanistic impact iLBPs may have on xenobiotic metabolism are largely undefined. This review examines the tissue-specific expression and functions of iLBPs, the ligand binding characteristics of iLBPs, their known endogenous and xenobiotic ligands, methods for measuring ligand binding, and mechanisms of ligand delivery from iLBPs to membranes and enzymes. Current knowledge of the importance of iLBPs in affecting disposition of xenobiotics is collectively described. SIGNIFICANCE STATEMENT: The data reviewed here show that FABPs bind many drugs and suggest that binding of drugs to FABPs in various tissues will affect drug distribution into tissues. The extensive work and findings with endogenous ligands suggest that FABPs may also alter the metabolism and transport of drugs. This review illustrates the potential significance of this understudied area.
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Affiliation(s)
- King Clyde B Yabut
- Department of Pharmaceutics, School of Pharmacy, University of Washington, Seattle, Washington
| | - Nina Isoherranen
- Department of Pharmaceutics, School of Pharmacy, University of Washington, Seattle, Washington
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Variabilities in global DNA methylation and β-sheet richness establish spectroscopic landscapes among subtypes of pancreatic cancer. Eur J Nucl Med Mol Imaging 2023; 50:1792-1810. [PMID: 36757432 PMCID: PMC10119063 DOI: 10.1007/s00259-023-06121-7] [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: 09/27/2022] [Accepted: 01/21/2023] [Indexed: 02/10/2023]
Abstract
PURPOSE Knowledge about pancreatic cancer (PC) biology has been growing rapidly in recent decades. Nevertheless, the survival of PC patients has not greatly improved. The development of a novel methodology suitable for deep investigation of the nature of PC tumors is of great importance. Molecular imaging techniques, such as Fourier transform infrared (FTIR) spectroscopy and Raman hyperspectral mapping (RHM) combined with advanced multivariate data analysis, were useful in studying the biochemical composition of PC tissue. METHODS Here, we evaluated the potential of molecular imaging in differentiating three groups of PC tumors, which originate from different precursor lesions. Specifically, we comprehensively investigated adenocarcinomas (ACs): conventional ductal AC, intraductal papillary mucinous carcinoma, and ampulla of Vater AC. FTIR microspectroscopy and RHM maps of 24 PC tissue slides were obtained, and comprehensive advanced statistical analyses, such as hierarchical clustering and nonnegative matrix factorization, were performed on a total of 211,355 Raman spectra. Additionally, we employed deep learning technology for the same task of PC subtyping to enable automation. The so-called convolutional neural network (CNN) was trained to recognize spectra specific to each PC group and then employed to generate CNN-prediction-based tissue maps. To identify the DNA methylation spectral markers, we used differently methylated, isolated DNA and compared the observed spectral differences with the results obtained from cellular nuclei regions of PC tissues. RESULTS The results showed significant differences among cancer tissues of the studied PC groups. The main findings are the varying content of β-sheet-rich proteins within the PC cells and alterations in the relative DNA methylation level. Our CNN model efficiently differentiated PC groups with 94% accuracy. The usage of CNN in the classification task did not require Raman spectral data preprocessing and eliminated the need for extensive knowledge of statistical methodologies. CONCLUSIONS Molecular spectroscopy combined with CNN technology is a powerful tool for PC detection and subtyping. The molecular fingerprint of DNA methylation and β-sheet cytoplasmic proteins established by our results is different for the main PC groups and allowed the subtyping of pancreatic tumors, which can improve patient management and increase their survival. Our observations are of key importance in understanding the variability of PC and allow translation of the methodology into clinical practice by utilizing liquid biopsy testing.
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Toke O. Structural and Dynamic Determinants of Molecular Recognition in Bile Acid-Binding Proteins. Int J Mol Sci 2022; 23:ijms23010505. [PMID: 35008930 PMCID: PMC8745080 DOI: 10.3390/ijms23010505] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2021] [Revised: 12/30/2021] [Accepted: 12/31/2021] [Indexed: 12/12/2022] Open
Abstract
Disorders in bile acid transport and metabolism have been related to a number of metabolic disease states, atherosclerosis, type-II diabetes, and cancer. Bile acid-binding proteins (BABPs), a subfamily of intracellular lipid-binding proteins (iLBPs), have a key role in the cellular trafficking and metabolic targeting of bile salts. Within the family of iLBPs, BABPs exhibit unique binding properties including positive binding cooperativity and site-selectivity, which in different tissues and organisms appears to be tailored to the local bile salt pool. Structural and biophysical studies of the past two decades have shed light on the mechanism of bile salt binding at the atomic level, providing us with a mechanistic picture of ligand entry and release, and the communication between the binding sites. In this review, we discuss the emerging view of bile salt recognition in intestinal- and liver-BABPs, with examples from both mammalian and non-mammalian species. The structural and dynamic determinants of the BABP-bile–salt interaction reviewed herein set the basis for the design and development of drug candidates targeting the transcellular traffic of bile salts in enterocytes and hepatocytes.
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Affiliation(s)
- Orsolya Toke
- Laboratory for NMR Spectroscopy, Structural Research Centre, Research Centre for Natural Sciences, 2 Magyar Tudósok Körútja, H-1117 Budapest, Hungary
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6
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Valadares VS, Martins LC, Roman EA, Valente AP, Cino EA, Moraes AH. Conformational dynamics of Tetracenomycin aromatase/cyclase regulate polyketide binding and enzyme aggregation propensity. Biochim Biophys Acta Gen Subj 2021; 1865:129949. [PMID: 34139289 DOI: 10.1016/j.bbagen.2021.129949] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2021] [Revised: 06/01/2021] [Accepted: 06/10/2021] [Indexed: 11/25/2022]
Abstract
BACKGROUND The N-terminal domain of Tetracenomycin aromatase/cyclase (TcmN), an enzyme derived from Streptomyces glaucescens, is involved in polyketide cyclization, aromatization, and folding. Polyketides are a diverse class of secondary metabolites produced by certain groups of bacteria, fungi, and plants with various pharmaceutical applications. Examples include antibiotics, such as tetracycline, and anticancer drugs, such as doxorubicin. Because TcmN is a promising enzyme for in vitro production of polyketides, it is important to identify conditions that enhance its thermal resistance and optimize its function. METHODS TcmN unfolding, stability, and dynamics were evaluated by fluorescence spectroscopy, circular dichroism, nuclear magnetic resonance 15N relaxation experiments, and microsecond molecular dynamics (MD) simulations. RESULTS TcmN thermal resistance was enhanced at low protein and high salt concentrations, was pH-dependent, and denaturation was irreversible. Conformational dynamics on the μs-ms timescale were detected for residues in the substrate-binding cavity, and two predominant conformers representing opened and closed cavity states were observed in the MD simulations. CONCLUSION Based on the results, a mechanism was proposed in which the thermodynamics and kinetics of the TcmN conformational equilibrium modulate enzyme function by favoring ligand binding and avoiding aggregation. GENERAL SIGNIFICANCE Understanding the principles underlying TcmN stability and dynamics may help in designing mutants with optimal properties for biotechnological applications.
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Affiliation(s)
- Veronica S Valadares
- Department of Biochemistry and Immunology, Universidade Federal de Minas Gerais, Belo Horizonte, Brazil
| | - Luan C Martins
- Graduate Program in Bioinformatics, Universidade Federal de Minas Gerais, Belo Horizonte, Brazil
| | - Ernesto A Roman
- Facultad de Farmacia y Bioquimica, Universidad de Buenos Aires, Buenos Aires, Argentina
| | - Ana Paula Valente
- National Center of Nuclear Magnetic Resonance, Leopoldo de Meis Institute of Medical Biochemistry, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil
| | - Elio A Cino
- Department of Biochemistry and Immunology, Universidade Federal de Minas Gerais, Belo Horizonte, Brazil.
| | - Adolfo H Moraes
- Departamento de Química, Instituto de Ciências Exatas, Universidade Federal de Minas Gerais, Belo Horizonte, Brazil; Department of NMR-based Structural Biology, Max-Planck Institute for Biophysical Chemistry, Göttingen, Germany.
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7
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Abstract
There is an opinion in professional literature that edge-strands in β-sheet are critical to the processes of amyloid transformation. Propagation of fibrillar forms mainly takes place on the basis of β-sheet type interactions. In many proteins, the edge strands represent only a partially matched form to the β-sheet. Therefore, the edge-strand takes slightly distorted forms. The assessment of the level of arrangement can be carried out based on studying the secondary structure as well as the structure of the hydrophobic core. For this purpose, a fuzzy oil drop model was used to determine the contribution of each fragment with a specific secondary structure to the construction of the system being the effect of a certain synergy, which results in the construction of a hydrophobic core. Studying the participation of β-sheets edge fragments in the hydrophobic core construction is the subject of the current analysis. Statuses of these edge fragments in β-sheets in ferredoxin-like folds are treated as factors that disturb the symmetry of the system.
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8
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Prabhu MPT, Sarkar N. Quantum Dots as Promising Theranostic Tools Against Amyloidosis: A Review. Protein Pept Lett 2019; 26:555-563. [PMID: 30543158 DOI: 10.2174/0929866526666181212113855] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2018] [Revised: 12/07/2018] [Accepted: 12/09/2018] [Indexed: 01/01/2023]
Abstract
Amyloids are highly ordered beta sheet rich stable protein aggregates, which have been found to play a significant role in the onset of several degenerative diseases such as Alzheimer's disease, Huntington's disease, Parkinson's disease, Type II diabetes mellitus and so on. Aggregation of proteins leading to amyloid fibril formation via intermediate(s), is thought to be a nucleated condensation polymerization process associated with many pathological conditions. There has been extensive research to identify inhibitors of these disease oriented aggregation processes. In recent times, quantum dots, with their unique physico-chemical properties have grabbed the attention of scientific community due to its applications in medical sciences. Quantum dots are nano-particles usually made of semiconductor materials which emit fluorescence upon radiation. The wavelength of fluorescence emission varies with changes in size of quantum dots. Several studies have reported significant inhibitory effects of these quantum dots towards amyloidogenesis, thereby presenting themselves as promising candidates against amyloidosis. Further, studies have also revealed amyloid detection capacity of quantum dots with sensitivity and specificity better than conventional probes. In the current review, we will discuss the various effects of quantum dots on protein aggregation pathways, their mechanism of actions and their potentials as effective therapeutics against amyloidosis.
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Affiliation(s)
- M P Taraka Prabhu
- Department of Biotechnology and Medical Engineering, National Institute of Technology Rourkela, Rourkela- 769008, Odisha, India
| | - Nandini Sarkar
- Department of Biotechnology and Medical Engineering, National Institute of Technology Rourkela, Rourkela- 769008, Odisha, India
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Ruggeri FS, Šneideris T, Vendruscolo M, Knowles TPJ. Atomic force microscopy for single molecule characterisation of protein aggregation. Arch Biochem Biophys 2019; 664:134-148. [PMID: 30742801 PMCID: PMC6420408 DOI: 10.1016/j.abb.2019.02.001] [Citation(s) in RCA: 80] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2018] [Revised: 02/03/2019] [Accepted: 02/05/2019] [Indexed: 12/22/2022]
Abstract
The development of atomic force microscopy (AFM) has opened up a wide range of novel opportunities in nanoscience and new modalities of observation in complex biological systems. AFM imaging has been widely employed to resolve the complex and heterogeneous conformational states involved in protein aggregation at the single molecule scale and shed light onto the molecular basis of a variety of human pathologies, including neurodegenerative disorders. The study of individual macromolecules at nanoscale, however, remains challenging, especially when fully quantitative information is required. In this review, we first discuss the principles of AFM with a special emphasis on the fundamental factors defining its sensitivity and accuracy. We then review the fundamental parameters and approaches to work at the limit of AFM resolution in order to perform single molecule statistical analysis of biomolecules and nanoscale protein aggregates. This single molecule statistical approach has proved to be powerful to unravel the molecular and hierarchical assembly of the misfolded species present transiently during protein aggregation, to visualise their dynamics at the nanoscale, as well to study the structural properties of amyloid-inspired functional nanomaterials.
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Affiliation(s)
- Francesco Simone Ruggeri
- Centre for Misfolding Disease, Department of Chemistry, University of Cambridge, Cambridge, CB2 1EW, United Kingdom.
| | - Tomas Šneideris
- Centre for Misfolding Disease, Department of Chemistry, University of Cambridge, Cambridge, CB2 1EW, United Kingdom; Institute of Biotechnology, Life Sciences Center, Vilnius University, Vilnius, Lithuania
| | - Michele Vendruscolo
- Centre for Misfolding Disease, Department of Chemistry, University of Cambridge, Cambridge, CB2 1EW, United Kingdom
| | - Tuomas P J Knowles
- Centre for Misfolding Disease, Department of Chemistry, University of Cambridge, Cambridge, CB2 1EW, United Kingdom; Cavendish Laboratory, University of Cambridge, Cambridge, CB3 0HE, United Kingdom.
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10
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Ding F, Peng W. Probing the local conformational flexibility in receptor recognition: mechanistic insight from an atomic-scale investigation. RSC Adv 2019; 9:13968-13980. [PMID: 35519308 PMCID: PMC9064033 DOI: 10.1039/c9ra01906e] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2019] [Accepted: 04/28/2019] [Indexed: 12/13/2022] Open
Abstract
Inherent protein conformational flexibility is important for biomolecular recognition, but this critical property is often neglected in several studies. This event can lead to large deviations in the research results. In the current contribution, we disclose the effects of the local conformational flexibility on receptor recognition by using an atomic-scale computational method. The results indicated that both static and dynamic reaction modes have noticeable differences, and these originated from the structural features of the protein molecules. Dynamic interaction results displayed that the structural stability and conformational flexibility of the proteins had a significant influence on the recognition processes. This point related closely to the characteristics of the flexible loop regions where bixin located within the protein structures. The energy decomposition analyses and circular dichroism results validated the rationality of the recognition studies. More importantly, the conformational and energy changes of some residues around the bixin binding domain were found to be vital to biological reactions. These microscopic findings clarified the nature of the phenomenon that the local conformational flexibility could intervene in receptor recognition. Obviously, this report may provide biophysical evidence for the exploration of the structure–function relationships of the biological receptors in the human body. The local conformational flexibility and dynamics have significant impacts on the receptor recognition processes, and this phenomenon is related closely to the structural characteristics of the flexible loop domains in biomacromolecules.![]()
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Affiliation(s)
- Fei Ding
- School of Environmental Science and Engineering
- Chang'an University
- Xi'an 710064
- China
- Key Laboratory of Subsurface Hydrology and Ecological Effect in Arid Region of Ministry of Education
| | - Wei Peng
- College of Chemistry and Chemical Engineering
- Xiamen University
- Xiamen 361005
- China
- Department of Chemistry
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11
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Thakur AK, Meng W, Gierasch LM. Local and non-local topological information in the denatured state ensemble of a β-barrel protein. Protein Sci 2018; 27:2062-2072. [PMID: 30252171 DOI: 10.1002/pro.3516] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2018] [Revised: 09/18/2018] [Accepted: 09/19/2018] [Indexed: 11/06/2022]
Abstract
The folding of predominantly β-sheet proteins is complicated by the presence of a large number of non-local interactions in their native states, which increase the ruggedness of their folding energy landscapes. However, forming non-local contacts early in folding or even in the unfolded state can smooth the energy landscape and facilitate productive folding. We report that several sequence regions of a β-barrel protein, cellular retinoic acid-binding protein 1 (CRABP1), populate native-like secondary structure to a significant extent in the denatured state in 8 M urea. In addition, we provide evidence for both local and non-local interactions in the denatured state of CRABP1. NMR chemical shift perturbations (CSPs) under denaturing conditions upon substitution of single residues by mutation support the presence of several non-local interactions in topologically key sites, arguing that the denatured state is conformationally restricted and contains topological information for the native fold. Among the most striking non-local interactions are those between the N- and C-terminal regions, which are involved in closure of the native β-barrel. In addition, CSPs support the presence of two features in the denatured state: a major hydrophobic cluster involving residues from various parts of the sequence and a native-like interaction similar to one identified in previous studies as forming early in folding (Budyak et al., Structure 21, 476 [2013]). Taken together, our data support a model in which transient structures involving nonlocal interactions prime early folding interactions in CRABP1, determine its barrel topology, and may protect this predominantly β-sheet protein against aggregation.
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Affiliation(s)
- Abhay K Thakur
- Departments of Biochemistry & Molecular Biology and Chemistry, University of Massachusetts Amherst, Amherst, Massachusetts, 01003
| | - Wenli Meng
- Departments of Biochemistry & Molecular Biology and Chemistry, University of Massachusetts Amherst, Amherst, Massachusetts, 01003
| | - Lila M Gierasch
- Departments of Biochemistry & Molecular Biology and Chemistry, University of Massachusetts Amherst, Amherst, Massachusetts, 01003
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12
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Moraes AH, Asam C, Almeida FCL, Wallner M, Ferreira F, Valente AP. Structural basis for cross-reactivity and conformation fluctuation of the major beech pollen allergen Fag s 1. Sci Rep 2018; 8:10512. [PMID: 30002383 PMCID: PMC6043577 DOI: 10.1038/s41598-018-28358-1] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2018] [Accepted: 03/20/2018] [Indexed: 01/08/2023] Open
Abstract
Fag s 1 is a member of the Pathogen Related protein family 10 (PR-10) and can elicit cross-reaction with IgE antibodies produced against the birch pollen allergen Bet v 1. The Nuclear Magnetic Resonance (NMR) structure of Fag s 1 is presented along with its dynamic properties. It shares 66% identity with Bet v 1 and exhibits the expected three α-helices and seven β-sheets arranged as a semi-beta barrel and exposing the residues mapped as the Bet v 1 IgE epitope. The structural dynamics of Fag s 1 were monitored on the fast and intermediate timescales, using relaxation rates. The complex dynamics of Fag s 1 are closely related to the internal cavity, and they modulate IgE and ligand binding.
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Affiliation(s)
- Adolfo H Moraes
- Chemistry Department, Federal University of Minas Gerais, Belo Horizonte, Brazil
| | - Claudia Asam
- Department of Molecular Biology, University of Salzburg, Salzburg, Austria
| | - Fabio C L Almeida
- National NMR Center, Department of Structural Biology, Federal University of Rio de Janeiro, Rio de Janeiro, Brazil
| | - Michael Wallner
- Department of Molecular Biology, University of Salzburg, Salzburg, Austria
| | - Fatima Ferreira
- Department of Molecular Biology, University of Salzburg, Salzburg, Austria
| | - Ana Paula Valente
- National NMR Center, Department of Structural Biology, Federal University of Rio de Janeiro, Rio de Janeiro, Brazil.
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13
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Chiti F, Dobson CM. Protein Misfolding, Amyloid Formation, and Human Disease: A Summary of Progress Over the Last Decade. Annu Rev Biochem 2017; 86:27-68. [DOI: 10.1146/annurev-biochem-061516-045115] [Citation(s) in RCA: 1658] [Impact Index Per Article: 236.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/30/2023]
Abstract
Peptides and proteins have been found to possess an inherent tendency to convert from their native functional states into intractable amyloid aggregates. This phenomenon is associated with a range of increasingly common human disorders, including Alzheimer and Parkinson diseases, type II diabetes, and a number of systemic amyloidoses. In this review, we describe this field of science with particular reference to the advances that have been made over the last decade in our understanding of its fundamental nature and consequences. We list the proteins that are known to be deposited as amyloid or other types of aggregates in human tissues and the disorders with which they are associated, as well as the proteins that exploit the amyloid motif to play specific functional roles in humans. In addition, we summarize the genetic factors that have provided insight into the mechanisms of disease onset. We describe recent advances in our knowledge of the structures of amyloid fibrils and their oligomeric precursors and of the mechanisms by which they are formed and proliferate to generate cellular dysfunction. We show evidence that a complex proteostasis network actively combats protein aggregation and that such an efficient system can fail in some circumstances and give rise to disease. Finally, we anticipate the development of novel therapeutic strategies with which to prevent or treat these highly debilitating and currently incurable conditions.
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Affiliation(s)
- Fabrizio Chiti
- Department of Experimental and Clinical Biomedical Sciences “Mario Serio,” Section of Biochemistry, Università di Firenze, 50134 Firenze, Italy
| | - Christopher M. Dobson
- Department of Chemistry, Centre for Misfolding Diseases, University of Cambridge, Cambridge CB2 1EW, United Kingdom
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14
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Elia F, Cantini F, Chiti F, Dobson CM, Bemporad F. Direct Conversion of an Enzyme from Native-like to Amyloid-like Aggregates within Inclusion Bodies. Biophys J 2017; 112:2540-2551. [PMID: 28636911 PMCID: PMC5479110 DOI: 10.1016/j.bpj.2017.05.011] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2016] [Revised: 05/02/2017] [Accepted: 05/08/2017] [Indexed: 01/29/2023] Open
Abstract
The acylphosphatase from Sulfolobus solfataricus (Sso AcP) is a globular protein able to aggregate in vitro from a native-like conformational ensemble without the need for a transition across the major unfolding energy barrier. This process leads to the formation of assemblies in which the protein retains its native-like structure, which subsequently convert into amyloid-like aggregates. Here, we investigate the mechanism by which Sso AcP aggregates in vivo to form bacterial inclusion bodies after expression in E. coli. Shortly after the initiation of expression, Sso AcP is incorporated into inclusion bodies as a native-like protein, still exhibiting small but significant enzymatic activity. Additional experiments revealed that this overall process of aggregation is enhanced by the presence of the unfolded N-terminal region of the sequence and by destabilization of the globular segment of the protein. At later times, the Sso AcP molecules in the inclusion bodies lose their native-like properties and convert into β-sheet-rich amyloid-like structures, as indicated by their ability to bind thioflavin T and Congo red. These results show that the aggregation behavior of this protein is similar in vivo to that observed in vitro, and that, at least for a predominant part of the protein population, the transition from a native to an amyloid-like structure occurs within the aggregate state.
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Affiliation(s)
- Francesco Elia
- Department of Experimental and Clinical Biomedical Sciences "Mario Serio," University of Florence, Firenze, Italy
| | - Francesca Cantini
- Centro Risonanze Magnetiche (CERM) and Department of Chemistry, University of Florence, Sesto Fiorentino, Italy
| | - Fabrizio Chiti
- Department of Experimental and Clinical Biomedical Sciences "Mario Serio," University of Florence, Firenze, Italy
| | | | - Francesco Bemporad
- Department of Experimental and Clinical Biomedical Sciences "Mario Serio," University of Florence, Firenze, Italy.
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15
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Hunter NH, Bakula BC, Bruce CD. Molecular dynamics simulations of apo and holo forms of fatty acid binding protein 5 and cellular retinoic acid binding protein II reveal highly mobile protein, retinoic acid ligand, and water molecules. J Biomol Struct Dyn 2017; 36:1893-1907. [PMID: 28566049 DOI: 10.1080/07391102.2017.1337591] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Structural and dynamic properties from a series of 300 ns molecular dynamics, MD, simulations of two intracellular lipid binding proteins, iLBPs, (Fatty Acid Binding Protein 5, FABP5, and Cellular Retinoic Acid Binding Protein II, CRABP-II) in both the apo form and when bound with retinoic acid reveal a high degree of protein and ligand flexibility. The ratio of FABP5 to CRABP-II in a cell may determine whether it undergoes natural apoptosis or unrestricted cell growth in the presence of retinoic acid. As a result, FABP5 is a promising target for cancer therapy. The MD simulations presented here reveal distinct differences in the two proteins and provide insight into the binding mechanism. CRABP-II is a much larger, more flexible protein that closes upon ligand binding, where FABP5 transitions to an open state in the holo form. The traditional understanding obtained from crystal structures of the gap between two β-sheets of the β-barrel common to iLBPs and the α-helix cap that forms the portal to the binding pocket is insufficient for describing protein conformation (open vs. closed) or ligand entry and exit. When the high degree of mobility between multiple conformations of both the ligand and protein are examined via MD simulation, a new mode of ligand motion that improves understanding of binding dynamics is revealed.
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Affiliation(s)
- Nathanael H Hunter
- a Department of Chemistry , John Carroll University , University Heights , OH , USA
| | - Blair C Bakula
- a Department of Chemistry , John Carroll University , University Heights , OH , USA
| | - Chrystal D Bruce
- a Department of Chemistry , John Carroll University , University Heights , OH , USA
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16
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Bemporad F, Ramazzotti M. From the Evolution of Protein Sequences Able to Resist Self-Assembly to the Prediction of Aggregation Propensity. INTERNATIONAL REVIEW OF CELL AND MOLECULAR BIOLOGY 2016; 329:1-47. [PMID: 28109326 DOI: 10.1016/bs.ircmb.2016.08.008] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
Folding of polypeptide chains into biologically active entities is an astonishingly complex process, determined by the nature and the sequence of residues emerging from ribosomes. While it has been long believed that evolution has pressed genomes so that specific sequences could adopt unique, functional three-dimensional folds, it is now clear that complex protein machineries act as quality control system and supervise folding. Notwithstanding that, events such as erroneous folding, partial folding, or misfolding are frequent during the life of a cell or a whole organism, and they can escape controls. One of the possible outcomes of this misbehavior is cross-β aggregation, a super secondary structure which represents the hallmark of self-assembled, well organized, and extremely ordered structures termed amyloid fibrils. What if evolution would have not taken into account such possibilities? Twenty years of research point toward the idea that, in fact, evolution has constantly supervised the risk of errors and minimized their impact. In this review we tried to survey the major findings in the amyloid field, trying to describe what the real pitfalls of protein folding are-from an evolutionary perspective-and how sequence and structural features have evolved to balance the need for perfect, dynamic, functionally efficient structures, and the detrimental effects implicit in the dangerous process of folding. We will discuss how the knowledge obtained from these studies has been employed to produce computational methods able to assess, predict, and discriminate the aggregation properties of protein sequences.
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Affiliation(s)
- F Bemporad
- Università degli Studi di Firenze, Firenze, Italy.
| | - M Ramazzotti
- Università degli Studi di Firenze, Firenze, Italy.
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17
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Ensemble Modeling and Intracellular Aggregation of an Engineered Immunoglobulin-Like Domain. J Mol Biol 2016; 428:1365-1374. [DOI: 10.1016/j.jmb.2016.02.016] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2015] [Revised: 01/28/2016] [Accepted: 02/12/2016] [Indexed: 11/21/2022]
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18
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Tomaselli S, Pagano K, Boulton S, Zanzoni S, Melacini G, Molinari H, Ragona L. Lipid binding protein response to a bile acid library: a combined NMR and statistical approach. FEBS J 2015; 282:4094-113. [PMID: 26260520 DOI: 10.1111/febs.13405] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2015] [Revised: 07/20/2015] [Accepted: 08/06/2015] [Indexed: 01/23/2023]
Abstract
Primary bile acids, differing in hydroxylation pattern, are synthesized from cholesterol in the liver and, once formed, can undergo extensive enzyme-catalysed glycine/taurine conjugation, giving rise to a complex mixture, the bile acid pool. Composition and concentration of the bile acid pool may be altered in diseases, posing a general question on the response of the carrier (bile acid binding protein) to the binding of ligands with different hydrophobic and steric profiles. A collection of NMR experiments (H/D exchange, HET-SOFAST, ePHOGSY NOESY/ROESY and (15) N relaxation measurements) was thus performed on apo and five different holo proteins, to monitor the binding pocket accessibility and dynamics. The ensemble of obtained data could be rationalized by a statistical approach, based on chemical shift covariance analysis, in terms of residue-specific correlations and collective protein response to ligand binding. The results indicate that the same residues are influenced by diverse chemical stresses: ligand binding always induces silencing of motions at the protein portal with a concomitant conformational rearrangement of a network of residues, located at the protein anti-portal region. This network of amino acids, which do not belong to the binding site, forms a contiguous surface, sensing the presence of the bound lipids, with a signalling role in switching protein-membrane interactions on and off.
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Affiliation(s)
- Simona Tomaselli
- NMR Laboratory, Istituto per lo Studio delle Macromolecole (ISMAC), Milano, Italy
| | - Katiuscia Pagano
- NMR Laboratory, Istituto per lo Studio delle Macromolecole (ISMAC), Milano, Italy
| | - Stephen Boulton
- Departments of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, Canada
| | | | - Giuseppe Melacini
- Departments of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, Canada.,Department of Chemistry and Chemical Biology, McMaster University, Hamilton, Canada
| | - Henriette Molinari
- NMR Laboratory, Istituto per lo Studio delle Macromolecole (ISMAC), Milano, Italy
| | - Laura Ragona
- NMR Laboratory, Istituto per lo Studio delle Macromolecole (ISMAC), Milano, Italy
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19
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Matsuoka D, Sugiyama S, Murata M, Matsuoka S. Molecular Dynamics Simulations of Heart-type Fatty Acid Binding Protein in Apo and Holo Forms, and Hydration Structure Analyses in the Binding Cavity. J Phys Chem B 2014; 119:114-27. [DOI: 10.1021/jp510384f] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Affiliation(s)
- Daisuke Matsuoka
- JST ERATO, Lipid Active
Structure Project, ‡Department of Chemistry, Graduate
School of Science, and §Project Research Center for Fundamental Science, Osaka University, 1-1
Machikaneyama, Toyonaka, Osaka 560-0043, Japan
| | - Shigeru Sugiyama
- JST ERATO, Lipid Active
Structure Project, ‡Department of Chemistry, Graduate
School of Science, and §Project Research Center for Fundamental Science, Osaka University, 1-1
Machikaneyama, Toyonaka, Osaka 560-0043, Japan
| | - Michio Murata
- JST ERATO, Lipid Active
Structure Project, ‡Department of Chemistry, Graduate
School of Science, and §Project Research Center for Fundamental Science, Osaka University, 1-1
Machikaneyama, Toyonaka, Osaka 560-0043, Japan
| | - Shigeru Matsuoka
- JST ERATO, Lipid Active
Structure Project, ‡Department of Chemistry, Graduate
School of Science, and §Project Research Center for Fundamental Science, Osaka University, 1-1
Machikaneyama, Toyonaka, Osaka 560-0043, Japan
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20
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Gershenson A, Gierasch LM, Pastore A, Radford SE. Energy landscapes of functional proteins are inherently risky. Nat Chem Biol 2014; 10:884-91. [PMID: 25325699 PMCID: PMC4416114 DOI: 10.1038/nchembio.1670] [Citation(s) in RCA: 80] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2014] [Accepted: 09/19/2014] [Indexed: 01/08/2023]
Abstract
Evolutionary pressure for protein function leads to unavoidable sampling of conformational states that are at risk of misfolding and aggregation. The resulting tension between functional requirements and the risk of misfolding and/or aggregation in the evolution of proteins is becoming more and more apparent. One outcome of this tension is sensitivity to mutation, in which only subtle changes in sequence that may be functionally advantageous can tip the delicate balance toward protein aggregation. Similarly, increasing the concentration of aggregation-prone species by reducing the ability to control protein levels or compromising protein folding capacity engenders increased risk of aggregation and disease. In this Perspective, we describe examples that epitomize the tension between protein functional energy landscapes and aggregation risk. Each case illustrates how the energy landscapes for the at-risk proteins are sculpted to enable them to perform their functions and how the risks of aggregation are minimized under cellular conditions using a variety of compensatory mechanisms.
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Affiliation(s)
- Anne Gershenson
- Department of Biochemistry and Molecular Biology, University of Massachusetts Amherst, Amherst, Massachusetts, USA
| | - Lila M Gierasch
- Department of Biochemistry and Molecular Biology, University of Massachusetts Amherst, Amherst, Massachusetts, USA
- Department of Chemistry, University of Massachusetts Amherst, Amherst, Massachusetts, USA
| | - Annalisa Pastore
- Department of Clinical Neurosciences, King’s College London, Denmark Hill Campus, London, UK
| | - Sheena E Radford
- Astbury Centre for Structural Molecular Biology, School of Molecular and Cellular Biology, University of Leeds, Leeds, UK
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21
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de Rosa M, Bemporad F, Pellegrino S, Chiti F, Bolognesi M, Ricagno S. Edge strand engineering prevents native-like aggregation in Sulfolobus solfataricus acylphosphatase. FEBS J 2014; 281:4072-84. [PMID: 24893801 DOI: 10.1111/febs.12861] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2014] [Revised: 05/19/2014] [Accepted: 05/23/2014] [Indexed: 01/09/2023]
Abstract
β-proteins are constantly threatened by the risk of aggregation because β-sheets are inherently structured for edge-to-edge interactions. To avoid native-like aggregation, evolution has resulted in a set of strategies that prevent intermolecular β-interactions. Acylphosphatase from Sulfolobus solfataricus (Sso AcP) represents a suitable model for the study of such a process. Under conditions promoting aggregation, Sso AcP acquires a native-like conformational state whereby an unstructured N-terminal segment interacts with the edge β-strand B4 of an adjacent Sso AcP molecule. Because B4 is poorly protected against aggregation, this interaction triggers the aggregation cascade without the need for unfolding. Recently, three single Sso AcP mutants (V84D, Y86E and V84P) were designed to engineer additional protection against aggregation in B4 and were observed to successfully impair native-like aggregation in all three variants at the expense of a lower stability. To understand the structural basis of the reduced aggregation propensity and lower stability, the crystal structures of the Sso AcP variants were determined in the present study. Structural analysis reveals that the V84D and Y86E mutations exert protection by the insertion of an edge negative charge. A conformationally less regular B4 underlies protection against aggregation in the V84P mutant. The thermodynamic basis of instability is discussed. Moreover, kinetic experiments indicate that aggregation of the three mutants is not native-like and is independent of the interaction between B4 and the unstructured N-terminal segment. The reported data rationalize previous evidence regarding Sso AcP native-like aggregation and provide a basis for the design of aggregation-free proteins. DATABASE The atomic coordinates and related experimental data for the Sso AcP mutants V84P, V84D, ΔN11 Y86E have been deposited in the Protein Data Bank under accession numbers 4OJ3, 4OJG and 4OJH, respectively. STRUCTURED DIGITAL ABSTRACT • Sso AcP and Sso AcP bind by fluorescence technology (View interaction).
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22
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Ragona L, Pagano K, Tomaselli S, Favretto F, Ceccon A, Zanzoni S, D'Onofrio M, Assfalg M, Molinari H. The role of dynamics in modulating ligand exchange in intracellular lipid binding proteins. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2014; 1844:1268-78. [PMID: 24768771 DOI: 10.1016/j.bbapap.2014.04.011] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/28/2014] [Revised: 04/14/2014] [Accepted: 04/16/2014] [Indexed: 11/29/2022]
Abstract
Lipids are essential for many biological processes and crucial in the pathogenesis of several diseases. Intracellular lipid-binding proteins (iLBPs) provide mobile hydrophobic binding sites that allow hydrophobic or amphipathic lipid molecules to penetrate into and across aqueous layers. Thus iLBPs mediate the lipid transport within the cell and participate to a spectrum of tissue-specific pathways involved in lipid homeostasis. Structural studies have shown that iLBPs' binding sites are inaccessible from the bulk, implying that substrate binding should involve a conformational change able to produce a ligand entry portal. Many studies have been reported in the last two decades on iLBPs indicating that their dynamics play a pivotal role in regulating ligand binding and targeted release. The ensemble of reported data has not been reviewed until today. This review is thus intended to summarize and possibly generalize the results up to now described, providing a picture which could help to identify the missing notions necessary to improve our understanding of the role of dynamics in iLBPs' molecular recognition. Such notions would clarify the chemistry of lipid binding to iLBPs and set the basis for the development of new drugs.
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Affiliation(s)
- Laura Ragona
- Laboratorio NMR, Istituto per lo Studio delle Macromolecole (ISMAC), CNR, Via Bassini 15, 20133 Milano, Italy
| | - Katiuscia Pagano
- Laboratorio NMR, Istituto per lo Studio delle Macromolecole (ISMAC), CNR, Via Bassini 15, 20133 Milano, Italy
| | - Simona Tomaselli
- Laboratorio NMR, Istituto per lo Studio delle Macromolecole (ISMAC), CNR, Via Bassini 15, 20133 Milano, Italy
| | - Filippo Favretto
- Dipartimento di Biotecnologie, Università degli Studi di Verona, Strada Le Grazie 15, 37134 Verona, Italy
| | - Alberto Ceccon
- Dipartimento di Biotecnologie, Università degli Studi di Verona, Strada Le Grazie 15, 37134 Verona, Italy
| | - Serena Zanzoni
- Dipartimento di Biotecnologie, Università degli Studi di Verona, Strada Le Grazie 15, 37134 Verona, Italy
| | - Mariapina D'Onofrio
- Dipartimento di Biotecnologie, Università degli Studi di Verona, Strada Le Grazie 15, 37134 Verona, Italy
| | - Michael Assfalg
- Dipartimento di Biotecnologie, Università degli Studi di Verona, Strada Le Grazie 15, 37134 Verona, Italy
| | - Henriette Molinari
- Laboratorio NMR, Istituto per lo Studio delle Macromolecole (ISMAC), CNR, Via Bassini 15, 20133 Milano, Italy.
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Sarkar S, Chattopadhyay K. Studies of Early Events of Folding of a Predominately β-Sheet Protein Using Fluorescence Correlation Spectroscopy and Other Biophysical Methods. Biochemistry 2014; 53:1393-402. [DOI: 10.1021/bi4014837] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Suparna Sarkar
- Protein Folding and Dynamics
Laboratory, Structural Biology and Bioinformatics Division, CSIR-Indian Institute of Chemical Biology, 4, Raja S. C. Mullick Road, Kolkata, India
| | - Krishnananda Chattopadhyay
- Protein Folding and Dynamics
Laboratory, Structural Biology and Bioinformatics Division, CSIR-Indian Institute of Chemical Biology, 4, Raja S. C. Mullick Road, Kolkata, India
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