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Khan S, Ansari B, Ansari NK, Naeem A. Protective role of chlorogenic acid in preserving cytochrome-c stability against HFIP-induced molten globule state at physiological pH. Int J Biol Macromol 2024; 261:129845. [PMID: 38302016 DOI: 10.1016/j.ijbiomac.2024.129845] [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: 08/31/2023] [Revised: 01/26/2024] [Accepted: 01/27/2024] [Indexed: 02/03/2024]
Abstract
Numerous neurodegenerative disorders are characterized by protein misfolding and aggregation. The mechanism of protein aggregation is intricate, and it is very challenging to study at cellular level. Inhibition of protein aggregation by interfering with its pathway is one of the ways to prevent neurodegenerative diseases. In the present work, we have evaluated the protective effect of a polyphenol compound chlorogenic acid (CGA) on the native and molten globule state of horse heart cytochrome c (cyt c). A molten globule state of this heme protein was achieved in the presence of fluorinated alcohol 1,1,1,3,3,3-hexafluoroisopropanol (HFIP) at physiological pH, as studied by UV-Vis absorption, circular dichroism, intrinsic and ANS fluorescence. We found that at 50 % (v/v) HFIP, the native cyt c transformed into a molten globule state. The same techniques were also used to analyze the protective effect of CGA on the molten globule state of cyt c, and the results show that the CGA prevented the molten globular state and retained the protein close to the native state at 1:1 protein:CGA sub molar ratio. Molecular dynamics study also revealed that CGA retains the stability of cyt c in HFIP medium by preserving it in an intermediate state close to native conformation.
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Affiliation(s)
- Sadaf Khan
- Department of Biochemistry, Faculty of Life Sciences, Aligarh Muslim University, Aligarh 202002, U.P., India.
| | - Bushra Ansari
- Department of Biochemistry, Faculty of Life Sciences, Aligarh Muslim University, Aligarh 202002, U.P., India
| | - Neha Kausar Ansari
- Department of Biochemistry, Faculty of Life Sciences, Aligarh Muslim University, Aligarh 202002, U.P., India.
| | - Aabgeena Naeem
- Department of Biochemistry, Faculty of Life Sciences, Aligarh Muslim University, Aligarh 202002, U.P., India.
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2
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Irukuvajjula SS, Jithender Reddy G, Rao K, Vadrevu LR. Contrasting effect of ficoll on apo and holo forms of bacterial chemotaxis protein Y: Selective destabilization of the conformationally altered holo form. Int J Biol Macromol 2023; 232:123505. [PMID: 36736516 DOI: 10.1016/j.ijbiomac.2023.123505] [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: 11/03/2022] [Revised: 01/13/2023] [Accepted: 01/28/2023] [Indexed: 02/04/2023]
Abstract
Chemotaxis Y (CheY), upon metal binding, displays a drastic alteration in its structure and stability. This premise prompted us to study the effect of crowding on the two conformationally distinct states of the same test protein. A comparative analysis on the structure and thermal stability in the presence and absence of the macromolecular crowder, ficoll, and its monomeric unit, sucrose, revealed a contrasting effect of ficoll on the apo and holo forms. In the presence of ficoll while the thermal stability (Tm) of the apo form is enhanced, the thermal stability of the holo form is reduced. The selective lowering of Tm for the holo form in the combined presence of ficoll and sucrose and not in sucrose alone suggests that the contrasting effect is due to the macromolecular nature of ficoll. Since metal-protein interaction remains unperturbed in the presence of ficoll and Mg2+ sequestration is ruled out in a systematic manner the alternative possibility for the exclusive reduction in the thermal stability of the holo form is the ficoll-induced modulation of the relative population of apo and holo forms of CheY.
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Affiliation(s)
- Shivkumar Sharma Irukuvajjula
- Department of Biological Sciences, Birla Institute of Science and Technology - Pilani, Hyderabad Campus, Shamirpet, Hyderabad 500078, India.
| | - G Jithender Reddy
- NMR Division, Department of Analytical & Structural Chemistry, CSIR-Indian Institute of Chemical Technology, Ministry of Science and Technology, Uppal Road, Tarnaka, Hyderabad 500007, India
| | - Krishna Rao
- Tata Institute of Fundamental Research, 36/P, Gopanpally Mandal, Ranga Reddy District, Hyderabad, Telangana State 500107, India
| | - Late Ramakrishna Vadrevu
- Department of Biological Sciences, Birla Institute of Science and Technology - Pilani, Hyderabad Campus, Shamirpet, Hyderabad 500078, India
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3
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Gupta MN, Uversky VN. Pre-Molten, Wet, and Dry Molten Globules en Route to the Functional State of Proteins. Int J Mol Sci 2023; 24:ijms24032424. [PMID: 36768742 PMCID: PMC9916686 DOI: 10.3390/ijms24032424] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2022] [Revised: 01/23/2023] [Accepted: 01/23/2023] [Indexed: 01/28/2023] Open
Abstract
Transitions between the unfolded and native states of the ordered globular proteins are accompanied by the accumulation of several intermediates, such as pre-molten globules, wet molten globules, and dry molten globules. Structurally equivalent conformations can serve as native functional states of intrinsically disordered proteins. This overview captures the characteristics and importance of these molten globules in both structured and intrinsically disordered proteins. It also discusses examples of engineered molten globules. The formation of these intermediates under conditions of macromolecular crowding and their interactions with nanomaterials are also reviewed.
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Affiliation(s)
- Munishwar Nath Gupta
- Department of Biochemical Engineering and Biotechnology, Indian Institute of Technology, Hauz Khas, New Delhi 110016, India
| | - Vladimir N. Uversky
- Department of Molecular Medicine and USF Health Byrd Alzheimer’s Research Institute, Morsani College of Medicine, University of South Florida, Tampa, FL 33612, USA
- Correspondence: ; Tel.: +1-813-494-5816
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4
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Parray ZA, Naqvi AAT, Ahanger IA, Shahid M, Ahmad F, Hassan MI, Islam A. Measuring Structural Changes in Cytochrome c under Crowded Conditions Using In Vitro and In Silico Approaches. Polymers (Basel) 2022; 14:polym14224808. [PMID: 36432935 PMCID: PMC9692323 DOI: 10.3390/polym14224808] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2022] [Revised: 07/26/2022] [Accepted: 07/28/2022] [Indexed: 11/11/2022] Open
Abstract
It is known from in vitro studies that macromolecular crowding in the cell effects protein structure, stability and function; but predictive studies are relatively unexplored. There are few reports where the effect of various crowder mixtures has been exploited to discern their combined effect on the structural stability of proteins. These studies are more significant because their effect can mimicked with in vivo conditions, where the environment is heterogeneous. Effects of two crowders, polyethylene glycol (PEG 400 Da), and its monomer ethylene glycol (EG) alone and in mixture on the structural stability of cytochrome c (cyt c) were determined using various spectroscopic and bioinformatics tools. The main conclusions of our study are (i) the monomer EG has a kosmotropic effect on the protein (stabilizes the protein), and has no significant effect on the tertiary structure; (ii) PEG 400 destabilizes the structure as well as the stability of the protein; and (iii) EG counteracts the destabilizing effect of PEG 400. From this investigation, it seems evident that proteins may fold or unfold in the crowded environment of the cell where various interactions assist them to maintain their structure for their functions. Bioinformatics approaches were also used to support all of the in vitro observations. Cyt c is functional protein; if the structure of the protein is modulated due to change in the environment its nature of function will also change. Our research addresses the question by modulating the environment around the protein, and the macromolecule (protein) conformation dynamics and interaction study via in vitro and in silico approaches which indirectly compares with that of the environment in-cellular milieu, which is highly crowded.
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Affiliation(s)
- Zahoor Ahmad Parray
- Centre for Interdisciplinary Research in Basic Sciences, Jamia Millia Islamia, Jamia Nagar, New Delhi 110025, India
- Department of Chemistry, Indian Institute of Technology Delhi, IIT Campus, Hauz Khas, New Delhi 110016, India
| | - Ahmad Abu Turab Naqvi
- Centre for Interdisciplinary Research in Basic Sciences, Jamia Millia Islamia, Jamia Nagar, New Delhi 110025, India
| | - Ishfaq Ahmad Ahanger
- Centre for Interdisciplinary Research in Basic Sciences, Jamia Millia Islamia, Jamia Nagar, New Delhi 110025, India
- Department of Chemistry, Biochemistry and Forensic Science, Amity School of Applied Sciences, Amity University Haryana, Gurugram 122413, India
| | - Mohammad Shahid
- Department of Basic Medical Sciences, College of Medicine, Prince Sattam Bin Abdulaziz University, Al Kharj 11942, Saudi Arabia
| | - Faizan Ahmad
- Department of Biochemistry, School of Chemical and Life Sciences, Jamia Hamdard, New Delhi 110062, India
| | - Md. Imtaiyaz Hassan
- Centre for Interdisciplinary Research in Basic Sciences, Jamia Millia Islamia, Jamia Nagar, New Delhi 110025, India
| | - Asimul Islam
- Centre for Interdisciplinary Research in Basic Sciences, Jamia Millia Islamia, Jamia Nagar, New Delhi 110025, India
- Correspondence: ; Tel.: +91-9312812007
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5
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Xu L, Zheng Y, Zhou C, Pan D, Geng F, Cao J, Xia Q. A structural explanation for enhanced binding behaviors between β-lactoglobulin and alkene-aldehydes upon heat- and ultrasonication-induced protein unfolding. Food Hydrocoll 2022. [DOI: 10.1016/j.foodhyd.2022.107682] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
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6
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Bazmi S, Wallin S. Crowding-induced protein destabilization in the absence of soft attractions. Biophys J 2022; 121:2503-2513. [PMID: 35672949 DOI: 10.1016/j.bpj.2022.06.005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2021] [Revised: 04/18/2022] [Accepted: 06/01/2022] [Indexed: 11/02/2022] Open
Abstract
It is generally assumed that volume exclusion by macromolecular crowders universally stabilizes the native states of proteins and destabilization suggests soft attractions between crowders and protein. Here we show that proteins can be destabilized even by crowders that are purely repulsive. With a coarse-grained sequence-based model, we study the folding thermodynamics of two sequences with different native folds, a helical hairpin and a β-barrel, in a range of crowder volume fractions, φc. We find that the native state, N, remains structurally unchanged under crowded conditions, while the size of the unfolded state, U, decreases monotonically with φc. Hence, for all φc>0, U is entropically disfavored relative to N. This entropy-centric view holds for the helical hairpin protein, which is stabilized under all crowded conditions as quantified by changes in either the folding midpoint temperature, Tm, or the free energy of folding. We find, however, that the β-barrel protein is destabilized under low-T, low-φc conditions. This destabilization can be understood from two characteristics of its folding: 1) a relatively compact U at T<Tm, such that U is only weakly disfavored entropically by the crowders; and 2) a transient, compact, and relatively low-energy nonnative state that has a maximum population of only a few percent at φc=0, but increasing monotonically with φc. Overall, protein destabilization driven by hard-core effects appears possible when a compaction of U leads to even a modest population of compact nonnative states that are energetically competitive with N.
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Affiliation(s)
- Saman Bazmi
- Department of Physics and Physical Oceanography, Memorial University of Newfoundland, St Johns, Newfoundland and Labrador, Canada
| | - Stefan Wallin
- Department of Physics and Physical Oceanography, Memorial University of Newfoundland, St Johns, Newfoundland and Labrador, Canada.
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7
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Parray ZA, Ahmad F, Chaudhary AA, Rudayni HA, Al-Zharani M, Hassan MI, Islam A. Size-Dependent Interplay of Volume Exclusion Versus Soft Interactions: Cytochrome c in Macromolecular Crowded Environment. Front Mol Biosci 2022; 9:849683. [PMID: 35693552 PMCID: PMC9174945 DOI: 10.3389/fmolb.2022.849683] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2022] [Accepted: 02/28/2022] [Indexed: 12/03/2022] Open
Abstract
Even though there are a great number of possible conformational states, how a protein generated as a linear unfolded polypeptide efficiently folds into its physiologically active form remained a fascinating and unanswered enigma inside crowded conditions of cells. In this study, various spectroscopic techniques have been exploited to know and understand the effect and mechanism of action of two different sizes of polyethylene glycols, or PEGs (molecular mass ∼10 and ∼20 kilo Daltons, kDa), on cytochrome c (cyt c). The outcomes showed that small size of the PEG leads to perturbation of the protein structure, and conversely, large size of the PEG has stabilizing effect on cyt c. Moreover, binding measurements showed that small size of PEG interacts strongly via soft interactions compared to the larger size of PEG, the latter being governed more by excluded volume effect or preferential exclusion from the protein. Overall, this finding suggests that conformations of protein may be influenced in cellular crowded conditions via interactions which depend upon the size of molecule in the environment. This study proposes that both volume exclusion and soft (chemical) interactions governs the protein’s conformation and functional activities. The cellular environment’s internal architecture as evident from crowder size and shape in this study has a significant role.
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Affiliation(s)
- Zahoor Ahmad Parray
- Centre for Interdisciplinary Research in Basic Sciences, Jamia Millia Islamia, New Delhi, India
- Department of Chemistry, Indian Institute of Technology Delhi, New Delhi, India
| | - Faizan Ahmad
- Centre for Interdisciplinary Research in Basic Sciences, Jamia Millia Islamia, New Delhi, India
- Department of Biochemistry, School of Chemical and Life Sciences, Jamia Hamdard, New Delhi, India
| | - Anis Ahmad Chaudhary
- Department of Biology, College of Science, Imam Mohammad Ibn Saud Islamic University (IMSIU), Riyadh, Saudi Arabia
| | - Hassan Ahmad Rudayni
- Department of Biology, College of Science, Imam Mohammad Ibn Saud Islamic University (IMSIU), Riyadh, Saudi Arabia
| | - Mohammed Al-Zharani
- Department of Biology, College of Science, Imam Mohammad Ibn Saud Islamic University (IMSIU), Riyadh, Saudi Arabia
| | - Md. Imtaiyaz Hassan
- Centre for Interdisciplinary Research in Basic Sciences, Jamia Millia Islamia, New Delhi, India
| | - Asimul Islam
- Centre for Interdisciplinary Research in Basic Sciences, Jamia Millia Islamia, New Delhi, India
- *Correspondence: Asimul Islam,
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8
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Parray ZA, Shahid M, Islam A. Insights into Fluctuations of Structure of Proteins: Significance of Intermediary States in Regulating Biological Functions. Polymers (Basel) 2022; 14:polym14081539. [PMID: 35458289 PMCID: PMC9025146 DOI: 10.3390/polym14081539] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2022] [Revised: 03/30/2022] [Accepted: 04/05/2022] [Indexed: 02/01/2023] Open
Abstract
Proteins are indispensable to cellular communication and metabolism. The structure on which cells and tissues are developed is deciphered from proteins. To perform functions, proteins fold into a three-dimensional structural design, which is specific and fundamentally determined by their characteristic sequence of amino acids. Few of them have structural versatility, allowing them to adapt their shape to the task at hand. The intermediate states appear momentarily, while protein folds from denatured (D) ⇔ native (N), which plays significant roles in cellular functions. Prolific effort needs to be taken in characterizing these intermediate species if detected during the folding process. Protein folds into its native structure through definite pathways, which involve a limited number of transitory intermediates. Intermediates may be essential in protein folding pathways and assembly in some cases, as well as misfolding and aggregation folding pathways. These intermediate states help to understand the machinery of proper folding in proteins. In this review article, we highlight the various intermediate states observed and characterized so far under in vitro conditions. Moreover, the role and significance of intermediates in regulating the biological function of cells are discussed clearly.
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Affiliation(s)
- Zahoor Ahmad Parray
- Centre for Interdisciplinary Research in Basic Sciences, Jamia Millia Islamia, New Delhi 110025, India;
- Department of Chemistry, Indian Institute of Technology Delhi, IIT Campus, Hauz Khas, New Delhi 110016, India
| | - Mohammad Shahid
- Department of Basic Medical Sciences, College of Medicine, Prince Sattam bin Abdulaziz University, Al Kharj 11942, Saudi Arabia;
| | - Asimul Islam
- Centre for Interdisciplinary Research in Basic Sciences, Jamia Millia Islamia, New Delhi 110025, India;
- Correspondence: ; Tel.: +91-93-1281-2007
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9
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Yao Y, Yang J, Li W, Zhang A. Confinements of Thermoresponsive Dendronized Polymers to Proteins. Polym Chem 2022. [DOI: 10.1039/d2py00957a] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Crowding environment created by host polymers plays crucial roles in manipulating interactions with proteins and modulating their bioactivity. Here, we report our investigation on interactions between polymers and proteins in...
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10
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Parray ZA, Naqvi AAT, Ahmad F, Hassan MI, Islam A. Characterization of different intermediate states in myoglobin induced by polyethylene glycol: A process of spontaneous molecular self-organization foresees the energy landscape theory via in vitro and in silico approaches. J Mol Liq 2021. [DOI: 10.1016/j.molliq.2021.117502] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
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11
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Xu L, Zheng Y, Zhou C, Pan D, Geng F, Cao J, Xia Q. Kinetic response of conformational variation of duck liver globular protein to ultrasonic stimulation and its impact on the binding behavior of n-alkenals. Lebensm Wiss Technol 2021. [DOI: 10.1016/j.lwt.2021.111890] [Citation(s) in RCA: 43] [Impact Index Per Article: 14.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
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12
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It is time to crowd your cell culture media - Physicochemical considerations with biological consequences. Biomaterials 2021; 275:120943. [PMID: 34139505 DOI: 10.1016/j.biomaterials.2021.120943] [Citation(s) in RCA: 30] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2020] [Revised: 05/24/2021] [Accepted: 05/29/2021] [Indexed: 12/12/2022]
Abstract
In vivo, the interior and exterior of cells is populated by various macromolecules that create an extremely crowded milieu. Yet again, in vitro eukaryotic cell culture is conducted in dilute culture media that hardly imitate the native tissue density. Herein, the concept of macromolecular crowding is discussed in both intracellular and extracellular context. Particular emphasis is given on how the physicochemical properties of the crowding molecules govern and determine kinetics, equilibria and mechanism of action of biochemical and biological reactions, processes and functions. It is evidenced that we are still at the beginning of appreciating, let alone effectively implementing, the potential of macromolecular crowding in permanently differentiated and stem cell culture systems.
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13
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Liu H, Li Q, Zhao D, Zhang M, Jiang S, Li C. Changes in the structure and digestibility of myoglobin treated with sodium chloride. Food Chem 2021; 363:130284. [PMID: 34120050 DOI: 10.1016/j.foodchem.2021.130284] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2021] [Revised: 06/01/2021] [Accepted: 06/01/2021] [Indexed: 10/21/2022]
Abstract
Myoglobin is a protein not easily broken down by digestive enzymes due to its rigid structure. This study evaluated the structural characteristics of myoglobin under various sodium chloride treatments (0.4-0.8 mol/L for 5-10 h) and the impacts on its digestibility using spectroscopic and molecular dynamics simulation techniques. Myoglobin digestibility was 40% following pepsin digestion and 60% after being sequentially digested by pepsin and trypsin. The α-helix content of myoglobin did not change significantly following sodium chloride treatment but hydrophobic amino acids were exposed and the binding of phenylalanine targeted by some digestive enzymes became more stable, leading to the reduced digestibility.
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Affiliation(s)
- Hui Liu
- Key Laboratory of Meat Processing and Quality Control, MOE, Key Laboratory of Meat Processing, MARA, Jiangsu Collaborative Innovation Center of Meat Production, Processing and Quality Control; College of Food Science and Technology, Nanjing Agricultural University, Nanjing 210095, China
| | - Qian Li
- Key Laboratory of Meat Processing and Quality Control, MOE, Key Laboratory of Meat Processing, MARA, Jiangsu Collaborative Innovation Center of Meat Production, Processing and Quality Control; College of Food Science and Technology, Nanjing Agricultural University, Nanjing 210095, China
| | - Di Zhao
- Key Laboratory of Meat Processing and Quality Control, MOE, Key Laboratory of Meat Processing, MARA, Jiangsu Collaborative Innovation Center of Meat Production, Processing and Quality Control; College of Food Science and Technology, Nanjing Agricultural University, Nanjing 210095, China
| | - Miao Zhang
- Key Laboratory of Meat Processing and Quality Control, MOE, Key Laboratory of Meat Processing, MARA, Jiangsu Collaborative Innovation Center of Meat Production, Processing and Quality Control; College of Food Science and Technology, Nanjing Agricultural University, Nanjing 210095, China
| | - Shuai Jiang
- Key Laboratory of Meat Processing and Quality Control, MOE, Key Laboratory of Meat Processing, MARA, Jiangsu Collaborative Innovation Center of Meat Production, Processing and Quality Control; College of Food Science and Technology, Nanjing Agricultural University, Nanjing 210095, China
| | - Chunbao Li
- Key Laboratory of Meat Processing and Quality Control, MOE, Key Laboratory of Meat Processing, MARA, Jiangsu Collaborative Innovation Center of Meat Production, Processing and Quality Control; College of Food Science and Technology, Nanjing Agricultural University, Nanjing 210095, China.
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14
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Garfagnini T, Levi-Kalisman Y, Harries D, Friedler A. Osmolytes and crowders regulate aggregation of the cancer-related L106R mutant of the Axin protein. Biophys J 2021; 120:3455-3469. [PMID: 34087214 DOI: 10.1016/j.bpj.2021.05.024] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2020] [Accepted: 05/28/2021] [Indexed: 11/16/2022] Open
Abstract
Protein aggregation is involved in a variety of diseases, including neurodegenerative diseases and cancer. The cellular environment is crowded by a plethora of cosolutes comprising small molecules and biomacromolecules at high concentrations, which may influence the aggregation of proteins in vivo. To account for the effect of cosolutes on cancer-related protein aggregation, we studied their effect on the aggregation of the cancer-related L106R mutant of the Axin protein. Axin is a key player in the Wnt signaling pathway, and the L106R mutation in its RGS domain results in a native molten globule that tends to form native-like aggregates. This results in uncontrolled activation of the Wnt signaling pathway, leading to cancer. We monitored the aggregation process of Axin RGS L106R in vitro in the presence of a wide ensemble of cosolutes including polyols, amino acids, betaine, and polyethylene glycol crowders. Except myo-inositol, all polyols decreased RGS L106R aggregation, with carbohydrates exerting the strongest inhibition. Conversely, betaine and polyethylene glycols enhanced aggregation. These results are consistent with the reported effects of osmolytes and crowders on the stability of molten globular proteins and with both amorphous and amyloid aggregation mechanisms. We suggest a model of Axin L106R aggregation in vivo, whereby molecularly small osmolytes keep the protein as a free soluble molecule but the increased crowding of the bound state by macromolecules induces its aggregation at the nanoscale. To our knowledge, this is the first systematic study on the effect of osmolytes and crowders on a process of native-like aggregation involved in pathology, as it sheds light on the contribution of cosolutes to the onset of cancer as a protein misfolding disease and on the relevance of aggregation in the molecular etiology of cancer.
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Affiliation(s)
- Tommaso Garfagnini
- Institute of Chemistry, The Hebrew University of Jerusalem, Jerusalem, Israel
| | - Yael Levi-Kalisman
- The Harvey M. Krueger Family Center for Nanoscience and Nanotechnology and The Alexander Silberman Life Sciences Institute, The Hebrew University of Jerusalem, Jerusalem, Israel
| | - Daniel Harries
- Institute of Chemistry, The Hebrew University of Jerusalem, Jerusalem, Israel; The Fritz Haber Center, The Hebrew University of Jerusalem, Jerusalem, Israel.
| | - Assaf Friedler
- Institute of Chemistry, The Hebrew University of Jerusalem, Jerusalem, Israel.
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15
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Structural Refolding and Thermal Stability of Myoglobin in the Presence of Mixture of Crowders: Importance of Various Interactions for Protein Stabilization in Crowded Conditions. Molecules 2021; 26:molecules26092807. [PMID: 34068693 PMCID: PMC8126177 DOI: 10.3390/molecules26092807] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2021] [Revised: 04/26/2021] [Accepted: 04/27/2021] [Indexed: 11/16/2022] Open
Abstract
The intracellular environment is overcrowded with a range of molecules (small and large), all of which influence protein conformation. As a result, understanding how proteins fold and stay functional in such crowded conditions is essential. Several in vitro experiments have looked into the effects of macromolecular crowding on different proteins. However, there are hardly any reports regarding small molecular crowders used alone and in mixtures to observe their effects on the structure and stability of the proteins, which mimics of the cellular conditions. Here we investigate the effect of different mixtures of crowders, ethylene glycol (EG) and its polymer polyethylene glycol (PEG 400 Da) on the structural and thermal stability of myoglobin (Mb). Our results show that monomer (EG) has no significant effect on the structure of Mb, while the polymer disrupts its structure and decreases its stability. Conversely, the additive effect of crowders showed structural refolding of the protein to some extent. Moreover, the calorimetric binding studies of the protein showed very weak interactions with the mixture of crowders. Usually, we can assume that soft interactions induce structural perturbations while exclusion volume effects stabilize the protein structure; therefore, we hypothesize that under in vivo crowded conditions, both phenomena occur and maintain the stability and function of proteins.
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16
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Parray ZA, Ahmad F, Alajmi MF, Hussain A, Hassan MI, Islam A. Interaction of polyethylene glycol with cytochrome c investigated via in vitro and in silico approaches. Sci Rep 2021; 11:6475. [PMID: 33742055 PMCID: PMC7979836 DOI: 10.1038/s41598-021-85792-4] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2020] [Accepted: 02/12/2021] [Indexed: 12/11/2022] Open
Abstract
One of the significant proteins that have attracted research groups due to virtue of being a potent selective anticancer drug target and property of triggering apoptosis upon release in cytoplasm is cytochrome c (cyt c). The mechanical transformations due to the macromolecular crowding in membrane in the mammalian cell are proposed to be useful inductors of changes in volume. It is very interesting to know that mitochondrial function were observed to be improved by polyethylene glycol (PEG) interaction, which in turn inhibits the cyt c (a pro-apoptotic cell death factor). In this work, the effect of polyethylene glycol of molecular weight 4 kilo Dalton (PEG 4 kDa) was investigated to highlight the structural transformations (tertiary and secondary structure) in cyt c using a choice of spectroscopic techniques (including UV-Vis absorption, near-UV, far-UV and Soret circular dichroism and fluorescence spectroscopy), which shows noteworthy shifts in the secondary and tertiary structures at higher concentrations of PEG 4 kDa with small changes in the heme-globular interactions. The size distribution changes of native protein treated with various concentrations of the crowder were observed and analyzed by dynamic light scattering (DLS). The interaction studies of the crowder with the protein was observed and analyzed by FTIR, isothermal titration calorimetry, time resolved fluorescence and molecular docking. The investigations suggested that the structural changes in the protein occurred due to soft interactions of PEG 4 kDa, which usually destabilizes proteins. The experimental evidence in this study proposed that crowding could be another approach to mechanical super-competition and free of certain markers that could aid in the identification and control of various diseases. This study suggests that crowders at specific concentrations, which softly interact with proteins, can be exploited as remedy for various diseases.
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Affiliation(s)
- Zahoor Ahmad Parray
- Centre for Interdisciplinary Research in Basic Sciences, Jamia Millia Islamia, Jamia Nagar, New Delhi, 110025, India
| | - Faizan Ahmad
- Centre for Interdisciplinary Research in Basic Sciences, Jamia Millia Islamia, Jamia Nagar, New Delhi, 110025, India
| | - Mohamed F Alajmi
- Department of Pharmacognosy College of Pharmacy, King Saud University, Riyadh, Saudi Arabia
| | - Afzal Hussain
- Department of Pharmacognosy College of Pharmacy, King Saud University, Riyadh, Saudi Arabia
| | - Md Imtaiyaz Hassan
- Centre for Interdisciplinary Research in Basic Sciences, Jamia Millia Islamia, Jamia Nagar, New Delhi, 110025, India
| | - Asimul Islam
- Centre for Interdisciplinary Research in Basic Sciences, Jamia Millia Islamia, Jamia Nagar, New Delhi, 110025, India.
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17
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Nasreen K, Parray ZA, Shamsi A, Ahmad F, Ahmed A, Malik A, Lakhrm NA, Hassan MI, Islam A. Crowding Milleu stabilizes apo-myoglobin against chemical-induced denaturation: Dominance of hardcore repulsions in the heme devoid protein. Int J Biol Macromol 2021; 181:552-560. [PMID: 33744250 DOI: 10.1016/j.ijbiomac.2021.03.089] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2020] [Revised: 03/11/2021] [Accepted: 03/15/2021] [Indexed: 12/27/2022]
Abstract
Macromolecular crowding can have significant consequences on the structure and dynamics of a protein. The size and shape of a co-solute molecule and the nature of protein contribute significantly in macromolecular crowding, which results in different outcomes in similar conditions. The structure of apo-myoglobin (apo-Mb) both in the absence and presence of denaturants (GdmCl and urea) was investigated in crowded conditions at pH 7.0, with a comparable size of crowders (~70 kDa) but of different shapes (ficoll and dextran) at various concentrations using spectroscopic techniques like absorption and circular dichroism to monitor changes in secondary and tertiary structure, respectively. The crowders in the absence of denaturants showed structural stabilization of the tertiary structure while no significant change in the secondary structure was observed. The effect of crowders on the stability of the protein was also investigated using probes such as Δε291 and θ222 using chemical denaturants. The analysis of chemical-induced denaturation curves showed that both the crowders stabilize apo-Mb by increasing the values of the midpoint of transition (Cm) and change in free energy in the absence of denaturant (∆GD°), and it was observed that dextran 70 shows more stabilization than ficoll 70 under similar conditions. In this study apo-Mb showed stabilization under crowded conditions, which is a deviation from earlier work from our group where holo form of the same protein was destabilized. This study emphasizes that volume exclusion is a dominant force in a simple protein while soft interactions may play important role in the proteins that are possessing prosthetic group. Hence, the effect of crowders is protein-dependent, and excluded volume plays a great role in the stabilization of apo-Mb, which does not interact with the crowders.
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Affiliation(s)
- Khalida Nasreen
- Centre for Interdisciplinary Research in Basic Sciences, Jamia Millia Islamia, Jamia Nagar, New Delhi 110025, India
| | - Zahoor Ahmad Parray
- Centre for Interdisciplinary Research in Basic Sciences, Jamia Millia Islamia, Jamia Nagar, New Delhi 110025, India
| | - Anas Shamsi
- Centre for Interdisciplinary Research in Basic Sciences, Jamia Millia Islamia, Jamia Nagar, New Delhi 110025, India
| | - Faizan Ahmad
- Centre for Interdisciplinary Research in Basic Sciences, Jamia Millia Islamia, Jamia Nagar, New Delhi 110025, India
| | - Anwar Ahmed
- Center of Excellence in Biotechnology Research, College of Science, King Saud University, Riyadh 11451, Saudi Arabia; Protein Research Chair, Department of Biochemistry, College of Science, King Saud University, Riyadh 11451, Saudi Arabia
| | - Ajamaluddin Malik
- Protein Research Chair, Department of Biochemistry, College of Science, King Saud University, Riyadh 11451, Saudi Arabia
| | - Nasser Abobakr Lakhrm
- Center of Excellence in Biotechnology Research, College of Science, King Saud University, Riyadh 11451, Saudi Arabia; Protein Research Chair, Department of Biochemistry, College of Science, King Saud University, Riyadh 11451, Saudi Arabia
| | - Md Imtaiyaz Hassan
- Centre for Interdisciplinary Research in Basic Sciences, Jamia Millia Islamia, Jamia Nagar, New Delhi 110025, India
| | - Asimul Islam
- Centre for Interdisciplinary Research in Basic Sciences, Jamia Millia Islamia, Jamia Nagar, New Delhi 110025, India.
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18
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Zeugolis DI. Bioinspired in vitro microenvironments to control cell fate: focus on macromolecular crowding. Am J Physiol Cell Physiol 2021; 320:C842-C849. [PMID: 33656930 DOI: 10.1152/ajpcell.00380.2020] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
The development of therapeutic regenerative medicine and accurate drug discovery cell-based products requires effective, with respect to obtaining sufficient numbers of viable, proliferative, and functional cell populations, cell expansion ex vivo. Unfortunately, traditional cell culture systems fail to recapitulate the multifaceted tissue milieu in vitro, resulting in cell phenotypic drift, loss of functionality, senescence, and apoptosis. Substrate-, environment-, and media-induced approaches are under intense investigation as a means to maintain cell phenotype and function while in culture. In this context, herein, the potential of macromolecular crowding, a biophysical phenomenon with considerable biological consequences, is discussed.
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Affiliation(s)
- Dimitrios I Zeugolis
- Regenerative, Modular, and Developmental Engineering Laboratory (REMODEL), Biomedical Sciences Building, National University of Ireland Galway, Galway, Ireland.,Science Foundation Ireland (SFI) Centre for Research in Medical Devices (CÚRAM), Biomedical Sciences Building, National University of Ireland Galway, Galway, Ireland.,Faculty of Biomedical Sciences, Regenerative, Modular, and Developmental Engineering Laboratory (REMODEL), Università della Svizzera Italiana, Lugano, Switzerland.,Regenerative, Modular & Developmental Engineering Laboratory (REMODEL), School of Mechanical and Materials Engineering, University College Dublin, Dublin, Ireland
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19
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Parray ZA, Ahmad F, Hassan MI, Islam A. Conformational changes in cytochrome c directed by ethylene glycol accompanying complex formation: Protein-solvent preferential interaction or/and kosmotropic effect. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2020; 242:118788. [PMID: 32810818 DOI: 10.1016/j.saa.2020.118788] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/28/2020] [Revised: 07/04/2020] [Accepted: 07/19/2020] [Indexed: 06/11/2023]
Abstract
When proteins interact with solvent or co-solutes with a high specificity and affinity, protein-ligand complexes may be formed. Such phenomenon may involve the processes like intra- and intermolecular interactions, which result in interaction based protein folding. In this study, cytochrome c (cyt c) was treated with different concentrations of ethylene glycol (EG) in crowded and confined media to check its structural stability using various spectroscopic techniques at pH 7.0 and 25 °C. The various spectroscopic techniques including circular dichroism (Soret, far- and near-UV regions), Fourier transform infrared (FTIR), absorption (UV and visible) and Trp fluorescence shows both secondary and tertiary structure of cyt c increases when treated with EG. The investigations using dynamic light scattering (DLS), time resolved fluorescence and isothermal titration calorimetry (ITC) for binding studies shows weak interaction between EG and cyt c. Small increase in the structure of the protein and insignificant decrease in hydrodynamic radii of the protein was observed from the studies. Molecular docking studies showed that EG has binding site on the protein and interact with few amino acid residues by weak interactions such as van der Waals and hydrogen bonding. This study helps in understanding the protein-ligand interactions, provides facts and the mechanisms that mediates the recognition of binding site for specific ligand to the receptor protein, which make possible of the discovery, design, and development of drugs at molecular level without affecting proteins within an organism.
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Affiliation(s)
- Zahoor Ahmad Parray
- Centre for Interdisciplinary Research in Basic Sciences, Jamia Millia Islamia, Jamia Nagar, New Delhi 110025, India
| | - Faizan Ahmad
- Centre for Interdisciplinary Research in Basic Sciences, Jamia Millia Islamia, Jamia Nagar, New Delhi 110025, India
| | - Md Imtaiyaz Hassan
- Centre for Interdisciplinary Research in Basic Sciences, Jamia Millia Islamia, Jamia Nagar, New Delhi 110025, India
| | - Asimul Islam
- Centre for Interdisciplinary Research in Basic Sciences, Jamia Millia Islamia, Jamia Nagar, New Delhi 110025, India.
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20
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Li Q, Zhao D, Liu H, Zhang M, Jiang S, Xu X, Zhou G, Li C. "Rigid" structure is a key determinant for the low digestibility of myoglobin. Food Chem X 2020; 7:100094. [PMID: 32617526 PMCID: PMC7322683 DOI: 10.1016/j.fochx.2020.100094] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2019] [Revised: 05/13/2020] [Accepted: 06/06/2020] [Indexed: 01/13/2023] Open
Abstract
Myoglobin, a critical protein responsible for meat color, has been shown insusceptible to digestion. The underlying mechanism is not clear. The present study aimed to evaluate whether the structural properties of myoglobin are associated with its insusceptibility to digestion using spectroscopic and computational techniques. Myoglobin was degraded by only 7.03% by pepsin and 33.00% by pancreatin. The structure of myoglobin still maintained α-helix after the two-step digestion, with the exposure of some aromatic residues. In addition, molecular dynamics modeling suggested that hydrophobic amino acid residues (Phe 111, Leu 10, Ala 115, Pro 116) in pepsin and polar amino acid residues (Tyr 146, Thr 95) in myoglobin were found in the proximity of binding sites, which could result in the low digestibility of myoglobin. Our findings provide a new insight into the underlying mechanisms on the difficulty in digestion of myoglobin.
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Affiliation(s)
- Qian Li
- Key Laboratory of Meat Processing and Quality Control, MOE, Key Laboratory of Meat Processing, MARA, Jiangsu Collaborative Innovation Center of Meat Production, Processing and Quality Control, College of Food Science and Technology, Nanjing Agricultural University, Nanjing 210095, China
| | - Di Zhao
- Key Laboratory of Meat Processing and Quality Control, MOE, Key Laboratory of Meat Processing, MARA, Jiangsu Collaborative Innovation Center of Meat Production, Processing and Quality Control, College of Food Science and Technology, Nanjing Agricultural University, Nanjing 210095, China
| | - Hui Liu
- Key Laboratory of Meat Processing and Quality Control, MOE, Key Laboratory of Meat Processing, MARA, Jiangsu Collaborative Innovation Center of Meat Production, Processing and Quality Control, College of Food Science and Technology, Nanjing Agricultural University, Nanjing 210095, China
| | - Miao Zhang
- Key Laboratory of Meat Processing and Quality Control, MOE, Key Laboratory of Meat Processing, MARA, Jiangsu Collaborative Innovation Center of Meat Production, Processing and Quality Control, College of Food Science and Technology, Nanjing Agricultural University, Nanjing 210095, China
| | - Shuai Jiang
- Key Laboratory of Meat Processing and Quality Control, MOE, Key Laboratory of Meat Processing, MARA, Jiangsu Collaborative Innovation Center of Meat Production, Processing and Quality Control, College of Food Science and Technology, Nanjing Agricultural University, Nanjing 210095, China
| | - Xinglian Xu
- Key Laboratory of Meat Processing and Quality Control, MOE, Key Laboratory of Meat Processing, MARA, Jiangsu Collaborative Innovation Center of Meat Production, Processing and Quality Control, College of Food Science and Technology, Nanjing Agricultural University, Nanjing 210095, China
| | - Guanghong Zhou
- Key Laboratory of Meat Processing and Quality Control, MOE, Key Laboratory of Meat Processing, MARA, Jiangsu Collaborative Innovation Center of Meat Production, Processing and Quality Control, College of Food Science and Technology, Nanjing Agricultural University, Nanjing 210095, China
| | - Chunbao Li
- Key Laboratory of Meat Processing and Quality Control, MOE, Key Laboratory of Meat Processing, MARA, Jiangsu Collaborative Innovation Center of Meat Production, Processing and Quality Control, College of Food Science and Technology, Nanjing Agricultural University, Nanjing 210095, China
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21
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Raina N, Singh AK, Hassan MI, Ahmad F, Islam A. Concentration dependent effect of ethylene glycol on the structure and stability of holo α-lactalbumin: Characterization of intermediate state amidst soft interactions. Int J Biol Macromol 2020; 164:2151-2161. [PMID: 32735932 DOI: 10.1016/j.ijbiomac.2020.07.224] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2020] [Revised: 07/22/2020] [Accepted: 07/24/2020] [Indexed: 12/16/2022]
Abstract
The interior of the cell is crowded with different kinds of biological molecules with varying sizes, shapes and compositions which may affect physiological processes especially protein folding, protein conformation and protein stability. To understand the consequences of such a crowded environment, pH-induced unfolding of holo alpha-lactalbumin (holo α-LA) was studied in the presence of ethylene glycol (EG). The effect of EG on the folding and stability of holo α-LA in aqueous solution was investigated using several spectroscopic techniques. The results indicate that stabilization/destabilization of holo α-LA by EG is concentration- and pH-dependent. Low concentration of EG stabilizes the protein at pH near its pI. From the results of far-UV CD, UV-visible and ANS fluorescence, intermediate state (MG state) was characterized in the presence of high concentration of ethylene glycol. The results invoke a new mechanism for the formation of MG state identical to active component of BAMLET. MG state of holo α-LA has a direct implication to cancer therapy. MG state of α-LA in complex with specific type of lipid is a novel class of protein-based anti-cancer complexes that incorporate oleic acid and deliver it to the cancer cells.
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Affiliation(s)
- Neha Raina
- Department of Biotechnology, Sharda University, Greater Noida, Uttar Pradesh 201310, India; Centre for Interdisciplinary Research in Basic Sciences, Jamia Millia Islamia, New Delhi 110025, India
| | - Amit Kumar Singh
- Department of Biotechnology, Sharda University, Greater Noida, Uttar Pradesh 201310, India.
| | - Md Imtaiyaz Hassan
- Centre for Interdisciplinary Research in Basic Sciences, Jamia Millia Islamia, New Delhi 110025, India
| | - Faizan Ahmad
- Centre for Interdisciplinary Research in Basic Sciences, Jamia Millia Islamia, New Delhi 110025, India
| | - Asimul Islam
- Centre for Interdisciplinary Research in Basic Sciences, Jamia Millia Islamia, New Delhi 110025, India.
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22
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Parray Z, Ahmad F, Hassan MI, Hasan I, Islam A. Effects of Ethylene Glycol on the Structure and Stability of Myoglobin Using Spectroscopic, Interaction, and In Silico Approaches: Monomer Is Different from Those of Its Polymers. ACS OMEGA 2020; 5:13840-13850. [PMID: 32566850 PMCID: PMC7301589 DOI: 10.1021/acsomega.0c01185] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/17/2020] [Accepted: 05/25/2020] [Indexed: 06/11/2023]
Abstract
Investigation of changes in thermal stabilities and structures of proteins in the presence of different co-solutes (ligands) is an integral part in the basic research, discovery, and development of drugs. Ethylene glycol (EG) is known to be toxic and causes teratogenic, inducing primarily skeletal and external malformations and other diseases. The effect of EG on the structure and thermal stability of myoglobin (Mb) was studied using various spectroscopic techniques at pH 7.0 and two different temperatures. As revealed by circular dichroism, Trp fluorescence, nano-DSF, and absorption (UV and visible) measurements, EG (i) has no significant effect on secondary and tertiary structures of Mb at 25 °C, and (ii) it decreases the thermal stability of the protein, which increases with increasing concentration of EG. As revealed by ANS (8-anilino-1-naphthalene sulfonic acid) fluorescence measurements, heat-induced denatured protein has newly exposed hydrophobic patches that bind to ANS. Isothermal titration calorimetry revealed that the interaction between EG and Mb is temperature dependent; the preferential interaction of EG is entropy driven at low temperature, 298 K (25 °C), and it is enthalpy driven at higher temperature, 343 K (70 °C). Molecular docking study showed that EG interacts with side chains of amino acid residues of Mb through van der Waals interactions and hydrogen bonding.
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Affiliation(s)
- Zahoor
Ahmad Parray
- Centre
for Interdisciplinary Research in Basic Sciences, Jamia Millia Islamia, Jamia Nagar, New Delhi 110025, India
| | - Faizan Ahmad
- Centre
for Interdisciplinary Research in Basic Sciences, Jamia Millia Islamia, Jamia Nagar, New Delhi 110025, India
| | - Md Imtaiyaz Hassan
- Centre
for Interdisciplinary Research in Basic Sciences, Jamia Millia Islamia, Jamia Nagar, New Delhi 110025, India
| | - Ikramul Hasan
- Department
of Basic Medical Science, Faculty of Applied Medical Sciences, Al-Baha University, Al-Baha 110025, KSA
| | - Asimul Islam
- Centre
for Interdisciplinary Research in Basic Sciences, Jamia Millia Islamia, Jamia Nagar, New Delhi 110025, India
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23
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Molecular and macromolecular crowding-induced stabilization of proteins: Effect of dextran and its building block alone and their mixtures on stability and structure of lysozyme. Int J Biol Macromol 2020; 150:1238-1248. [DOI: 10.1016/j.ijbiomac.2019.10.135] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2018] [Revised: 10/13/2019] [Accepted: 10/14/2019] [Indexed: 11/22/2022]
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24
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Interactions Under Crowding Milieu: Chemical-Induced Denaturation of Myoglobin is Determined by the Extent of Heme Dissociation on Interaction with Crowders. Biomolecules 2020; 10:biom10030490. [PMID: 32210191 PMCID: PMC7175338 DOI: 10.3390/biom10030490] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2020] [Revised: 03/06/2020] [Accepted: 03/08/2020] [Indexed: 12/13/2022] Open
Abstract
Generally, in vivo function and structural changes are studied by probing proteins in a dilute solution under in vitro conditions, which is believed to be mimicking proteins in intracellular milieu. Earlier, thermal-induced denaturation of myoglobin, in the milieu of crowder molecule showed destabilization of the metal protein. Destabilization of protein by thermal-induced denaturation involves a large extrapolation, so, the reliability is questionable. This led us to measure the effects of macromolecular crowding on its stability by chemical-induced denaturation of the protein using probes like circular dichroism and absorption spectroscopy in the presence of dextran 70 and ficoll 70 at various pHs (acidic: 6.0, almost neutral: 7.0 and basic: 8.0). Observations showed that the degree of destabilization of myoglobin was greater due to ficoll 70 as compared to that of dextran 70 so it can be understood that the nature of the crowder or the shape of the crowder has an important role towards the stability of proteins. Additionally, the degree of destabilization was observed as pH dependent, however the pH dependence is different for different crowders. Furthermore, isothermal titration calorimetry and molecular docking studies confirmed that both the crowders (ficoll and dextran) bind to heme moiety of myoglobin and a single binding site was observed for each.
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25
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Parray ZA, Ahmad F, Alajmi MF, Hussain A, Hassan MI, Islam A. Formation of molten globule state in horse heart cytochrome c under physiological conditions: Importance of soft interactions and spectroscopic approach in crowded milieu. Int J Biol Macromol 2020; 148:192-200. [PMID: 31945437 DOI: 10.1016/j.ijbiomac.2020.01.119] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2019] [Revised: 01/07/2020] [Accepted: 01/12/2020] [Indexed: 11/17/2022]
Abstract
To understand protein folding problem under physiological condition, usually taken as dilute aqueous buffer at pH 7.0 and 25 °C, knowledge of properties of folding intermediates is important, such as molten globule (MG). We observed that polyethylene glycol 400 Da (PEG 400) induces molten globule state conformation in cytochrome c at pH 7.0 and 25 °C. This PEG-induced MG state has: (i) native tertiary structure partially perturbed, (ii) unperturbed native secondary structure, (iii) newly exposed hydrophobic patches, and (iv) has 1.58 times more hydrodynamic volume than that of the native protein. Isothermal titration calorimetry and docking studies showed specific binding between PEG 400 and cytochrome c. The study delineates that PEG-protein interactions are more complex than the excluded-volume. The soft interactions need to be seriously studied in crowding milieu that leads to destabilization of protein and overcome stabilizing exclusion volume effect. This study not only can help in unraveling the mystery of steps involved in the proper folding of proteins to solve the massively complicated problems of protein folding but also provides novel insights towards importance of structural change in proteins inside cell where intermediate states of protein import-export easily via membranes rather than native form of proteins.
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Affiliation(s)
- Zahoor Ahmad Parray
- Centre for Interdisciplinary Research in Basic Sciences, Jamia Millia Islamia, Jamia Nagar, New Delhi 110025, India
| | - Faizan Ahmad
- Centre for Interdisciplinary Research in Basic Sciences, Jamia Millia Islamia, Jamia Nagar, New Delhi 110025, India
| | - Mohamed F Alajmi
- Department of Pharmacognosy, College of Pharmacy, King Saud University, Riyadh, Saudi Arabia
| | - Afzal Hussain
- Department of Pharmacognosy, College of Pharmacy, King Saud University, Riyadh, Saudi Arabia
| | - Md Imtaiyaz Hassan
- Centre for Interdisciplinary Research in Basic Sciences, Jamia Millia Islamia, Jamia Nagar, New Delhi 110025, India
| | - Asimul Islam
- Centre for Interdisciplinary Research in Basic Sciences, Jamia Millia Islamia, Jamia Nagar, New Delhi 110025, India.
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26
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Biswas B, Singh PC. Does Fungicide "Dodine" Unfold Protein like Kosmo-Chaotropic Agent? J Phys Chem B 2019; 123:8240-8246. [PMID: 31487177 DOI: 10.1021/acs.jpcb.9b08129] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The nontargeted action of fungicides affects the structure of protein, which leads to several serious diseases such as nausea, cancer, fetus malformations, movement dysfunction, and behavioral changes in human and animals. Hence, understanding of the structural change in protein induced by fungicides is of utmost importance to decode its mode of nontargeted action. In this study, we have investigated the structural change of myoglobin by an important fungicide, namely, dodine (n-dodecylguanidinium acetate), as well as its analogues n-hexylguanidinium acetate (HGA) and guanidinium chloride (GdmCl) using spectroscopic and thermodynamic methods. The amount of dodine and HGA required for the unfolding of myoglobin is significantly less than GdmCl. GdmCl, dodine, and HGA unfold the myoglobin by decreasing the content of the helical and tertiary structures. However, the decrease in the content of tertiary structure is significantly higher than that of the secondary structure for dodine and HGA, in contrast to GdmCl, where the decrease in secondary and tertiary contents of protein is not biased. Thermodynamic and spectroscopic data depict that the unfolding of the dodine and HGA is driven by the hydrophobic interaction, whereas the hydrogen bonding of GdmCl with the amino acids of protein plays a key role in the unfolding. The long alkyl chain of dodine and HGA get accommodated at the surface of the helices of myoglobin, inducing strong hydrophobic interaction, which causes its unfolding. This study depicts that dodine unfolds protein by the chaotropic effect in which its hydrocarbon chain destabilizes the protein by the hydrophobic effect, unlike in an earlier study, where dodine was claimed to be a kosmo-chaotropic agent as its hydrocarbon group stabilizes the protein.
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Affiliation(s)
- Biswajit Biswas
- School of Chemical Science , Indian Association for the Cultivation of Science , Jadavpur, Kolkata 700032 , India
| | - Prashant Chandra Singh
- School of Chemical Science , Indian Association for the Cultivation of Science , Jadavpur, Kolkata 700032 , India
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27
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Carbohydrate-Based Macromolecular Crowding-Induced Stabilization of Proteins: Towards Understanding the Significance of the Size of the Crowder. Biomolecules 2019; 9:biom9090477. [PMID: 31547256 PMCID: PMC6769620 DOI: 10.3390/biom9090477] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2019] [Revised: 09/02/2019] [Accepted: 09/06/2019] [Indexed: 11/23/2022] Open
Abstract
There are a large number of biomolecules that are accountable for the extremely crowded intracellular environment, which is totally different from the dilute solutions, i.e., the idealized conditions. Such crowded environment due to the presence of macromolecules of different sizes, shapes, and composition governs the level of crowding inside a cell. Thus, we investigated the effect of different sizes and shapes of crowders (ficoll 70, dextran 70, and dextran 40), which are polysaccharide in nature, on the thermodynamic stability, structure, and functional activity of two model proteins using UV-Vis spectroscopy and circular dichroism techniques. We observed that (a) the extent of stabilization of α-lactalbumin and lysozyme increases with the increasing concentration of the crowding agents due to the excluded volume effect and the small-sized and rod-shaped crowder, i.e., dextran 40 resulted in greater stabilization of both proteins than dextran 70 and ficoll 70; (b) structure of both the proteins remains unperturbed; and (c) enzymatic activity of lysozyme decreases with the increasing concentration of the crowder.
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28
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Khan MS, Rehman MT, Bhat SA, Tabrez S, Hussain A, Husain FM, AlAjmi MF, Alamery SF, Sumbul S. Food additive dye (quinoline yellow) promotes unfolding and aggregation of myoglobin: A spectroscopic and molecular docking analysis. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2019; 214:216-226. [PMID: 30785041 DOI: 10.1016/j.saa.2019.01.090] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/02/2018] [Revised: 01/31/2019] [Accepted: 01/31/2019] [Indexed: 06/09/2023]
Abstract
Protein aggregation leads to vast conformational changes and plays a key role in the pathogenesis of various neurodegenerative diseases including Alzheimer's and Parkinson's. In the current piece of work, we have explored the interaction of quinoline yellow (QY) with myoglobin (Mb) at two different pH (3.5 and 7.4). Various spectroscopic techniques such as turbidity, Rayleigh light scattering (RLS), UV-Vis absorbance, fluorescence resonance energy transfer (FRET), far UV-CD along with transmission electron microscopy (TEM) and molecular docking have been utilized to characterize dye-induced aggregation in Mb. Binding results showed that interaction between QY and myoglobin is spontaneous and static in nature with high KSV value of 2.14 × 104 M-1. On the other hand, thermodynamics studies (∆H & ∆S) revealed that complex formation was driven by hydrogen and Van der Walls forces. Molecular docking analysis showed strong binding affinity (Kd = 4.95 × 104 M-1) between QY and Mb at Pro100, Ile101, Lys102, Glu105, Glu136, Arg139, Lys140, and Ala143 residues. The intrinsic fluorescence and circular dichroism studies indicated that QY induced conformational changes in Mb at pH 3.5. Turbidity and RLS studies showed aggregation of Mb in the presence of QY (0.2-5 mM). Moreover, kinetics data revealed nucleation independent aggregation of myoglobin in the presence of QY. TEM analysis further established amorphous nature of Mb aggregate induced by QY. At pH (7.4), QY was unable to induce aggregation in myoglobin; it might be due to repulsive nature of negatively charged dye and myoglobin or partially altered states of protein could be pre-requisite for binding and aggregation.
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Affiliation(s)
- Mohd Shahnawaz Khan
- Department of Biochemistry, College of Sciences, King Saud University, Riyadh, Saudi Arabia.
| | - Md Tabish Rehman
- Department of Pharmacognosy, College of Pharmacy, King Saud University, Riyadh, Saudi Arabia
| | - Sheraz Ahmad Bhat
- Department of Biochemistry, Kashmir University, Jammu and Kashmir, India
| | - Shams Tabrez
- King Fahd Medical Research Centre, King Abdulaziz University, Jeddah, Saudi Arabia; Department of Medical Laboratory Technology, Faculty of Applied Medical Sciences, King AbdulAziz University, Jeddah, Saudi Arabia
| | - Afzal Hussain
- Department of Pharmacognosy, College of Pharmacy, King Saud University, Riyadh, Saudi Arabia
| | - Fohad Mabood Husain
- Department of Food and Agriculture Science, King Saud University, Riyadh, Saudi Arabia
| | - Mohamed F AlAjmi
- Department of Pharmacognosy, College of Pharmacy, King Saud University, Riyadh, Saudi Arabia
| | - Salman Freeh Alamery
- Department of Biochemistry, College of Sciences, King Saud University, Riyadh, Saudi Arabia
| | - Sadia Sumbul
- Department of Chemistry, Collage of Science Princess Noura Bint Abdul Rahman University, Riyadh, Saudi Arabia.
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29
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Parray ZA, Ahamad S, Ahmad F, Hassan MI, Islam A. First evidence of formation of pre-molten globule state in myoglobin: A macromolecular crowding approach towards protein folding in vivo. Int J Biol Macromol 2018; 126:1288-1294. [PMID: 30586590 DOI: 10.1016/j.ijbiomac.2018.12.170] [Citation(s) in RCA: 30] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2018] [Revised: 12/14/2018] [Accepted: 12/18/2018] [Indexed: 01/04/2023]
Abstract
Myoglobin is known to show formation of intermediate states under various environmental conditions, in spite of that, this is the first evidence of formation pre-molten globule (PMG) in myoglobin. Polyethylene glycol (PEG) of various molecular sizes shows assorted effects on different proteins. Out of too short and too long PEGs, only PEGs of optimal size interact with proteins leading to change in protein structure that form intermediate state. We are the first one to report the formation of PMG in a protein in the presence of a crowding agent. The PEG-induced intermediate state was characterized by various techniques like absorption, fluorescence, near- and far-UV circular dichroism spectroscopy, ANS binding, and dynamic light scattering measurements to be PMG. Isothermal titration calorimetry and docking studies were further carried out to delineate the mechanism of formation of PMG in myoglobin in physiological conditions. The intermediate formed due to interaction of PEG with myoglobin has physiological implications which are essential to unravel the mystery to solve the massively complicated problems involved in the proper folding of proteins in vivo. Further, outcomes from this study are expected to gain mechanistic insights on the native structure and functions of proteins under in vivo conditions.
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Affiliation(s)
- Zahoor Ahmad Parray
- Centre for Interdisciplinary Research in Basic Sciences, Jamia Millia Islamia, Jamia Nagar, New Delhi 110025, India
| | - Shahzaib Ahamad
- Centre for Interdisciplinary Research in Basic Sciences, Jamia Millia Islamia, Jamia Nagar, New Delhi 110025, India
| | - Faizan Ahmad
- Centre for Interdisciplinary Research in Basic Sciences, Jamia Millia Islamia, Jamia Nagar, New Delhi 110025, India
| | - Md Imtaiyaz Hassan
- Centre for Interdisciplinary Research in Basic Sciences, Jamia Millia Islamia, Jamia Nagar, New Delhi 110025, India
| | - Asimul Islam
- Centre for Interdisciplinary Research in Basic Sciences, Jamia Millia Islamia, Jamia Nagar, New Delhi 110025, India.
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Kumar R, Kumar R, Sharma D, Garg M, Kumar V, Agarwal MC. Macromolecular crowding-induced molten globule states of the alkali pH-denatured proteins. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2018; 1866:1102-1114. [DOI: 10.1016/j.bbapap.2018.08.012] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/23/2018] [Revised: 07/07/2018] [Accepted: 08/30/2018] [Indexed: 11/26/2022]
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Kumar R, Sharma D, Kumar V, Kumar R. Factors defining the effects of macromolecular crowding on dynamics and thermodynamic stability of heme proteins in-vitro. Arch Biochem Biophys 2018; 654:146-162. [DOI: 10.1016/j.abb.2018.07.018] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2018] [Revised: 07/18/2018] [Accepted: 07/20/2018] [Indexed: 11/28/2022]
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32
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Ahamad S, Hassan MI, Dwivedi N. Designing of phenol-based β-carbonic anhydrase1 inhibitors through QSAR, molecular docking, and MD simulation approach. 3 Biotech 2018; 8:256. [PMID: 29765814 DOI: 10.1007/s13205-018-1278-z] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2018] [Accepted: 05/04/2018] [Indexed: 12/18/2022] Open
Abstract
Tuberculosis (Tb) is an airborne infectious disease caused by Mycobacterium tuberculosis. Beta-carbonic anhydrase 1 (β-CA1) has emerged as one of the potential targets for new antitubercular drug development. In this work, three-dimensional quantitative structure-activity relationships (3D-QSAR), molecular docking, and molecular dynamics (MD) simulation approaches were performed on a series of natural and synthetic phenol-based β-CA1 inhibitors. The developed 3D-QSAR model (r2 = 0.94, q2 = 0.86, and pred_r2 = 0.74) indicated that the steric and electrostatic factors are important parameters to modulate the bioactivity of phenolic compounds. Based on this indication, we designed 72 new phenolic inhibitors, out of which two compounds (D25 and D50) effectively stabilized β-CA1 receptor and, thus, are potential candidates for new generation antitubercular drug discovery program.
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Affiliation(s)
- Shahzaib Ahamad
- 1School of Biotechnology, IFTM University, Lodhipur Rajpoot, Delhi Road, Moradabad, India
| | - Md Imtaiyaz Hassan
- 2Centre for Interdisciplinary Research in Basic Sciences, Jamia Millia Islamia, New Delhi, 110025 India
| | - Neeraja Dwivedi
- 1School of Biotechnology, IFTM University, Lodhipur Rajpoot, Delhi Road, Moradabad, India
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