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Lipid nanoparticles with erythrocyte cell-membrane proteins. J Mol Liq 2022. [DOI: 10.1016/j.molliq.2022.120791] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
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Arai K, Iwaoka M. Flexible Folding: Disulfide-Containing Peptides and Proteins Choose the Pathway Depending on the Environments. Molecules 2021; 26:E195. [PMID: 33401729 PMCID: PMC7794709 DOI: 10.3390/molecules26010195] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2020] [Revised: 12/24/2020] [Accepted: 12/29/2020] [Indexed: 11/18/2022] Open
Abstract
In the last few decades, development of novel experimental techniques, such as new types of disulfide (SS)-forming reagents and genetic and chemical technologies for synthesizing designed artificial proteins, is opening a new realm of the oxidative folding study where peptides and proteins can be folded under physiologically more relevant conditions. In this review, after a brief overview of the historical and physicochemical background of oxidative protein folding study, recently revealed folding pathways of several representative peptides and proteins are summarized, including those having two, three, or four SS bonds in the native state, as well as those with odd Cys residues or consisting of two peptide chains. Comparison of the updated pathways with those reported in the early years has revealed the flexible nature of the protein folding pathways. The significantly different pathways characterized for hen-egg white lysozyme and bovine milk α-lactalbumin, which belong to the same protein superfamily, suggest that the information of protein folding pathways, not only the native folded structure, is encoded in the amino acid sequence. The application of the flexible pathways of peptides and proteins to the engineering of folded three-dimensional structures is an interesting and important issue in the new realm of the current oxidative protein folding study.
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Affiliation(s)
| | - Michio Iwaoka
- Department of Chemistry, School of Science, Tokai University, Kitakaname, Hiratsuka-shi, Kanagawa 259-1292, Japan;
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Sindhu A, Kumar S, Mondal D, Bahadur I, Venkatesu P. Protein packaging in ionic liquid mixtures: an ecofriendly approach towards the improved stability of β-lactoglobulin in cholinium-based mixed ionic liquids. Phys Chem Chem Phys 2020; 22:14811-14821. [DOI: 10.1039/d0cp02151b] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
The present work demonstrates a pioneering approach for the packaging of β-LG with improved stability in the presence of aqueous solutions containing cholinium-based ionic liquid mixtures.
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Affiliation(s)
| | - Sumit Kumar
- Department of Chemistry
- University of Delhi
- Delhi
- India
| | - Dibyendu Mondal
- Centre for Nano & Material Science
- JAIN (deemed to be University)
- Jain Global Campus
- Bangalore-562112
- India
| | - Indra Bahadur
- Department of Chemistry, School of Physical and Chemical Sciences, Material Science Innovation & Modelling (MaSIM) Focus Area, Faculty of Natural and Agricultural Sciences
- North-West University (Mafikeng Campus)
- Private Bag X2046
- Mmabatho 2735
- South Africa
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4
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Uversky VN, Finkelstein AV. Life in Phases: Intra- and Inter- Molecular Phase Transitions in Protein Solutions. Biomolecules 2019; 9:E842. [PMID: 31817975 PMCID: PMC6995567 DOI: 10.3390/biom9120842] [Citation(s) in RCA: 45] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2019] [Revised: 12/05/2019] [Accepted: 12/06/2019] [Indexed: 02/06/2023] Open
Abstract
Proteins, these evolutionarily-edited biological polymers, are able to undergo intramolecular and intermolecular phase transitions. Spontaneous intramolecular phase transitions define the folding of globular proteins, whereas binding-induced, intra- and inter- molecular phase transitions play a crucial role in the functionality of many intrinsically-disordered proteins. On the other hand, intermolecular phase transitions are the behind-the-scenes players in a diverse set of macrosystemic phenomena taking place in protein solutions, such as new phase nucleation in bulk, on the interface, and on the impurities, protein crystallization, protein aggregation, the formation of amyloid fibrils, and intermolecular liquid-liquid or liquid-gel phase transitions associated with the biogenesis of membraneless organelles in the cells. This review is dedicated to the systematic analysis of the phase behavior of protein molecules and their ensembles, and provides a description of the major physical principles governing intramolecular and intermolecular phase transitions in protein solutions.
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Affiliation(s)
- Vladimir N. Uversky
- Department of Molecular Medicine, Morsani College of Medicine, University of South Florida, Tampa, FL 33612, USA
- Laboratory of New Methods in Biology, Institute for Biological Instrumentation, Russian Academy of Sciences, Federal Research Center “Pushchino Scientific Center for Biological Research of the Russian Academy of Sciences”, 142290 Pushchino, Moscow, Russia
| | - Alexei V. Finkelstein
- Institute of Protein Research, Russian Academy of Sciences, 142290 Pushchino, Moscow, Russia
- Biology Department, Lomonosov Moscow State University, 119192 Moscow, Russia
- Bioltechnogy Department, Lomonosov Moscow State University, 142290 Pushchino, Moscow, Russia
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Abstract
Cells of the vast majority of organisms are subject to temperature, pressure, pH, ionic strength, and other stresses. We discuss these effects in the light of protein folding and protein interactions in vitro, in complex environments, in cells, and in vivo. Protein phase diagrams provide a way of organizing different structural ensembles that occur under stress and how one can move among ensembles. Experiments that perturb biomolecules in vitro or in cells by stressing them have revealed much about the underlying forces that are competing to control protein stability, folding, and function. Two phenomena that emerge and serve to broadly classify effects of the cellular environment are crowding (mainly due to repulsive forces) and sticking (mainly due to attractive forces). The interior of cells is closely balanced between these emergent effects, and stress can tip the balance one way or the other. The free energy scale involved is small but significant on the scale of the "on/off switches" that control signaling in cells or of protein-protein association with a favorable function such as increased enzyme processivity. Quantitative tools from biophysical chemistry will play an important role in elucidating the world of crowding and sticking under stress.
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Affiliation(s)
- Mayank Boob
- Center for Biophysics and Quantitative Biology, University of Illinois at Urbana-Champaign, Champaign, IL 61801, United States
| | - Yuhan Wang
- Center for Biophysics and Quantitative Biology, University of Illinois at Urbana-Champaign, Champaign, IL 61801, United States
| | - Martin Gruebele
- Center for Biophysics and Quantitative Biology, University of Illinois at Urbana-Champaign, Champaign, IL 61801, United States
- Department of Chemistry, Department of Physics, Center for the Physics of Living Cells, and Beckman Institute for Advanced Science and Technology, University of Illinois at Urbana-Champaign, Champaign, IL 61801, United States
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Iwaoka M, Mitsuji T, Shinozaki R. Oxidative folding pathways of bovine milk β-lactoglobulin with odd cysteine residues. FEBS Open Bio 2019; 9:1379-1391. [PMID: 31087497 PMCID: PMC6668375 DOI: 10.1002/2211-5463.12656] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2019] [Accepted: 05/13/2019] [Indexed: 01/06/2023] Open
Abstract
Bovine β‐lactoglobulin (BLG) is a major whey protein with unique structural characteristics: it possesses a free Cys thiol (SH) and two disulfide (SS) bonds and consists of a β‐barrel core surrounded by one long and several short α helices. Although SS‐intact conformational folding has been studied in depth, the oxidative folding pathways and accompanying SS formation/rearrangement are poorly understood. In this study, we used trans‐3,4‐dihydroxyselenolane oxide, a water‐soluble selenoxide reagent which undergoes rapid and quantitative SS formation, to determine the oxidative folding pathways of BLG variant A (BLGA) at pH 8.0 and 25 °C. This was done by characterizing two key one‐SS intermediates, a particular folding intermediate having a Cys66–Cys160 SS bond (I‐1) and a particular folding intermediate having a Cys106–Cys119 SS bond (I‐2), which have a native Cys66–Cys160 and Cys106–Cys119 SS bond, respectively. In the major folding pathway, the reduced protein (R) with abundant α helices was oxidized to I‐1, which was then transformed to I‐2 through SS rearrangement. The native protein (N) was formed by oxidation of I‐2. The redundant Cys121 thiol facilitates SS rearrangement. N is also generated from an ensemble of folding intermediates having two SS bonds (2SS) intermediates with scrambled SS bonds through SS rearrangement, but this minor pathway is deteriorative due to aggregation or overoxidation of 2SS. During oxidative folding of BLGA, α→β conformational transition occurred as previously observed in SS‐intact folding. These findings are informative not only for elucidating oxidative folding pathways of other members of the β‐lactoglobulin family, but also for understanding the roles of a redundant Cys thiol in the oxidative folding process of a protein with odd Cys residues.
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Affiliation(s)
- Michio Iwaoka
- Department of Chemistry, School of Science, Tokai University, Hiratsuka-shi, Kanagawa, Japan
| | - Takumi Mitsuji
- Department of Chemistry, School of Science, Tokai University, Hiratsuka-shi, Kanagawa, Japan
| | - Reina Shinozaki
- Department of Chemistry, School of Science, Tokai University, Hiratsuka-shi, Kanagawa, Japan
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Andoyo R, Dianti Lestari V, Mardawati E, Nurhadi B. Fractal Dimension Analysis of Texture Formation of Whey Protein-Based Foods. INTERNATIONAL JOURNAL OF FOOD SCIENCE 2018; 2018:7673259. [PMID: 29951523 PMCID: PMC5987291 DOI: 10.1155/2018/7673259] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/26/2017] [Revised: 03/21/2018] [Accepted: 04/15/2018] [Indexed: 11/17/2022]
Abstract
Whey protein in the form of isolate or concentrate is widely used in food industries due to its functionality to form gel under certain condition and its nutritive value. Controlling or manipulating the formation of gel aggregates is used often to evaluate food texture. Many researchers made use of fractal analysis that provides the quantitative data (i.e., fractal dimension) for fundamentally and rationally analyzing and designing whey protein-based food texture. This quantitative analysis is also done to better understand how the texture of whey protein-based food is formed. Two methods for fractal analysis were discussed in this review: image analysis (microscopy) and rheology. These methods, however, have several limitations which greatly affect the accuracy of both fractal dimension values and types of aggregation obtained. This review therefore also discussed problem encountered and ways to reduce the potential errors during fractal analysis of each method.
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Affiliation(s)
- Robi Andoyo
- Department of Food Industrial Technology, Faculty of Agro-Industrial Technology, Universitas Padjadjaran, Jl. Raya Bandung Sumedang Km. 21, Jatinangor, Sumedang 40600, Indonesia
| | - Vania Dianti Lestari
- Department of Food Industrial Technology, Faculty of Agro-Industrial Technology, Universitas Padjadjaran, Jl. Raya Bandung Sumedang Km. 21, Jatinangor, Sumedang 40600, Indonesia
| | - Efri Mardawati
- Department of Food Industrial Technology, Faculty of Agro-Industrial Technology, Universitas Padjadjaran, Jl. Raya Bandung Sumedang Km. 21, Jatinangor, Sumedang 40600, Indonesia
| | - Bambang Nurhadi
- Department of Food Industrial Technology, Faculty of Agro-Industrial Technology, Universitas Padjadjaran, Jl. Raya Bandung Sumedang Km. 21, Jatinangor, Sumedang 40600, Indonesia
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Vazquez L, e Lima LMTDR, Almeida MDS. Comprehensive structural analysis of designed incomplete polypeptide chains of the replicase nonstructural protein 1 from the severe acute respiratory syndrome coronavirus. PLoS One 2017; 12:e0182132. [PMID: 28750053 PMCID: PMC5531528 DOI: 10.1371/journal.pone.0182132] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2017] [Accepted: 07/12/2017] [Indexed: 11/18/2022] Open
Abstract
The cotranslational folding is recognized as a very cooperative process that occurs after the nearly completion of the polypeptide sequence of a domain. Here we investigated the challenges faced by polypeptide segments of a non-vectorial β-barrel fold. Besides the biological interest behind the SARS coronavirus non-structural protein 1 (nsp1, 117 amino acids), this study model has two structural features that motivated its use in this work: 1- its recombinant production is dependent on the temperature, with greater solubility when expressed at low temperatures. This is an indication of the cotranslational guidance to the native protein conformation. 2- Conversely, nsp1 has a six-stranded, mixed parallel/antiparallel β-barrel with intricate long-range interactions, indicating it will need the full-length protein to fold properly. We used non-denaturing purification conditions that allowed the characterization of polypeptide chains of different lengths, mimicking the landscape of the cotranslational fold of a β-barrel, and avoiding the major technical hindrances of working with the nascent polypeptide bound to the ribosome. Our results showed partially folded states formed as soon as the amino acids of the second β-strand were present (55 amino acids). These partially folded states are different based on the length of polypeptide chain. The native α-helix (amino acids 24-37) was identified as a transient structure (~20-30% propensity). We identified the presence of regular secondary structure after the fourth native β-strand is present (89 amino acids), in parallel to the collapse to a non-native 3D structure. Interestingly the polypeptide sequences of the native strands β2, β3 and β4 have characteristics of α-helices. Our comprehensive analyses support the idea that incomplete polypeptide chains, such as the ones of nascent proteins much earlier than the end of the translation, adopt an abundance of specific transient folds, instead of disordered conformations.
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Affiliation(s)
- Leonardo Vazquez
- Instituto de Bioquímica Médica Leopoldo de Meis, Centro Nacional de Biologia Estrutural e Bioimagem (CENABIO), Universidade Federal do Rio de Janeiro, Rio de Janeiro, RJ, Brazil
| | | | - Marcius da Silva Almeida
- Instituto de Bioquímica Médica Leopoldo de Meis, Centro Nacional de Biologia Estrutural e Bioimagem (CENABIO), Universidade Federal do Rio de Janeiro, Rio de Janeiro, RJ, Brazil
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Sarkar-Banerjee S, Chowdhury S, Paul SS, Dutta D, Ghosh A, Chattopadhyay K. The Non-native Helical Intermediate State May Accumulate at Low pH in the Folding and Aggregation Landscape of the Intestinal Fatty Acid Binding Protein. Biochemistry 2016; 55:4457-68. [DOI: 10.1021/acs.biochem.6b00390] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Suparna Sarkar-Banerjee
- Protein Folding and Dynamics
Laboratory, Structural Biology and Bioinformatics Division, CSIR-Indian Institute of Chemical Biology, Kolkata 700032, India
| | - Sourav Chowdhury
- Protein Folding and Dynamics
Laboratory, Structural Biology and Bioinformatics Division, CSIR-Indian Institute of Chemical Biology, Kolkata 700032, India
| | - Simanta Sarani Paul
- Protein Folding and Dynamics
Laboratory, Structural Biology and Bioinformatics Division, CSIR-Indian Institute of Chemical Biology, Kolkata 700032, India
| | - Debashis Dutta
- Protein Folding and Dynamics
Laboratory, Structural Biology and Bioinformatics Division, CSIR-Indian Institute of Chemical Biology, Kolkata 700032, India
| | - Anisa Ghosh
- Protein Folding and Dynamics
Laboratory, Structural Biology and Bioinformatics Division, CSIR-Indian Institute of Chemical Biology, Kolkata 700032, India
| | - Krishnananda Chattopadhyay
- Protein Folding and Dynamics
Laboratory, Structural Biology and Bioinformatics Division, CSIR-Indian Institute of Chemical Biology, Kolkata 700032, India
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Konuma T, Sakurai K, Yagi M, Goto Y, Fujisawa T, Takahashi S. Highly Collapsed Conformation of the Initial Folding Intermediates of β-Lactoglobulin with Non-Native α-Helix. J Mol Biol 2015; 427:3158-65. [DOI: 10.1016/j.jmb.2015.07.018] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2015] [Revised: 07/21/2015] [Accepted: 07/22/2015] [Indexed: 10/23/2022]
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