1
|
Ou X, Tang Z, Ye Y, Chen X, Huang Y. Macromolecular Crowding Effect on Chitosan-Hyaluronic Acid Complexation and the Activity of Encapsulated Catalase. Biomacromolecules 2024; 25:3840-3849. [PMID: 38801711 DOI: 10.1021/acs.biomac.4c00445] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/29/2024]
Abstract
The associative phase separation of charged biomacromolecules plays a key role in many biophysical events that take place in crowded intracellular environments. Such natural polyelectrolyte complexation and phase separation often occur at nonstoichiometric charge ratios with the incorporation of bioactive proteins, which is not studied as extensively as those complexations at stoichiometric ratios. In this work, we investigated how the addition of a crowding agent (polyethylene glycol, PEG) affected the complexation between chitosan (CS) and hyaluronic acid (HA), especially at nonstoichiometric ratios, and the encapsulation of enzyme (catalase, CAT) by the colloidal complexes. The crowded environment promoted colloidal phase separation at low charge ratios, forming complexes with increased colloidal and dissolution stability, which resulted in a smaller size and polydispersity (PDI). The binding isotherms revealed that the addition of PEG greatly enhanced the ion-pairing strength (with increased ion-pairing equilibrium constant Ka from 4.92 × 104 without PEG to 1.08 × 106 with 200 g/L PEG) and switched the coacervation from endothermic to exothermic, which explained the promoted complexation and phase separation. At the stoichiometric charge ratio, the enhanced CS-HA interaction in crowded media generated a more solid-like coacervate phase with a denser network, slower chain relaxation, and higher modulus. Moreover, both crowding and complex encapsulation enhanced the activity and catalytic efficiency of CAT, represented by a 2-fold increase in catalytic efficiency (Kcat/Km) under 100 g/L PEG crowding and CS-HA complex encapsulation. This is likely due to the lower polarity in the microenvironment surrounding the enzyme molecules. By a systematic investigation of both nonstoichiometric and stoichiometric charge ratios under macromolecular crowding, this work provided new insights into the complexation between natural polyelectrolytes in a scenario closer to an intracellular environment.
Collapse
Affiliation(s)
- Xiatong Ou
- College of Biological Science and Engineering, Fuzhou University, No.2 Xueyuan Road, Minhou County, Fuzhou 350108, Fujian, China
| | - Ziyao Tang
- College of Biological Science and Engineering, Fuzhou University, No.2 Xueyuan Road, Minhou County, Fuzhou 350108, Fujian, China
| | - Yanqi Ye
- College of Biological Science and Engineering, Fuzhou University, No.2 Xueyuan Road, Minhou County, Fuzhou 350108, Fujian, China
| | - Xiaochao Chen
- College of Biological Science and Engineering, Fuzhou University, No.2 Xueyuan Road, Minhou County, Fuzhou 350108, Fujian, China
- Chuanhua Kechuang Building, Ningwei Street, Xiaoshan District, Zhejiang Novofacies Biotech Co., Ltd., Hangzhou 311215, Zhejiang, China
| | - Yan Huang
- College of Biological Science and Engineering, Fuzhou University, No.2 Xueyuan Road, Minhou County, Fuzhou 350108, Fujian, China
| |
Collapse
|
2
|
Sadarangani V, Kalia A, Kausar T, Murarka P, Sau AK. Effect of the Macromolecular Crowding Agents on the Structure and Function of Human Arginase-I, a Therapeutically Important Enzyme. J Phys Chem B 2023; 127:8749-8761. [PMID: 37796726 DOI: 10.1021/acs.jpcb.3c02940] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/07/2023]
Abstract
Macromolecular crowding has been known to influence the structure and function of many enzymes through excluded volume effects and/or soft interactions. Here, we employed two synthetic macromolecular crowders, Dextrans and poly(ethylene glycol)s (PEGs) with varying molecular masses, to examine how they affected the structure and function of a therapeutically important enzyme, human arginase-I that catalyzes the conversion of l-arginine to l-ornithine and urea. Except at greater concentrations of Dextran 200, Dextrans were observed to slightly reduce the enzymatic activity, indicating that they exert their influence mainly through the excluded volume effects. Similar outcomes were seen with PEGs, with the exception of PEG 1000, where the activity decreased with increasing PEG concentrations, showing the maximum effect at a 20 g/L concentration. This finding suggests that the enzyme function is reduced by the soft interactions of this macromolecule with the enzyme, supported by the binding measurement. Secondary and local tertiary structures and thermodynamic stability were also affected, suggesting that PEG 1000 has an impact on the protein's structure. Furthermore, molecular dynamics simulation studies suggest that the catalytic pocket is disturbed, presumably by the unwinding of neighboring helix 9. As a result, the positioning of nearby Glu277 is altered, which prevents His141 and Glu277 from making contact. This hampers the proton transfer from the catalytic His141 to the intermediate species to form ornithine, a crucial step for the substrate hydrolysis reaction by this arginase. Overall, the knowledge gained from this study might be helpful for understanding how different enzymes work in a crowded/cellular environment.
Collapse
Affiliation(s)
- Vineet Sadarangani
- Protein Engineering Laboratory, National Institute of Immunology, Aruna Asaf Ali Marg, New Delhi 110067, India
| | - Anjali Kalia
- Protein Engineering Laboratory, National Institute of Immunology, Aruna Asaf Ali Marg, New Delhi 110067, India
| | - Tasneem Kausar
- Protein Engineering Laboratory, National Institute of Immunology, Aruna Asaf Ali Marg, New Delhi 110067, India
| | - Pooja Murarka
- Protein Engineering Laboratory, National Institute of Immunology, Aruna Asaf Ali Marg, New Delhi 110067, India
| | - Apurba Kumar Sau
- Protein Engineering Laboratory, National Institute of Immunology, Aruna Asaf Ali Marg, New Delhi 110067, India
| |
Collapse
|
3
|
Hanselmann RG, Welter C. Origin of Cancer: Cell work is the Key to Understanding Cancer Initiation and Progression. Front Cell Dev Biol 2022; 10:787995. [PMID: 35300431 PMCID: PMC8921603 DOI: 10.3389/fcell.2022.787995] [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: 10/01/2021] [Accepted: 01/31/2022] [Indexed: 11/16/2022] Open
Abstract
The cell is the smallest unit of life. It is a structure that maintains order through self-organization, characterized by a high level of dynamism, which in turn is characterized by work. For this work to take place, a continuous high flow of energy is necessary. However, a focused view of the physical relationship between energy and work is inadequate for describing complex biological/medical mechanisms or systems. In this review, we try to make a connection between the fundamental laws of physics and the mechanisms and functions of biology, which are characterized by self-organization. Many different physical work processes (work) in human cells are called cell work and can be grouped into five forms: synthetic, mechanical, electrical, concentration, and heat generation cell work. In addition to the flow of energy, these cell functions are based on fundamental processes of self-organization that we summarize with the term Entirety of molecular interaction (EoMI). This illustrates that cell work is caused by numerous molecular reactions, flow equilibrium, and mechanisms. Their number and interactions are so complex that they elude our perception in their entirety. To be able to describe cell functions in a biological/medical context, the parameters influencing cell work should be summarized in overarching influencing variables. These are “biological” energy, information, matter, and cell mechanics (EMIM). This makes it possible to describe and characterize the cell work involved in cell systems (e.g., respiratory chain, signal transmission, cell structure, or inheritance processes) and to demonstrate changes. If cell work and the different influencing parameters (EMIM influencing variables) are taken as the central property of the cell, specific gene mutations cannot be regarded as the sole cause for the initiation and progression of cancer. This reductionistic monocausal view does not do justice to the dynamic and highly complex system of a cell. Therefore, we postulate that each of the EMIM influencing variables described above is capable of changing the cell work and thus the order of a cell in such a way that it can develop into a cancer cell.
Collapse
|
4
|
Köhn B, Schwarz P, Wittung-Stafshede P, Kovermann M. Impact of crowded environments on binding between protein and single-stranded DNA. Sci Rep 2021; 11:17682. [PMID: 34480058 PMCID: PMC8417293 DOI: 10.1038/s41598-021-97219-1] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2021] [Accepted: 08/20/2021] [Indexed: 11/09/2022] Open
Abstract
The concept of Molecular Crowding depicts the high density of diverse molecules present in the cellular interior. Here, we determine the impact of low molecular weight and larger molecules on binding capacity of single-stranded DNA (ssDNA) to the cold shock protein B (CspB). Whereas structural features of ssDNA-bound CspB are fully conserved in crowded environments as probed by high-resolution NMR spectroscopy, intrinsic fluorescence quenching experiments reveal subtle changes in equilibrium affinity. Kinetic stopped-flow data showed that DNA-to-protein association is significantly retarded independent of choice of the molecule that is added to the solution, but dissociation depends in a nontrivial way on its size and chemical characteristics. Thus, for this DNA-protein interaction, excluded volume effect does not play the dominant role but instead observed effects are dictated by the chemical properties of the crowder. We propose that surrounding molecules are capable of specific modification of the protein's hydration shell via soft interactions that, in turn, tune protein-ligand binding dynamics and affinity.
Collapse
Affiliation(s)
- Birgit Köhn
- Department of Chemistry, University of Konstanz, Universitätsstrasse 10, 78457, Konstanz, Germany.,Konstanz Research School Chemical Biology KoRS-CB, University of Konstanz, Universitätsstrasse 10, 78457, Konstanz, Germany
| | - Patricia Schwarz
- Department of Chemistry, University of Konstanz, Universitätsstrasse 10, 78457, Konstanz, Germany
| | - Pernilla Wittung-Stafshede
- Department of Biology and Biological Engineering, Chalmers University of Technology, 41296, Gothenburg, Sweden
| | - Michael Kovermann
- Department of Chemistry, University of Konstanz, Universitätsstrasse 10, 78457, Konstanz, Germany. .,Konstanz Research School Chemical Biology KoRS-CB, University of Konstanz, Universitätsstrasse 10, 78457, Konstanz, Germany.
| |
Collapse
|
5
|
Mannering SI, Rubin AF, Wang R, Bhattacharjee P. Identifying New Hybrid Insulin Peptides (HIPs) in Type 1 Diabetes. Front Immunol 2021; 12:667870. [PMID: 33995402 PMCID: PMC8120023 DOI: 10.3389/fimmu.2021.667870] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2021] [Accepted: 04/15/2021] [Indexed: 11/13/2022] Open
Abstract
In 2016 Delong et al. discovered a new type of neoepitope formed by the fusion of two unrelated peptide fragments. Remarkably these neoepitopes, called hybrid insulin peptides, or HIPs, are recognized by pathogenic CD4+ T cells in the NOD mouse and human pancreatic islet-infiltrating T cells in people with type 1 diabetes. Current data implicates CD4+ T-cell responses to HIPs in the immune pathogenesis of human T1D. Because of their role in the immune pathogenesis of human T1D it is important to identify new HIPs that are recognized by CD4+ T cells in people at risk of, or with, T1D. A detailed knowledge of T1D-associated HIPs will allow HIPs to be used in assays to monitor changes in T cell mediated beta-cell autoimmunity. They will also provide new targets for antigen-specific therapies for T1D. However, because HIPs are formed by the fusion of two unrelated peptides there are an enormous number of potential HIPs which makes it technically challenging to identify them. Here we review the discovery of HIPs, how they form and discuss approaches to identifying new HIPs relevant to the immune pathogenesis of human type 1 diabetes.
Collapse
Affiliation(s)
- Stuart I Mannering
- Immunology and Diabetes Unit, St. Vincent's Institute of Medical Research, Melbourne, VIC, Australia.,Department of Medicine, University of Melbourne, St. Vincent's Hospital, Melbourne, VIC, Australia
| | - Alan F Rubin
- Bioinformatics Division, Walter and Eliza Hall Institute of Medical Research, Melbourne, VIC, Australia.,Department of Medical Biology, University of Melbourne, Melbourne, VIC, Australia
| | - Ruike Wang
- Immunology and Diabetes Unit, St. Vincent's Institute of Medical Research, Melbourne, VIC, Australia
| | - Pushpak Bhattacharjee
- Immunology and Diabetes Unit, St. Vincent's Institute of Medical Research, Melbourne, VIC, Australia
| |
Collapse
|
6
|
Abstract
Historically, ligase activity by proteases was theoretically derived due to their catalyst nature, and it was experimentally observed as early as around 1900. Initially, the digestive proteases, such as pepsin, chymotrypsin, and trypsin were employed to perform in vitro syntheses of small peptides. Protease-catalyzed ligation is more efficient than peptide bond hydrolysis in organic solvents, representing control of the thermodynamic equilibrium. Peptide esters readily form acyl intermediates with serine and cysteine proteases, followed by peptide bond synthesis at the N-terminus of another residue. This type of reaction is under kinetic control, favoring aminolysis over hydrolysis. Although only a few natural peptide ligases are known, such as ubiquitin ligases, sortases, and legumains, the principle of proteases as general catalysts could be adapted to engineer some proteases accordingly. In particular, the serine proteases subtilisin and trypsin were converted to efficient ligases, which are known as subtiligase and trypsiligase. Together with sortases and legumains, they turned out to be very useful in linking peptides and proteins with a great variety of molecules, including biomarkers, sugars or building blocks with non-natural amino acids. Thus, these engineered enzymes are a promising branch for academic research and for pharmaceutical progress.
Collapse
|
7
|
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]
|
8
|
Mannering SI, So M, Elso CM, Kay TWH. Shuffling peptides to create T-cell epitopes: does the immune system play cards? Immunol Cell Biol 2017; 96:34-40. [PMID: 29359347 DOI: 10.1111/imcb.1015] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2017] [Revised: 09/17/2017] [Accepted: 09/18/2017] [Indexed: 11/27/2022]
Abstract
For a long time, immunologists have believed that classical CD4+ and CD8+ T cells recognize peptides (referred to as epitopes), derived from protein antigens presented by MHC/HLA class I or II. Over the past 10-15 years, it has become clear that epitopes recognized by CD8+, and more recently CD4+ T cells, can be formed by protein splicing. Here, we review the discovery of spliced epitopes recognized by tumor-specific human CD8+ T cells. We discuss how these epitopes are formed and some of the unusual variants that have been reported. Now, over a decade since the first report, evidence is emerging that spliced CD8+ T-cell epitopes are much more common, and potentially much more important, than previously imagined. Recent work has shown that epitopes recognized by CD4+ T cells can also be formed by protein splicing. We discuss the recent discovery of spliced CD4+ T-cell epitopes and their potential role as targets of autoimmune T-cell responses. Finally, we highlight some of the new questions raised from our growing appreciation of T-cell epitopes formed by peptide splicing.
Collapse
Affiliation(s)
- Stuart I Mannering
- Immunology and Diabetes Unit, St. Vincent's Institute of Medical Research, Fitzroy, Vic., Australia
| | - Michelle So
- Immunology and Diabetes Unit, St. Vincent's Institute of Medical Research, Fitzroy, Vic., Australia
| | - Colleen M Elso
- Immunology and Diabetes Unit, St. Vincent's Institute of Medical Research, Fitzroy, Vic., Australia
| | - Thomas W H Kay
- Immunology and Diabetes Unit, St. Vincent's Institute of Medical Research, Fitzroy, Vic., Australia
| |
Collapse
|
9
|
Brudzynski K, Miotto D, Kim L, Sjaarda C, Maldonado-Alvarez L, Fukś H. Active macromolecules of honey form colloidal particles essential for honey antibacterial activity and hydrogen peroxide production. Sci Rep 2017; 7:7637. [PMID: 28794506 PMCID: PMC5550472 DOI: 10.1038/s41598-017-08072-0] [Citation(s) in RCA: 36] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2017] [Accepted: 06/30/2017] [Indexed: 11/09/2022] Open
Abstract
Little is known about the global structure of honey and the arrangement of its main macromolecules. We hypothesized that the conditions in ripened honeys resemble macromolecular crowding in the cell and affect the concentration, reactivity, and conformation of honey macromolecules. Combined results from UV spectroscopy, DLS and SEM showed that the concentration of macromolecules was a determining factor in honey structure. The UV spectral scans in 200-400 nm visualized and allowed quantification of UV-absorbing compounds in the following order: dark > medium > light honeys (p < 0.0001). The high concentration of macromolecules promoted their self-assembly to micron-size superstructures, visible in SEM as two-phase system consisting of dense globules distributed in sugar solution. These particles showed increased conformational stability upon dilution. At the threshold concentration, the system underwent phase transition with concomitant fragmentation of large micron-size particles to nanoparticles in hierarchical order. Honey two-phase conformation was an essential requirement for antibacterial activity and hydrogen peroxide production. These activities disappeared beyond the phase transition point. The realization that active macromolecules of honey are arranged into compact, stable multicomponent assemblies with colloidal properties reframes our view on global structure of honey and emerges as a key property to be considered in investigating its biological activity.
Collapse
Affiliation(s)
- Katrina Brudzynski
- Department of Biological Sciences, Brock University, 1812 Sir Isaac Brock Way, St. Catharines, Ontario, Canada.
| | - Danielle Miotto
- Department of Biological Sciences, Brock University, 1812 Sir Isaac Brock Way, St. Catharines, Ontario, Canada
| | - Linda Kim
- Department of Biological Sciences, Brock University, 1812 Sir Isaac Brock Way, St. Catharines, Ontario, Canada
| | - Calvin Sjaarda
- Department of Biological Sciences, Brock University, 1812 Sir Isaac Brock Way, St. Catharines, Ontario, Canada
| | - Liset Maldonado-Alvarez
- Department of Biological Sciences, Brock University, 1812 Sir Isaac Brock Way, St. Catharines, Ontario, Canada
| | - Henryk Fukś
- Department of Mathematics & Statistics, Brock University, 1812 Sir Isaac Brock Way, St. Catharines, Ontario, Canada
| |
Collapse
|
10
|
Crèvecoeur I, Vig S, Mathieu C, Overbergh L. Understanding type 1 diabetes through proteomics. Expert Rev Proteomics 2017. [DOI: 10.1080/14789450.2017.1345633] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Affiliation(s)
- Inne Crèvecoeur
- Laboratory for Clinical and Experimental Endocrinology, KU Leuven, Leuven, Belgium
| | - Saurabh Vig
- Laboratory for Clinical and Experimental Endocrinology, KU Leuven, Leuven, Belgium
| | - Chantal Mathieu
- Laboratory for Clinical and Experimental Endocrinology, KU Leuven, Leuven, Belgium
| | - Lut Overbergh
- Laboratory for Clinical and Experimental Endocrinology, KU Leuven, Leuven, Belgium
| |
Collapse
|
11
|
Wieczorek R, Adamala K, Gasperi T, Polticelli F, Stano P. Small and Random Peptides: An Unexplored Reservoir of Potentially Functional Primitive Organocatalysts. The Case of Seryl-Histidine. Life (Basel) 2017; 7:E19. [PMID: 28397774 PMCID: PMC5492141 DOI: 10.3390/life7020019] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2017] [Revised: 04/03/2017] [Accepted: 04/05/2017] [Indexed: 12/11/2022] Open
Abstract
Catalysis is an essential feature of living systems biochemistry, and probably, it played a key role in primordial times, helping to produce more complex molecules from simple ones. However, enzymes, the biocatalysts par excellence, were not available in such an ancient context, and so, instead, small molecule catalysis (organocatalysis) may have occurred. The best candidates for the role of primitive organocatalysts are amino acids and short random peptides, which are believed to have been available in an early period on Earth. In this review, we discuss the occurrence of primordial organocatalysts in the form of peptides, in particular commenting on reports about seryl-histidine dipeptide, which have recently been investigated. Starting from this specific case, we also mention a peptide fragment condensation scenario, as well as other potential roles of peptides in primordial times. The review actually aims to stimulate further investigation on an unexplored field of research, namely one that specifically looks at the catalytic activity of small random peptides with respect to reactions relevant to prebiotic chemistry and early chemical evolution.
Collapse
Affiliation(s)
- Rafal Wieczorek
- Faculty of Chemistry, University of Warsaw, Pasteura 1, 02-093 Warsaw, Poland.
| | - Katarzyna Adamala
- Department of Genetics, Cell Biology, and Development, University of Minnesota, Minneapolis, MN 55455, USA.
| | - Tecla Gasperi
- Department of Science, Roma Tre University, Viale G. Marconi 446, 00146 Rome, Italy.
| | - Fabio Polticelli
- Department of Science, Roma Tre University, Viale G. Marconi 446, 00146 Rome, Italy.
- National Institute of Nuclear Physics, Roma Tre Section, Via della Vasca Navale 84, 00146 Rome, Italy.
| | - Pasquale Stano
- Department of Biological and Environmental Sciences and Technologies (DiSTeBA), University of Salento, Campus Ecotekne (S.P. 6 Lecce-Monteroni), 73100 Lecce, Italy.
| |
Collapse
|
12
|
Jia J, Peng X, Qi W, Su R, He Z. Effects of macromolecular crowding on alkaline phosphatase unfolding, conformation and stability. Int J Biol Macromol 2017; 101:373-382. [PMID: 28344089 DOI: 10.1016/j.ijbiomac.2017.03.113] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2017] [Revised: 02/27/2017] [Accepted: 03/21/2017] [Indexed: 10/19/2022]
Abstract
The interior of the cell is tightly packed with various biological macromolecules, which affects physiological processes, especially protein folding process. To explore how macromolecular crowding may influence protein folding process, alkaline phosphatase (ALP) was chosen as a model protein, and the unfolding process of ALP induced by GdnHCl was studied in the presence of crowding agents such as PEG 4000, Dextran 70 and Ficoll 70. The effect of macromolecular crowding on the denatured state of ALP was directly probed by measuring enzyme activities, fluorescence spectroscopy and circular dichroism. From the results of circular dichroism, GdnHCl induced a biphasic change, suggesting that a three-state unfolding mechanism was involved in the denaturation process irrespective of the absence or presence of crowding agents. It was also found that crowding agents had a little impact on the unfolding process of ALP. The results of phase diagrams also demonstrated that the unfolding process of ALP induced by GdnHCl was three-state mechanism. Moreover, the results of fluorescence spectra demonstrated that with the increase of GdnHCl concentration, the structure of protein had changed, but existence of crowding agents can make protein structure more stable. Our results can provide valuable information for understanding the protein folding in vivo.
Collapse
Affiliation(s)
- Jiajia Jia
- Chemical Engineering Research Center, School of Chemical Engineering and Technology, Tianjin University, Tianjin 300072, PR China
| | - Xin Peng
- School of Life Sciences, Tianjin University, Tianjin 300072, PR China.
| | - Wei Qi
- Chemical Engineering Research Center, School of Chemical Engineering and Technology, Tianjin University, Tianjin 300072, PR China; State Key Laboratory of Chemical Engineering, Tianjin University, Tianjin 300072, PR China; Collaborative Innovation Center of Chemistry Science and Engineering (Tianjin), Tianjin 300072, PR China; Tianjin Key Laboratory of Membrane Science and Desalination Technology, Tianjin, 300072, PR China.
| | - Rongxin Su
- Chemical Engineering Research Center, School of Chemical Engineering and Technology, Tianjin University, Tianjin 300072, PR China; State Key Laboratory of Chemical Engineering, Tianjin University, Tianjin 300072, PR China; Collaborative Innovation Center of Chemistry Science and Engineering (Tianjin), Tianjin 300072, PR China; Tianjin Key Laboratory of Membrane Science and Desalination Technology, Tianjin, 300072, PR China
| | - Zhimin He
- Chemical Engineering Research Center, School of Chemical Engineering and Technology, Tianjin University, Tianjin 300072, PR China; State Key Laboratory of Chemical Engineering, Tianjin University, Tianjin 300072, PR China
| |
Collapse
|
13
|
Pan W, Wen H, Liang D. Enzymatic activity inside a DNA/peptide complex. Phys Chem Chem Phys 2017; 19:22487-22493. [DOI: 10.1039/c7cp04066k] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The dissociation of the DNA/peptide complex is controlled by the enzyme, while only 1/3 of the enzyme is active inside the complex.
Collapse
Affiliation(s)
- Wei Pan
- Beijing National Laboratory for Molecular Sciences and the Key Laboratory of Polymer Chemistry and Physics of Ministry of Education
- College of Chemistry and Molecular Engineering
- Peking University
- Bejing 100871
- China
| | - Hao Wen
- Beijing National Laboratory for Molecular Sciences and the Key Laboratory of Polymer Chemistry and Physics of Ministry of Education
- College of Chemistry and Molecular Engineering
- Peking University
- Bejing 100871
- China
| | - Dehai Liang
- Beijing National Laboratory for Molecular Sciences and the Key Laboratory of Polymer Chemistry and Physics of Ministry of Education
- College of Chemistry and Molecular Engineering
- Peking University
- Bejing 100871
- China
| |
Collapse
|
14
|
Paul SS, Sil P, Chakraborty R, Haldar S, Chattopadhyay K. Molecular Crowding Affects the Conformational Fluctuations, Peroxidase Activity, and Folding Landscape of Yeast Cytochrome c. Biochemistry 2016; 55:2332-43. [DOI: 10.1021/acs.biochem.6b00053] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Simanta Sarani Paul
- Protein
Folding and Dynamics Laboratory, Structural Biology and Bioinformatics
Division, CSIR-Indian Institute of Chemical Biology, 4, Raja S. C.
Mullick Road, Kolkata 700032, India
| | - Pallabi Sil
- Protein
Folding and Dynamics Laboratory, Structural Biology and Bioinformatics
Division, CSIR-Indian Institute of Chemical Biology, 4, Raja S. C.
Mullick Road, Kolkata 700032, India
| | - Ritobrita Chakraborty
- Protein
Folding and Dynamics Laboratory, Structural Biology and Bioinformatics
Division, CSIR-Indian Institute of Chemical Biology, 4, Raja S. C.
Mullick Road, Kolkata 700032, India
| | - Shubhasis Haldar
- Department
of Cellular Biochemistry, Max Planck Institute of Biochemistry, Am Klopferspitz
18, 82152 Martinsried, Germany
| | - 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 700032, India
| |
Collapse
|
15
|
Proteasomes generate spliced epitopes by two different mechanisms and as efficiently as non-spliced epitopes. Sci Rep 2016; 6:24032. [PMID: 27049119 PMCID: PMC4822137 DOI: 10.1038/srep24032] [Citation(s) in RCA: 82] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2016] [Accepted: 03/15/2016] [Indexed: 12/24/2022] Open
Abstract
Proteasome-catalyzed peptide splicing represents an additional catalytic activity of proteasomes contributing to the pool of MHC-class I-presented epitopes. We here biochemically and functionally characterized a new melanoma gp100 derived spliced epitope. We demonstrate that the gp100mel47–52/40–42 antigenic peptide is generated in vitro and in cellulo by a not yet described proteasomal condensation reaction. gp100mel47–52/40–42 generation is enhanced in the presence of the β5i/LMP7 proteasome-subunit and elicits a peptide-specific CD8+ T cell response. Importantly, we demonstrate that different gp100mel-derived spliced epitopes are generated and presented to CD8+ T cells with efficacies comparable to non-spliced canonical tumor epitopes and that gp100mel-derived spliced epitopes trigger activation of CD8+ T cells found in peripheral blood of half of the melanoma patients tested. Our data suggest that both transpeptidation and condensation reactions contribute to the frequent generation of spliced epitopes also in vivo and that their immune relevance may be comparable to non-spliced epitopes.
Collapse
|
16
|
Delong T, Wiles TA, Baker RL, Bradley B, Barbour G, Reisdorph R, Armstrong M, Powell RL, Reisdorph N, Kumar N, Elso CM, DeNicola M, Bottino R, Powers AC, Harlan DM, Kent SC, Mannering SI, Haskins K. Pathogenic CD4 T cells in type 1 diabetes recognize epitopes formed by peptide fusion. Science 2016; 351:711-4. [PMID: 26912858 DOI: 10.1126/science.aad2791] [Citation(s) in RCA: 360] [Impact Index Per Article: 45.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
T cell-mediated destruction of insulin-producing β cells in the pancreas causes type 1 diabetes (T1D). CD4 T cell responses play a central role in β cell destruction, but the identity of the epitopes recognized by pathogenic CD4 T cells remains unknown. We found that diabetes-inducing CD4 T cell clones isolated from nonobese diabetic mice recognize epitopes formed by covalent cross-linking of proinsulin peptides to other peptides present in β cell secretory granules. These hybrid insulin peptides (HIPs) are antigenic for CD4 T cells and can be detected by mass spectrometry in β cells. CD4 T cells from the residual pancreatic islets of two organ donors who had T1D also recognize HIPs. Autoreactive T cells targeting hybrid peptides may explain how immune tolerance is broken in T1D.
Collapse
Affiliation(s)
- Thomas Delong
- Department of Immunology and Microbiology, University of Colorado School of Medicine, Denver, Anschutz Medical Campus, Aurora, CO 80045, USA.
| | - Timothy A Wiles
- Department of Immunology and Microbiology, University of Colorado School of Medicine, Denver, Anschutz Medical Campus, Aurora, CO 80045, USA
| | - Rocky L Baker
- Department of Immunology and Microbiology, University of Colorado School of Medicine, Denver, Anschutz Medical Campus, Aurora, CO 80045, USA
| | - Brenda Bradley
- Department of Immunology and Microbiology, University of Colorado School of Medicine, Denver, Anschutz Medical Campus, Aurora, CO 80045, USA
| | - Gene Barbour
- Department of Immunology and Microbiology, University of Colorado School of Medicine, Denver, Anschutz Medical Campus, Aurora, CO 80045, USA
| | - Richard Reisdorph
- Pharmaceutical Sciences, University of Colorado School of Medicine, Aurora, CO 80045, USA
| | - Michael Armstrong
- Pharmaceutical Sciences, University of Colorado School of Medicine, Aurora, CO 80045, USA
| | - Roger L Powell
- Pharmaceutical Sciences, University of Colorado School of Medicine, Aurora, CO 80045, USA
| | - Nichole Reisdorph
- Pharmaceutical Sciences, University of Colorado School of Medicine, Aurora, CO 80045, USA
| | - Nitesh Kumar
- Immunology and Diabetes Unit, St. Vincent's Institute of Medical Research, 9 Princes Street, Fitzroy, Victoria 3065, Australia
| | - Colleen M Elso
- Immunology and Diabetes Unit, St. Vincent's Institute of Medical Research, 9 Princes Street, Fitzroy, Victoria 3065, Australia
| | - Megan DeNicola
- Department of Medicine, Diabetes Division, Diabetes Center of Excellence, University of Massachusetts Medical School, Worcester, MA, USA
| | - Rita Bottino
- Institute of Cellular Therapeutics, Allegheny-Singer Research Institute, Allegheny Health Network, Pittsburgh, PA, USA
| | - Alvin C Powers
- Division of Diabetes, Endocrinology, and Metabolism, Department of Medicine, and Department of Molecular Physiology and Biophysics, Vanderbilt University Medical Center, Nashville, TN, USA. VA Tennessee Valley Healthcare System, Nashville, TN, USA
| | - David M Harlan
- Department of Medicine, Diabetes Division, Diabetes Center of Excellence, University of Massachusetts Medical School, Worcester, MA, USA
| | - Sally C Kent
- Department of Medicine, Diabetes Division, Diabetes Center of Excellence, University of Massachusetts Medical School, Worcester, MA, USA
| | - Stuart I Mannering
- Immunology and Diabetes Unit, St. Vincent's Institute of Medical Research, 9 Princes Street, Fitzroy, Victoria 3065, Australia. University of Melbourne, Department of Medicine, St. Vincent's Hospital, Fitzroy, Victoria 3065, Australia
| | - Kathryn Haskins
- Department of Immunology and Microbiology, University of Colorado School of Medicine, Denver, Anschutz Medical Campus, Aurora, CO 80045, USA.
| |
Collapse
|
17
|
Gorczyca SM, Chapman CD, Robertson-Anderson RM. Universal scaling of crowding-induced DNA mobility is coupled with topology-dependent molecular compaction and elongation. SOFT MATTER 2015; 11:7762-8. [PMID: 26303877 DOI: 10.1039/c5sm01882j] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/23/2023]
Abstract
Using single-molecule fluorescence microscopy and particle-tracking techniques, we elucidate the role DNA topology plays in the diffusion and conformational dynamics of crowded DNA molecules. We focus on large (115 kbp), double-stranded ring and linear DNA crowded by varying concentrations (0-40%) of dextran (10, 500 kDa) that mimic cellular conditions. By tracking the center-of-mass and measuring the lengths of the major and minor axes of single DNA molecules, we characterize both DNA mobility reduction as well as crowding-induced conformational changes (from random spherical coils). We reveal novel topology-dependent conformations, with single ring molecules undergoing compaction to ordered spherical configurations ∼20% smaller than dilute random coils, while linear DNA elongates by ∼2-fold. Surprisingly, these highly different conformations result in nearly identical exponential mobility reduction dependent solely on crowder volume fraction Φ, revealing a universal critical crowding concentration of Φc≅ 2.3. Beyond Φc DNA exhibits topology-independent conformational relaxation dynamics despite highly distinct topology-driven conformations. Our collective results reveal that topology-dependent conformational changes, unique to crowded environments, enable DNA to overcome the classically expected mobility reduction that high-viscosity crowded environments impose. Such coupled universal dynamics suggest a mechanism for DNA to maintain sufficient mobility required for wide-ranging biological processes despite severe cellular crowding.
Collapse
Affiliation(s)
- Stephanie M Gorczyca
- Department of Physics, University of San Diego, 5998 Alcala Park, San Diego, CA 92110, USA.
| | | | | |
Collapse
|
18
|
Kuznetsova IM, Zaslavsky BY, Breydo L, Turoverov KK, Uversky VN. Beyond the excluded volume effects: mechanistic complexity of the crowded milieu. Molecules 2015; 20:1377-409. [PMID: 25594347 PMCID: PMC6272634 DOI: 10.3390/molecules20011377] [Citation(s) in RCA: 135] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2014] [Accepted: 01/09/2015] [Indexed: 11/16/2022] Open
Abstract
Macromolecular crowding is known to affect protein folding, binding of small molecules, interaction with nucleic acids, enzymatic activity, protein-protein interactions, and protein aggregation. Although for a long time it was believed that the major mechanism of the action of crowded environments on structure, folding, thermodynamics, and function of a protein can be described in terms of the excluded volume effects, it is getting clear now that other factors originating from the presence of high concentrations of “inert” macromolecules in crowded solution should definitely be taken into account to draw a more complete picture of a protein in a crowded milieu. This review shows that in addition to the excluded volume effects important players of the crowded environments are viscosity, perturbed diffusion, direct physical interactions between the crowding agents and proteins, soft interactions, and, most importantly, the effects of crowders on solvent properties.
Collapse
Affiliation(s)
- Irina M. Kuznetsova
- Laboratory of Structural Dynamics, Stability and Folding of Proteins, Institute of Cytology, Russian Academy of Sciences, 4 Tikhoretsky Ave., St. Petersburg 194064, Russia; E-Mails: (I.M.K.); (K.K.T.)
- St. Petersburg State Polytechnical University, 29 Polytechnicheskaya st., St. Petersburg 195251, Russia
| | - Boris Y. Zaslavsky
- Cleveland Diagnostics, 3615 Superior Ave., Suite 4407B, Cleveland, OH 44114, USA; E-Mail:
| | - Leonid Breydo
- Department of Molecular Medicine and USF Health Byrd Alzheimer’s Research Institute, Morsani College of Medicine, University of South Florida, 12901 Bruce B. Downs Blvd. MDC07, Tampa, FL 33612, USA; E-Mails:
| | - Konstantin K. Turoverov
- Laboratory of Structural Dynamics, Stability and Folding of Proteins, Institute of Cytology, Russian Academy of Sciences, 4 Tikhoretsky Ave., St. Petersburg 194064, Russia; E-Mails: (I.M.K.); (K.K.T.)
- St. Petersburg State Polytechnical University, 29 Polytechnicheskaya st., St. Petersburg 195251, Russia
| | - Vladimir N. Uversky
- Laboratory of Structural Dynamics, Stability and Folding of Proteins, Institute of Cytology, Russian Academy of Sciences, 4 Tikhoretsky Ave., St. Petersburg 194064, Russia; E-Mails: (I.M.K.); (K.K.T.)
- Department of Molecular Medicine and USF Health Byrd Alzheimer’s Research Institute, Morsani College of Medicine, University of South Florida, 12901 Bruce B. Downs Blvd. MDC07, Tampa, FL 33612, USA; E-Mails:
- Biology Department, Faculty of Science, King Abdulaziz University, P.O. Box 80203, Jeddah 21589, Saudi Arabia
- Author to whom correspondence should be addressed; E-Mail: ; Tel.: +1-813-974-5816; Fax: +1-813-974-7357
| |
Collapse
|
19
|
What macromolecular crowding can do to a protein. Int J Mol Sci 2014; 15:23090-140. [PMID: 25514413 PMCID: PMC4284756 DOI: 10.3390/ijms151223090] [Citation(s) in RCA: 355] [Impact Index Per Article: 35.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2014] [Revised: 12/04/2014] [Accepted: 12/05/2014] [Indexed: 01/17/2023] Open
Abstract
The intracellular environment represents an extremely crowded milieu, with a limited amount of free water and an almost complete lack of unoccupied space. Obviously, slightly salted aqueous solutions containing low concentrations of a biomolecule of interest are too simplistic to mimic the “real life” situation, where the biomolecule of interest scrambles and wades through the tightly packed crowd. In laboratory practice, such macromolecular crowding is typically mimicked by concentrated solutions of various polymers that serve as model “crowding agents”. Studies under these conditions revealed that macromolecular crowding might affect protein structure, folding, shape, conformational stability, binding of small molecules, enzymatic activity, protein-protein interactions, protein-nucleic acid interactions, and pathological aggregation. The goal of this review is to systematically analyze currently available experimental data on the variety of effects of macromolecular crowding on a protein molecule. The review covers more than 320 papers and therefore represents one of the most comprehensive compendia of the current knowledge in this exciting area.
Collapse
|
20
|
Abstract
Macromolecular crowding decreases the diffusion rate, shifts the equilibrium of protein-protein and protein-substrate interactions, and changes protein conformational dynamics. Collectively, these effects contribute to enzyme catalysis. Here we describe how crowding may bias the conformational change and dynamics of enzyme populations and in this way affect catalysis. Crowding effects have been studied using artificial crowding agents and in vivo-like environments. These studies revealed a correlation between protein dynamics and function in the crowded environment. We suggest that crowded environments be classified into uniform crowding and structured crowding. Uniform crowding represents random crowding conditions created by synthetic particles with a narrow size distribution. Structured crowding refers to the highly coordinated cellular environment, where proteins and other macromolecules are clustered and organized. In structured crowded environments the perturbation of protein thermal stability may be lower; however, it may still be able to modulate functions effectively and dynamically. Dynamic, allosteric enzymes could be more sensitive to cellular perturbations if their free energy landscape is flatter around the native state; on the other hand, if their free energy landscape is rougher, with high kinetic barriers separating deep minima, they could be more robust. Above all, cells are structured; and this holds both for the cytosol and for the membrane environment. The crowded environment is organized, which limits the search, and the crowders are not necessarily inert. More likely, they too transmit allosteric effects, and as such play important functional roles. Overall, structured cellular crowding may lead to higher enzyme efficiency and specificity.
Collapse
Affiliation(s)
- Judith Klinman
- Department of Chemistry Department of Molecular and Cell Biology, University of California The california institute for Quantitativ, Berkeley, CA, USA
| | | |
Collapse
|
21
|
Promoting immobilization and catalytic activity of horseradish peroxidase on mesoporous silica through template micelles. J Colloid Interface Sci 2012; 377:497-503. [DOI: 10.1016/j.jcis.2012.03.057] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2012] [Revised: 03/16/2012] [Accepted: 03/17/2012] [Indexed: 11/18/2022]
|
22
|
Sharma A, Radha Kishan KV. Serine protease inhibitor mediated peptide bond re-synthesis in diverse protein molecules. FEBS Lett 2011; 585:3465-70. [PMID: 22001203 DOI: 10.1016/j.febslet.2011.10.004] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2011] [Revised: 09/27/2011] [Accepted: 10/04/2011] [Indexed: 11/29/2022]
Abstract
Protease inhibitors have been extensively used in research to prevent unwanted degradation of proteins during purification and analysis. Here, we report a remarkable discovery of protease inhibitor mediated reformation of peptide bonds by the serine protease inhibitor, PMSF in a diverse set of proteolyzed molecules. Interestingly, the religation reaction in the presence of PMSF occurs in a very short time period and with very high yields of the religated product. We also investigate the plausible mechanism of such a reaction and demonstrate through biochemical studies and X-ray crystallography that proximity of reacting termini is essential for the feasibility of this reaction.
Collapse
Affiliation(s)
- Amit Sharma
- Institute of Microbial Technology, Sector 39-A, Chandigarh 160 036, India
| | | |
Collapse
|
23
|
Berkers CR, de Jong A, Ovaa H, Rodenko B. Transpeptidation and reverse proteolysis and their consequences for immunity. Int J Biochem Cell Biol 2008; 41:66-71. [PMID: 18817889 DOI: 10.1016/j.biocel.2008.08.036] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2008] [Revised: 08/29/2008] [Accepted: 08/29/2008] [Indexed: 11/27/2022]
Abstract
Reverse proteolysis and transpeptidation lead to the generation of polypeptide sequences that cannot be inferred directly from genome sequences as they are post-translational phenomena. These phenomena have so far received little attention although the physiological consequences may reach far. The protease-mediated synthesis of several immunodominant MHC class I antigens was recently reported, underscoring its importance to immunity. Reverse proteolytic and transpeptidation mechanisms as well as conditions that favor successful protease-catalyzed synthetic events are discussed here.
Collapse
Affiliation(s)
- Celia R Berkers
- Division of Cellular Biochemistry, The Netherlands Cancer Institute, Plesmanlaan 121, 1066 CX Amsterdam, The Netherlands
| | | | | | | |
Collapse
|
24
|
Influence of macromolecular crowding on protein-protein association rates--a Brownian dynamics study. Biophys J 2008; 95:5030-6. [PMID: 18757562 DOI: 10.1529/biophysj.108.136291] [Citation(s) in RCA: 74] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The high total concentration of macromolecules, often referred to as macromolecular crowding, is one of the characteristic features of living cells. Macromolecular crowding influences interactions between many types of macromolecules, with consequent effects on, among others, the rates of reactions occurring in the cell. Simulations to study the influence of crowding on macromolecular association rate were performed using a modified Brownian dynamics protocol. The calculated values of the time-dependent self-diffusion coefficients in different crowding conditions are in a very good agreement with those obtained by other authors. Simulations of the complex formation between the monoclonal antibody HyHEL-5 and its antigen hen egg lysozyme, both represented at atomic level detail, show that the calculated association rates strongly depend on the volume excluded by crowding. The rate obtained for the highest concentration of crowding particles is greater than twofold higher than the rate for proteins without crowding.
Collapse
|
25
|
Saska I, Craik DJ. Protease-catalysed protein splicing: a new post-translational modification? Trends Biochem Sci 2008; 33:363-8. [DOI: 10.1016/j.tibs.2008.04.016] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2008] [Revised: 04/30/2008] [Accepted: 04/30/2008] [Indexed: 10/21/2022]
|
26
|
Munishkina LA, Ahmad A, Fink AL, Uversky VN. Guiding protein aggregation with macromolecular crowding. Biochemistry 2008; 47:8993-9006. [PMID: 18665616 DOI: 10.1021/bi8008399] [Citation(s) in RCA: 133] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Macromolecular crowding is expected to have a significant effect on protein aggregation. In the present study we analyzed the effect of macromolecular crowding on fibrillation of four proteins, bovine S-carboxymethyl-alpha-lactalbumin (a disordered form of the protein with reduced three out of four disulfide bridges), human insulin, bovine core histones, and human alpha-synuclein. These proteins are structurally different, varying from natively unfolded (alpha-synuclein and core histones) to folded proteins with rigid tertiary and quaternary structures (monomeric and hexameric forms of insulin). All these proteins are known to fibrillate in diluted solutions, however their aggregation mechanisms are very divers and some of them are able to form different aggregates in addition to fibrils. We studied how macromolecular crowding guides protein between different aggregation pathways by analyzing the effect of crowding agents on the aggregation patterns under the variety of conditions favoring different aggregated end products in diluted solutions.
Collapse
Affiliation(s)
- Larissa A Munishkina
- Department of Chemistry and Biochemistry, University of California at Santa Cruz, Santa Cruz, California 95064, USA
| | | | | | | |
Collapse
|
27
|
Totani K, Ihara Y, Matsuo I, Ito Y. Effects of Macromolecular Crowding on Glycoprotein Processing Enzymes. J Am Chem Soc 2008; 130:2101-7. [DOI: 10.1021/ja077570k] [Citation(s) in RCA: 76] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
|
28
|
Jiang M, Guo Z. Effects of Macromolecular Crowding on the Intrinsic Catalytic Efficiency and Structure of Enterobactin-Specific Isochorismate Synthase. J Am Chem Soc 2007; 129:730-1. [PMID: 17243787 DOI: 10.1021/ja065064+] [Citation(s) in RCA: 89] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Ming Jiang
- Department of Chemistry, The Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong SAR, China
| | | |
Collapse
|
29
|
Rivas G, Ferrone F, Herzfeld J. Life in a crowded world. EMBO Rep 2004; 5:23-7. [PMID: 14710181 PMCID: PMC1298967 DOI: 10.1038/sj.embor.7400056] [Citation(s) in RCA: 151] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2003] [Accepted: 11/20/2003] [Indexed: 11/08/2022] Open
Affiliation(s)
- Germán Rivas
- Centro de Investigaciones Biológicas, CSIC, Ramiro de Maeztu 9, E-28040 Madrid, Spain.
| | | | | |
Collapse
|
30
|
Hall D, Minton AP. Macromolecular crowding: qualitative and semiquantitative successes, quantitative challenges. BIOCHIMICA ET BIOPHYSICA ACTA 2003; 1649:127-39. [PMID: 12878031 DOI: 10.1016/s1570-9639(03)00167-5] [Citation(s) in RCA: 337] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
The concept of excluded volume and the theory of effects of excluded volume on the equilibria and rates of macromolecular reactions in fluid media containing high total concentrations of macromolecules ('crowded' media) are summarized. Reports of experimental studies of crowding effects published during the last year are tabulated. Limitations of current excluded volume theory are discussed, and a determination is made of conditions under which this theory may and may not be validly applied. Recently suggested novel approaches to quantitative analysis of crowding phenomena, which may help to overcome some of the limitations of current theory, are summarized.
Collapse
Affiliation(s)
- Damien Hall
- Section on Physical Biochemistry, Laboratory of Biochemistry and Genetics, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, US Department of Health and Human Services, Bethesda, MD 20892-0830, USA
| | | |
Collapse
|