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Ghosh S, Prabhu NP. Heterogeneous Macromolecular crowding effect on nucleation-independent fibril formation of Lysozyme: Spectroscopic analysis of Structure, Stability, and fibrillation rate. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2024; 315:124276. [PMID: 38626673 DOI: 10.1016/j.saa.2024.124276] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/06/2023] [Revised: 04/05/2024] [Accepted: 04/09/2024] [Indexed: 04/18/2024]
Affiliation(s)
- Subhasree Ghosh
- Department of Biotechnology & Bioinformatics, School of Life Sciences, University of Hyderabad, Hyderabad 500046, India
| | - N Prakash Prabhu
- Department of Biotechnology & Bioinformatics, School of Life Sciences, University of Hyderabad, Hyderabad 500046, India.
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Singh A, Gupta M, Rastogi H, Khare K, Chowdhury PK. Deeper Insights into Mixed Crowding through Enzyme Activity, Dynamics, and Crowder Diffusion. J Phys Chem B 2024; 128:5293-5309. [PMID: 38808573 DOI: 10.1021/acs.jpcb.4c00337] [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: 05/30/2024]
Abstract
Given the fact that the cellular interior is crowded by many different kinds of macromolecules, it is important that in vitro studies be carried out in the presence of mixed crowder systems. In this regard, we have used binary crowders formed by the combination of some of the commonly used crowding agents, namely, Ficoll 70, Dextran 70, Dextran 40, and PEG 8000 (PEG 8), to study how these affect enzyme activity, dynamics, and crowder diffusion. The enzyme chosen is AK3L1, an isoform of adenylate kinase. To investigate its dynamics, we have carried out three single point mutations (A74C, A132C, and A209C) with the cysteine residues being labeled with a coumarin-based solvatochromic probe [CPM: (7-diethylamino-3-(4-maleimido-phenyl)-4-methylcoumarin)]. Both enzyme activity and dynamics decreased in the binary mixtures as compared with the sum of the individual crowders, suggesting a reduction in excluded volume (in the mixture). To gain deeper insights into the binary mixtures, fluorescence correlation spectroscopy studies were carried out using fluorescein isothiocyanate-labeled Dextran 70 and tetramethylrhodamine-labeled AK3L1 as the diffusion probes. Diffusion in binary mixtures was observed to be much more constrained (relative to the sum of the individual crowders) for the labeled enzyme as compared to the labeled crowder showing different environments being faced by the two species. This was further confirmed during imaging of the phase-separated droplets formed in the binary mixtures having PEG as one of the crowding agents. The interior of these droplets was found to be rich in crowders and densely packed, as shown by confocal and digital holographic microscopy images, with the enzymes predominantly residing outside these droplets, that is, in the relatively less crowded regions. Taken together, our data provide important insights into various aspects of the simplest form of mixed crowding, that is, composed of just two components, and also hint at the enhanced complexity that the cellular interior presents toward having a detailed and comprehensive understanding of the same.
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Affiliation(s)
- Arvind Singh
- Department of Chemistry, Indian Institute of Technology Delhi, Hauz Khas, New Delhi 110016, India
| | - Monika Gupta
- Department of Chemistry, Indian Institute of Technology Delhi, Hauz Khas, New Delhi 110016, India
| | - Harshita Rastogi
- Department of Chemistry, Indian Institute of Technology Delhi, Hauz Khas, New Delhi 110016, India
| | - Kedar Khare
- Optics and Photonics Centre, Indian Institute of Technology Delhi, Hauz Khas, New Delhi 110016, India
| | - Pramit K Chowdhury
- Department of Chemistry, Indian Institute of Technology Delhi, Hauz Khas, New Delhi 110016, India
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3
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Pierro A, Tamburrini KC, Leguenno H, Gerbaud G, Etienne E, Guigliarelli B, Belle V, Zambelli B, Mileo E. In-cell investigation of the conformational landscape of the GTPase UreG by SDSL-EPR. iScience 2023; 26:107855. [PMID: 37766968 PMCID: PMC10520941 DOI: 10.1016/j.isci.2023.107855] [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: 04/07/2023] [Revised: 07/07/2023] [Accepted: 09/06/2023] [Indexed: 09/29/2023] Open
Abstract
UreG is a cytosolic GTPase involved in the maturation network of urease, an Ni-containing bacterial enzyme. Previous investigations in vitro showed that UreG features a flexible tertiary organization, making this protein the first enzyme discovered to be intrinsically disordered. To determine whether this heterogeneous behavior is maintained in the protein natural environment, UreG structural dynamics was investigated directly in intact bacteria by in-cell EPR. This approach, based on site-directed spin labeling coupled to electron paramagnetic resonance (SDSL-EPR) spectroscopy, enables the study of proteins in their native environment. The results show that UreG maintains heterogeneous structural landscape in-cell, existing in a conformational ensemble of two major conformers, showing either random coil-like or compact properties. These data support the physiological relevance of the intrinsically disordered nature of UreG and indicates a role of protein flexibility for this specific enzyme, possibly related to the regulation of promiscuous protein interactions for metal ion delivery.
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Affiliation(s)
- Annalisa Pierro
- Aix Marseille Univ, CNRS, BIP, IMM, 13009 Marseille, France
- Department of Chemistry, University of Konstanz, Universitätsstraße 10, 78457 Konstanz, Germany
| | - Ketty Concetta Tamburrini
- Aix Marseille Univ, CNRS, AFMB, 13009 Marseille, France
- INRAE, Aix Marseille Univ, BBF, 13009 Marseille, France
| | - Hugo Leguenno
- Aix Marseille Univ, CNRS, IMM, Microscopy Core Facility, 13009 Marseille, France
| | | | | | | | - Valérie Belle
- Aix Marseille Univ, CNRS, BIP, IMM, 13009 Marseille, France
| | - Barbara Zambelli
- Laboratory of Bioinorganic Chemistry, Department of Pharmacy and Biotechnology, University of Bologna, 40127 Bologna, Italy
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J-aggregation of 5, 10, 15, 20-tetraphenyl-21H, 23H-porphinetetrasulfonic acid in a molecular crowding environment simulated using dextran. ANAL SCI 2022; 38:1505-1512. [PMID: 36050568 DOI: 10.1007/s44211-022-00185-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2022] [Accepted: 08/23/2022] [Indexed: 11/01/2022]
Abstract
In a molecular crowding environment, different thermodynamics is often observed in a dilute solution. One such example is the promotion of the formation of amyloids, which are causal agents of Alzheimer's disease. Although a considerable number of molecular crowding studies have been reported, its effect remains unclear. In this study, we investigated a J-aggregation of a porphyrin derivative, 5, 10, 15, 20-tetraphenyl-21H,23H-porphinetetrasulfonic acid (TPPS), in a molecular crowding environment simulated by dextran (Dex) in HClO4, HCl, and NaCl solutions. The changes in the number of monomers in the J-aggregate (n) with the concentration of Dex (CDex) depended on the type of solution. No change in n was observed in the NaCl solution, which indicated that the Dex solution did not affect the J-aggregation because of the ionic strength effect. In the HCl solution, the aggregation behavior changed with the pH. Further, at a low pH, the electrostatic interactions promoted J-aggregation by the volume exclusion of Dex, while the aggregation was suppressed at a high pH owing to steric hindrance. A different aggregation mechanism, involving the hydrogen bonding between NH in the center of the TPPS macrocyclic frame and the SO3H and ClO4- functional groups, was responsible for the J-aggregation in the HClO4 solution. Moreover, the n value increased owing to the volume exclusion effect. We expect that this study will be useful for further elucidation of the molecular crowding effect.
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Gong Z, Yang J, Qin LY, Tang C, Jiang H, Ke Y, Dong X. Preferential Regulation of Transient Protein-Protein Interaction by the Macromolecular Crowders. J Phys Chem B 2022; 126:4840-4848. [PMID: 35731981 DOI: 10.1021/acs.jpcb.2c02713] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The environmental condition is a critical regulation factor for protein behavior in solution. Several studies have shown that macromolecular crowders can modulate protein structures, interactions, and functions. Recent publications described the regulation of specific interaction by macromolecular crowders. However, the other category of protein-protein interaction, namely, the transient interaction, is rarely investigated, especially from the perspective of protein structure to study transient interactions between proteins. Here, we used nuclear magnetic resonance and small-angle X-ray/neutron scattering methods to structurally investigate the ensemble of the protein complex in dilute buffer and crowded environments. Histidine phosphocarrier protein (HPr) and the N-terminal domain of enzyme I (EIN) are the important components of the bacterial phosphotransfer system. Our results show that the addition of Ficoll-70 promotes HPr molecules to form the encounter complex with EIN maintained by long-range electrostatic interaction. However, when macromolecular crowder BSA is used, the soft interaction between BSA and HPr perturbs the active site of HPr, driving HPr to form an encounter complex with EIN at the weakly charged interface. Our results indicate that different macromolecular crowders could influence transient EIN-HPr interaction through different mechanisms and provide new insights into protein-protein interaction regulation in native environments.
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Affiliation(s)
- Zhou Gong
- State Key Laboratory of Magnetic Resonance and Atomic Molecular Physics, National Center for Magnetic Resonance at Wuhan, Innovation Academy for Precision Measurement Science and Technology, Chinese Academy of Sciences, Wuhan, Hubei 430071, China
| | - Ju Yang
- State Key Laboratory of Magnetic Resonance and Atomic Molecular Physics, National Center for Magnetic Resonance at Wuhan, Innovation Academy for Precision Measurement Science and Technology, Chinese Academy of Sciences, Wuhan, Hubei 430071, China
| | - Ling-Yun Qin
- State Key Laboratory of Magnetic Resonance and Atomic Molecular Physics, National Center for Magnetic Resonance at Wuhan, Innovation Academy for Precision Measurement Science and Technology, Chinese Academy of Sciences, Wuhan, Hubei 430071, China
| | - Chun Tang
- Beijing National Laboratory for Molecular Sciences, College of Chemistry and Molecular Engineering, and Peking-Tsinghua Center for Life Sciences, Peking University, Beijing 100871, China
| | - Hanqiu Jiang
- Spallation Neutron Source Science Center (SNSSC), Dalang, Dongguan 523803, China.,Institute of High Energy Physics, Chinese Academy of Sciences (CAS), Beijing 100049, China
| | - Yubin Ke
- Spallation Neutron Source Science Center (SNSSC), Dalang, Dongguan 523803, China.,Institute of High Energy Physics, Chinese Academy of Sciences (CAS), Beijing 100049, China
| | - Xu Dong
- State Key Laboratory of Magnetic Resonance and Atomic Molecular Physics, National Center for Magnetic Resonance at Wuhan, Innovation Academy for Precision Measurement Science and Technology, Chinese Academy of Sciences, Wuhan, Hubei 430071, China
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Chen Y, Liu Q, Yang F, Yu H, Xie Y, Yao W. Lysozyme amyloid fibril: Regulation, application, hazard analysis, and future perspectives. Int J Biol Macromol 2022; 200:151-161. [PMID: 34995654 DOI: 10.1016/j.ijbiomac.2021.12.163] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2021] [Revised: 12/15/2021] [Accepted: 12/25/2021] [Indexed: 12/11/2022]
Abstract
Self-assembly of misfolded proteins into ordered fibrillar aggregates known as amyloid results in various human diseases. However, more and more proteins, whether in human body or in food, have been found to be able to form amyloid fibrils with in-depth researches. As a model protein for amyloid research, lysozyme has always been the focus of research in various fields. Firstly, the formation mechanisms of amyloid fibrils are discussed concisely. Researches on the regulation of lysozyme amyloid fibrils are helpful to find suitable therapeutic drugs and unfriendly substances. And this review article summarizes a number of exogenous substances including small molecules, nanoparticles, macromolecules, and polymers. Small molecules are mainly connected to lysozyme through hydrophobic interaction, electrostatic interaction, π-π interaction, van der Waals force and hydrogen bond. Nanoparticles inhibit the formation of amyloid fibers by stabilizing lysozyme and fixing β-sheet. Besides, the applications of lysozyme amyloid fibrils in food-related fields are considered furtherly due to outstanding physical and mechanical properties. Nevertheless, the potential health threats are still worthy of our attention. Finally, we also give suggestions and opinions on the future research direction of lysozyme amyloid fibrils.
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Affiliation(s)
- Yulun Chen
- State Key Laboratory of Food Science and Technology, Jiangnan University, No.1800 Lihu Avenue, Wuxi 214122, Jiangsu Province, China; Engineering Research Center of Dairy Quality and Safety Control Technology, Ministry of Education, Inner Mongolia University, No.235 Daxue West Road, Hohhot 010021, Inner Mongolia Autonomous Region, China; School of Food Science and Technology, Jiangnan University, No.1800 Lihu Avenue, Wuxi 214122, Jiangsu Province, China; Joint International Research Laboratory of Food Safety, Jiangnan University, No.1800 Lihu Avenue, Wuxi 214122, Jiangsu Province, China
| | - Qingrun Liu
- State Key Laboratory of Food Science and Technology, Jiangnan University, No.1800 Lihu Avenue, Wuxi 214122, Jiangsu Province, China; School of Food Science and Technology, Jiangnan University, No.1800 Lihu Avenue, Wuxi 214122, Jiangsu Province, China; Joint International Research Laboratory of Food Safety, Jiangnan University, No.1800 Lihu Avenue, Wuxi 214122, Jiangsu Province, China
| | - Fangwei Yang
- State Key Laboratory of Food Science and Technology, Jiangnan University, No.1800 Lihu Avenue, Wuxi 214122, Jiangsu Province, China; Engineering Research Center of Dairy Quality and Safety Control Technology, Ministry of Education, Inner Mongolia University, No.235 Daxue West Road, Hohhot 010021, Inner Mongolia Autonomous Region, China; School of Food Science and Technology, Jiangnan University, No.1800 Lihu Avenue, Wuxi 214122, Jiangsu Province, China; Joint International Research Laboratory of Food Safety, Jiangnan University, No.1800 Lihu Avenue, Wuxi 214122, Jiangsu Province, China
| | - Hang Yu
- State Key Laboratory of Food Science and Technology, Jiangnan University, No.1800 Lihu Avenue, Wuxi 214122, Jiangsu Province, China; School of Food Science and Technology, Jiangnan University, No.1800 Lihu Avenue, Wuxi 214122, Jiangsu Province, China; Joint International Research Laboratory of Food Safety, Jiangnan University, No.1800 Lihu Avenue, Wuxi 214122, Jiangsu Province, China
| | - Yunfei Xie
- State Key Laboratory of Food Science and Technology, Jiangnan University, No.1800 Lihu Avenue, Wuxi 214122, Jiangsu Province, China; Engineering Research Center of Dairy Quality and Safety Control Technology, Ministry of Education, Inner Mongolia University, No.235 Daxue West Road, Hohhot 010021, Inner Mongolia Autonomous Region, China; School of Food Science and Technology, Jiangnan University, No.1800 Lihu Avenue, Wuxi 214122, Jiangsu Province, China; Joint International Research Laboratory of Food Safety, Jiangnan University, No.1800 Lihu Avenue, Wuxi 214122, Jiangsu Province, China
| | - Weirong Yao
- State Key Laboratory of Food Science and Technology, Jiangnan University, No.1800 Lihu Avenue, Wuxi 214122, Jiangsu Province, China; School of Food Science and Technology, Jiangnan University, No.1800 Lihu Avenue, Wuxi 214122, Jiangsu Province, China; Joint International Research Laboratory of Food Safety, Jiangnan University, No.1800 Lihu Avenue, Wuxi 214122, Jiangsu Province, China.
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7
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Gupta M, Chowdhury PK. Protein dynamics as a sensor for macromolecular crowding: Insights into mixed crowding. J Mol Liq 2022. [DOI: 10.1016/j.molliq.2021.117969] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
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8
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The kinetics of islet amyloid polypeptide phase-separated system and hydrogel formation are critically influenced by macromolecular crowding. Biochem J 2021; 478:3025-3046. [PMID: 34313292 PMCID: PMC8370757 DOI: 10.1042/bcj20210384] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2021] [Revised: 07/19/2021] [Accepted: 07/26/2021] [Indexed: 11/17/2022]
Abstract
Many protein misfolding diseases (e.g. type II diabetes and Alzheimer's disease) are characterised by amyloid deposition. Human islet amyloid polypeptide (hIAPP, involved in type II diabetes) spontaneously undergoes liquid-liquid phase separation (LLPS) and a kinetically complex hydrogelation, both catalysed by hydrophobic-hydrophilic interfaces (e.g. air-water interface and/or phospholipids-water interfaces). Gelation of hIAPP phase-separated liquid droplets initiates amyloid aggregation and the formation of clusters of interconnected aggregates, which grow and fuse to eventually percolate the whole system. Droplet maturation into irreversible hydrogels via amyloid aggregation is thought to be behind the pathology of several diseases. Biological fluids contain a high volume fraction of macromolecules, leading to macromolecular crowding. Despite crowding agent addition in in vitro studies playing a significant role in changing protein phase diagrams, the mechanism underlying enhanced LLPS, and the effect(s) on stages beyond LLPS remain poorly or not characterised.We investigated the effect of macromolecular crowding and increased viscosity on the kinetics of hIAPP hydrogelation using rheology and the evolution of the system beyond LLPS by microscopy. We demonstrate that increased viscosity exacerbated the kinetic variability of hydrogelation and of the phase separated-aggregated system, whereas macromolecular crowding abolished heterogeneity. Increased viscosity also strengthened the gel meshwork and accelerated aggregate cluster fusion. In contrast, crowding either delayed cluster fusion onset (dextran) or promoted it (Ficoll). Our study highlights that an in vivo crowded environment would critically influence amyloid stages beyond LLPS and pathogenesis.
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Siddiqui GA, Naeem A. The contrasting effect of macromolecular crowding and confinement on fibril formation of globular protein: Underlying cause of proteopathies. J Mol Liq 2021. [DOI: 10.1016/j.molliq.2020.114602] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
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10
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Abstract
Multiple therapeutic proteins can be combined into a single dose for synergistic targeting to multiple sites of action. Such proteins would be mixed in dose-specific ratios to provide the correct potency for each component, and yet the formulations must also preserve their activity and keep degradation to a minimum. Mixing different therapeutic proteins could adversely affect their stability, and reduce the shelf life of each individual component, making the control of such products very challenging. In this study, a therapeutic monoclonal antibody and a related Fab fragment, were combined to investigate the impact of coformulation on their degradation kinetics. Under mildly destabilizing conditions, these proteins were found to protect each other from degradation. The protective effect appeared to originate from the interaction of Fab and IgG1 in small soluble oligomers, or through the rapid coalescence of pre-existing monomeric IgG1 nuclei into a dead-end aggregate, rather than through macromolecular crowding or diffusion-limitations.
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Ross ML, Kunkel J, Long S, Asuri P. Combined Effects of Confinement and Macromolecular Crowding on Protein Stability. Int J Mol Sci 2020; 21:ijms21228516. [PMID: 33198190 PMCID: PMC7697604 DOI: 10.3390/ijms21228516] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2020] [Revised: 11/09/2020] [Accepted: 11/10/2020] [Indexed: 01/18/2023] Open
Abstract
Confinement and crowding have been shown to affect protein fates, including folding, functional stability, and their interactions with self and other proteins. Using both theoretical and experimental studies, researchers have established the independent effects of confinement or crowding, but only a few studies have explored their effects in combination; therefore, their combined impact on protein fates is still relatively unknown. Here, we investigated the combined effects of confinement and crowding on protein stability using the pores of agarose hydrogels as a confining agent and the biopolymer, dextran, as a crowding agent. The addition of dextran further stabilized the enzymes encapsulated in agarose; moreover, the observed increases in enhancements (due to the addition of dextran) exceeded the sum of the individual enhancements due to confinement and crowding. These results suggest that even though confinement and crowding may behave differently in how they influence protein fates, these conditions may be combined to provide synergistic benefits for protein stabilization. In summary, our study demonstrated the successful use of polymer-based platforms to advance our understanding of how in vivo like environments impact protein function and structure.
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Huo XZ, Wang X, Yang R, Qu LB, Zeng HJ. Studies on the effect of a Fupenzi glycoprotein on the fibrillation of bovine serum albumin and its antioxidant activity. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2020; 237:118387. [PMID: 32416513 DOI: 10.1016/j.saa.2020.118387] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/21/2019] [Revised: 02/04/2020] [Accepted: 04/18/2020] [Indexed: 06/11/2023]
Abstract
In this study, the effect of a glycoprotein obtained from Fupenzi (FPZ) (Rubus chingii Hu.) on the fibrillation of bovine serum album (BSA) was investigated by multi-spectroscopic methods and transmission electron microscopy. Moreover, the cytotoxicity of the glycoprotein and the effect of it on H2O2-induced cell viability were investigated by cell counting kit and β-galactosidase kit, respectively. The experimental results indicated that the glycoprotein showed very low toxicity to NRK-52E cells and could obviously delay cell senescence and improve cell viability. Moreover, the glycoprotein could effectively inhibit the formation of BSA fibrils and destroy the stability of preformed BSA fibrils in a concentration-dependent manner. Generally, antioxidant capacities are thought to be related to the anti-amyloidogenic activity of inhibitors; therefore, to reveal the inhibitory mechanism, the anti-oxidative property of the glycoprotein was examined by DPPH and ABTS assays. The results demonstrated that FPZ glycoprotein had a remarkable antioxidant activity and the IC50 values of DPPH and ABTS were 0.249 mg mL-1 and 0.092 mg mL-1, respectively. This work suggested that the FPZ glycoprotein had the potential to be designed a new therapeutic agent for attenuating aging and preventing the age-related diseases.
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Affiliation(s)
- Xiu-Zhu Huo
- School of Pharmaceutical Sciences, Zhengzhou University, Zhengzhou 450001, PR China
| | - Xia Wang
- School of Pharmaceutical Sciences, Zhengzhou University, Zhengzhou 450001, PR China
| | - Ran Yang
- College of Chemistry, Green Catalysis Center, Henan Joint International Research Laboratory of Green Construction of Functional Molecules and Their Bioanalytical Applications, Zhengzhou University, Zhengzhou 450001, PR China
| | - Ling-Bo Qu
- College of Chemistry, Green Catalysis Center, Henan Joint International Research Laboratory of Green Construction of Functional Molecules and Their Bioanalytical Applications, Zhengzhou University, Zhengzhou 450001, PR China
| | - Hua-Jin Zeng
- School of Pharmaceutical Sciences, Zhengzhou University, Zhengzhou 450001, PR China.
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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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Sengupta P, Banerjee N, Roychowdhury T, Dutta A, Chattopadhyay S, Chatterjee S. Site-specific amino acid substitution in dodecameric peptides determines the stability and unfolding of c-MYC quadruplex promoting apoptosis in cancer cells. Nucleic Acids Res 2019; 46:9932-9950. [PMID: 30239898 PMCID: PMC6212778 DOI: 10.1093/nar/gky824] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2018] [Accepted: 09/11/2018] [Indexed: 12/11/2022] Open
Abstract
c-MYC proto-oncogene harbours a transcription-inhibitory quadruplex-forming scaffold (Pu27) upstream P1 promoter providing anti-neoplastic therapeutic target. Previous reports showed the binding profile of human Cathelicidin peptide (LL37) and telomeric G-quadruplex. Here, we truncated the quadruplex-binding domain of LL37 to prepare a small library of peptides through site-specific amino acid substitution. We investigated the intracellular selectivity of peptides for Pu27 over other oncogenic quadruplexes and their role in c-MYC promoter repression by dual-luciferase assays. We analysed their thermodynamics of binding reactions with c-MYC quadruplex isomers (Pu27, Myc22, Pu19) by Isothermal Titration Calorimetry. We discussed how amino acid substitutions and peptide helicity enhanced/weakened their affinities for c-MYC quadruplexes and characterized specific non-covalent inter-residual interactions determining their selectivity. Solution NMR structure indicated that KR12C, the best peptide candidate, selectively stabilized the 5′-propeller loop of c-MYC quadruplex by arginine-driven electrostatic-interactions at the sugar-phosphate backbone while KR12A peptide destabilized the quadruplex inducing a single-stranded hairpin-like conformation. Chromatin immunoprecipitations envisaged that KR12C and KR12A depleted and enriched Sp1 and NM23-H2 (Nucleoside diphosphate kinase) occupancy at Pu27 respectively supporting their regulation in stabilizing and unfolding c-MYC quadruplex in MCF-7 cells. We deciphered that selective arresting of c-MYC transcription by KR12C triggered apoptotic-signalling pathway via VEGF-A-BCL-2 axis.
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Affiliation(s)
- Pallabi Sengupta
- Department of Biophysics, Bose Institute, P-1/12 CIT Scheme VII (M), Kolkata 700054, India
| | - Nilanjan Banerjee
- Department of Biophysics, Bose Institute, P-1/12 CIT Scheme VII (M), Kolkata 700054, India
| | - Tanaya Roychowdhury
- Cancer Biology and Inflammatory Disorder Division, CSIR-Indian Institute of Chemical Biology, 4, Raja S.C. Mullick Road, Kolkata 700032, India
| | - Anindya Dutta
- Department of Biophysics, Bose Institute, P-1/12 CIT Scheme VII (M), Kolkata 700054, India
| | - Samit Chattopadhyay
- Cancer Biology and Inflammatory Disorder Division, CSIR-Indian Institute of Chemical Biology, 4, Raja S.C. Mullick Road, Kolkata 700032, India
| | - Subhrangsu Chatterjee
- Department of Biophysics, Bose Institute, P-1/12 CIT Scheme VII (M), Kolkata 700054, India
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Jansens KJA, Lambrecht MA, Rombouts I, Monge Morera M, Brijs K, Rousseau F, Schymkowitz J, Delcour JA. Conditions Governing Food Protein Amyloid Fibril Formation-Part I: Egg and Cereal Proteins. Compr Rev Food Sci Food Saf 2019; 18:1256-1276. [PMID: 33336994 DOI: 10.1111/1541-4337.12462] [Citation(s) in RCA: 34] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2019] [Revised: 04/26/2019] [Accepted: 05/13/2019] [Indexed: 12/18/2022]
Abstract
Conditions including heating mode, time, temperature, pH, moisture and protein concentration, shear, and the presence of alcohols, chaotropic/reducing agents, enzymes, and/or salt influence amyloid fibril (AF) formation as they can affect the accessibility of amino acid sequences prone to aggregate. As some conditions applied on model protein resemble conditions in food processing unit operations, we here hypothesize that food processing can lead to formation of protein AFs with a compact cross β-sheet structure. This paper reviews conditions and food constituents that affect amyloid fibrillation of egg and cereal proteins. While egg and cereal proteins often coexist in food products, their impact on each other's fibrillation remains unknown. Hen egg ovalbumin and lysozyme form AFs when subjected to moderate heating at acidic pH separately. AFs can also be formed at higher pH, especially in the presence of alcohols or chaotropic/reducing agents. Tryptic wheat gluten digests can form fibrillar structures at neutral pH and maize and rice proteins do so in aqueous ethanol or at acidic pH, respectively.
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Affiliation(s)
- Koen J A Jansens
- KU Leuven, Laboratory of Food Chemistry and Biochemistry and Leuven Food Science and Nutrition Research Centre (LFoRCe), Kasteelpark Arenberg 20, B-3001, Leuven, Belgium.,Nutrex NV, Achterstenhoek 5, B-2275, Lille, Belgium
| | - Marlies A Lambrecht
- KU Leuven, Laboratory of Food Chemistry and Biochemistry and Leuven Food Science and Nutrition Research Centre (LFoRCe), Kasteelpark Arenberg 20, B-3001, Leuven, Belgium
| | - Ine Rombouts
- KU Leuven, Laboratory of Food Chemistry and Biochemistry and Leuven Food Science and Nutrition Research Centre (LFoRCe), Kasteelpark Arenberg 20, B-3001, Leuven, Belgium.,KU Leuven, ECOVO, Kasteelpark Arenberg 21, B-3001, Leuven, Belgium
| | - Margarita Monge Morera
- KU Leuven, Laboratory of Food Chemistry and Biochemistry and Leuven Food Science and Nutrition Research Centre (LFoRCe), Kasteelpark Arenberg 20, B-3001, Leuven, Belgium
| | - Kristof Brijs
- KU Leuven, Laboratory of Food Chemistry and Biochemistry and Leuven Food Science and Nutrition Research Centre (LFoRCe), Kasteelpark Arenberg 20, B-3001, Leuven, Belgium
| | - Frederic Rousseau
- Switch Laboratory, VIB, and Dept. of Cellular and Molecular Medicine, KU Leuven, B-3000, Leuven, Belgium
| | - Joost Schymkowitz
- Switch Laboratory, VIB, and Dept. of Cellular and Molecular Medicine, KU Leuven, B-3000, Leuven, Belgium
| | - Jan A Delcour
- KU Leuven, Laboratory of Food Chemistry and Biochemistry and Leuven Food Science and Nutrition Research Centre (LFoRCe), Kasteelpark Arenberg 20, B-3001, Leuven, Belgium
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16
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Sun LJ, Qu L, Yang R, Yin L, Zeng HJ. Cysteamine functionalized MoS2 quantum dots inhibit amyloid aggregation. Int J Biol Macromol 2019; 128:870-876. [DOI: 10.1016/j.ijbiomac.2019.01.212] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2018] [Revised: 01/31/2019] [Accepted: 01/31/2019] [Indexed: 01/28/2023]
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17
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Brudar S, Hribar-Lee B. The Role of Buffers in Wild-Type HEWL Amyloid Fibril Formation Mechanism. Biomolecules 2019; 9:E65. [PMID: 30769878 PMCID: PMC6406783 DOI: 10.3390/biom9020065] [Citation(s) in RCA: 31] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2019] [Revised: 02/04/2019] [Accepted: 02/05/2019] [Indexed: 01/06/2023] Open
Abstract
Amyloid fibrils, highly ordered protein aggregates, play an important role in the onset of several neurological disorders. Many studies have assessed amyloid fibril formation under specific solution conditions, but they all lack an important phenomena in biological solutions-buffer specific effects. We have focused on the formation of hen egg-white lysozyme (HEWL) fibrils in aqueous solutions of different buffers in both acidic and basic pH range. By means of UV-Vis spectroscopy, fluorescence measurements and CD spectroscopy, we have managed to show that fibrillization of HEWL is affected by buffer identity (glycine, TRIS, phosphate, KCl-HCl, cacodylate, HEPES, acetate), solution pH, sample incubation (agitated vs. static) and added excipients (NaCl and PEG). HEWL only forms amyloid fibrils at pH = 2.0 under agitated conditions in glycine and KCl-HCl buffers of high enough ionic strength. Phosphate buffer on the other hand stabilizes the HEWL molecules. Similar stabilization effect was achieved by addition of PEG12000 molecules to the solution.
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Affiliation(s)
- Sandi Brudar
- Faculty of Chemistry and Chemical Technology, University of Ljubljana, Večna pot 113, SI-1000 Ljubljana, Slovenia.
| | - Barbara Hribar-Lee
- Faculty of Chemistry and Chemical Technology, University of Ljubljana, Večna pot 113, SI-1000 Ljubljana, Slovenia.
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18
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Mixture of Macromolecular Crowding Agents Has a Non-additive Effect on the Stability of Proteins. Appl Biochem Biotechnol 2019; 188:927-941. [PMID: 30737628 DOI: 10.1007/s12010-019-02972-9] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2018] [Accepted: 02/01/2019] [Indexed: 10/27/2022]
Abstract
The folding and unfolding of proteins inside a cell take place in the presence of macromolecules of various shapes and sizes. Such crowded conditions can significantly affect folding, stability, and biophysical properties of proteins. Thus, to logically mimic the intracellular environment, the thermodynamic stability of two different proteins (lysozyme and α-lactalbumin) was investigated in the presence of mixtures of three crowding agents (ficoll 70, dextran 70, and dextran 40) at different pH values. These crowders possess different shapes and sizes. It was observed that the stabilizing effect of mixtures of crowders is more than the sum effects of the individual crowder, i.e., the stabilizing effect is non-additive in nature. Moreover, dextran 40 (in the mixture) has been found to exhibit the greatest stabilization when compared with other crowders in the mixture. In other words, the small size of the crowder has been observed to be a dominant factor in stabilization of the proteins. Graphical Abstract.
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19
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Liu Z, Li X, Wu X, Zhu C. A dual-inhibitor system for the effective antifibrillation of Aβ40 peptides by biodegradable EGCG–Fe(iii)/PVP nanoparticles. J Mater Chem B 2019; 7:1292-1299. [DOI: 10.1039/c8tb03266a] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
By the synergistic effect of dual inhibition, EFPP NPs exhibited a significant effect on the inhibition of Aβ40 fibrillation and on the disaggregation of existing Aβ40 fibrils.
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Affiliation(s)
- Zexiu Liu
- Institute of Food Safety and Environment Monitoring
- College of Chemistry
- Fuzhou University
- Fuzhou 350116
- P. R. China
| | - Xianglong Li
- Institute of Food Safety and Environment Monitoring
- College of Chemistry
- Fuzhou University
- Fuzhou 350116
- P. R. China
| | - Xiaoping Wu
- Institute of Food Safety and Environment Monitoring
- College of Chemistry
- Fuzhou University
- Fuzhou 350116
- P. R. China
| | - Chunling Zhu
- Institute of Food Safety and Environment Monitoring
- College of Chemistry
- Fuzhou University
- Fuzhou 350116
- P. R. China
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20
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Multiphasic effect of vinyl pyrrolidone polymers on amyloidogenesis, from macromolecular crowding to inhibition. Biochem J 2018; 475:3417-3436. [DOI: 10.1042/bcj20180715] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2018] [Revised: 10/02/2018] [Accepted: 10/04/2018] [Indexed: 11/17/2022]
Abstract
Deposition of misfolded amyloid polypeptides, associated with cell death, is the hallmark of many degenerative diseases (e.g. type II diabetes mellitus and Alzheimer's disease). In vivo, cellular and extracellular spaces are occupied by a high volume fraction of macromolecules. The resulting macromolecular crowding energetically affects reactions. Amyloidogenesis can either be promoted by macromolecular crowding through the excluded volume effect or inhibited due to a viscosity increase reducing kinetics. Macromolecular crowding can be mimicked in vitro by the addition of non-specific polymers, e.g. Ficoll, dextran and polyvinyl pyrrolidone (PVP), the latter being rarely used to study amyloid systems. We investigated the effect of PVP on amyloidogenesis of full-length human islet amyloid polypeptide (involved in type II diabetes) using fibrillisation and surface activity assays, ELISA, immunoblot and microscale thermophoresis. We demonstrate that high molecular mass PVP360 promotes amyloidogenesis due to volume exclusion and increase in effective amyloidogenic monomer concentration, like other crowders, but without the confounding effects of viscosity and surface activity. Interestingly, we also show that low molecular mass PVP10 has unique inhibitory properties as inhibition of fibril elongation occurs mainly in the bulk solution and is due to PVP10 directly and strongly interacting with amyloid species rather than the increase in viscosity typically associated with macromolecular crowding. In vivo, amyloidogenesis might be affected by the properties and proximity of endogenous macromolecular crowders, which could contribute to changes in associated pathogenesis. More generally, the PVP10 molecular backbone could be used to design small compounds as potential inhibitors of toxic species formation.
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21
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Liang C, Ye Z, Xue B, Zeng L, Wu W, Zhong C, Cao Y, Hu B, Messersmith PB. Self-Assembled Nanofibers for Strong Underwater Adhesion: The Trick of Barnacles. ACS APPLIED MATERIALS & INTERFACES 2018; 10:25017-25025. [PMID: 29990429 DOI: 10.1021/acsami.8b04752] [Citation(s) in RCA: 32] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
Developing adhesives that can function underwater remains a major challenge for bioengineering, yet many marine creatures, exemplified as mussels and barnacles, have evolved their unique proteinaceous adhesives for strong wet adhesion. The mechanisms underlying the strong adhesion of these natural adhesive proteins provide rich information for biomimetic efforts. Here, combining atomic force microscopy (AFM) imaging and force spectroscopy, we examine the effects of pH on the self-assembly and adhesive properties of cp19k, a key barnacle underwater adhesive protein. For the first time, we confirm that the bacterial recombinant Balanus albicostatus cp19k (rBalcp19k), which contains no 3,4-dihydroxyphenylalanine (DOPA) or any other amino acids with post-translational modifications, can self-assemble into aggregated nanofibers at acidic pHs. Under moderately acidic conditions, the adhesion strength of unassembled monomeric rBalcp19k on mica is only slightly lower than that of a commercially available mussel adhesive protein mixture, yet the adhesion ability of rBalcp19k monomers decreases significantly at increased pH. In contrast, upon preassembly at acidic and low-salinity conditions, rBalcp19k nanofibers keep stable in basic and high-salinity seawater and display much stronger adhesion and thus show resistance to its adverse impacts. Besides, we find that the adhesion ability of Balcp19k is not impaired when it is combined with an N-terminal Thioredoxin (Trx) tag, yet whether the self-assembly property will be disrupted is not determined. Collectively, the self-assembly-enhanced adhesion presents a previously unexplored mechanism for the strong wet adhesion of barnacle cement proteins and may lead to the design of barnacle-inspired adhesive materials.
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Affiliation(s)
- Chao Liang
- Department of Chemistry and Biology, College of Science , National University of Defense Technology , Changsha 410073 , P. R. China
- Collaborative Innovation Center of Advanced Microstructures, National Laboratory of Solid State Microstructures, Department of Physics , Nanjing University , Nanjing 210093 , P. R. China
| | - Zonghuang Ye
- Department of Chemistry and Biology, College of Science , National University of Defense Technology , Changsha 410073 , P. R. China
| | - Bin Xue
- Collaborative Innovation Center of Advanced Microstructures, National Laboratory of Solid State Microstructures, Department of Physics , Nanjing University , Nanjing 210093 , P. R. China
| | - Ling Zeng
- Department of Chemistry and Biology, College of Science , National University of Defense Technology , Changsha 410073 , P. R. China
| | - Wenjian Wu
- Department of Chemistry and Biology, College of Science , National University of Defense Technology , Changsha 410073 , P. R. China
| | - Chao Zhong
- School of Physical Science and Technology , ShanghaiTech University , Shanghai 201210 , P. R. China
| | - Yi Cao
- Collaborative Innovation Center of Advanced Microstructures, National Laboratory of Solid State Microstructures, Department of Physics , Nanjing University , Nanjing 210093 , P. R. China
| | - Biru Hu
- Department of Chemistry and Biology, College of Science , National University of Defense Technology , Changsha 410073 , P. R. China
| | - Phillip B Messersmith
- Departments of Materials Science and Engineering and Bioengineering , University of California , Berkeley , California 94720 , United States
- Materials Science Division , Lawrence Berkeley National Laboratory , Berkeley , California 94720 , United States
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22
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Martin EB, Williams AD, Heidel RE, Foster JS, Lands RH, Kennel SJ, Wall JS. A functional assay to identify amyloidogenic light chains. Amyloid 2018; 25:93-100. [PMID: 29571269 PMCID: PMC6333307 DOI: 10.1080/13506129.2018.1456425] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
INTRODUCTION Multiple myeloma (MM) and light chain monoclonal gammopathy of undetermined significance (LCMGUS) are plasma cell disorders associated with the secretion of monoclonal free light-chain (LC) proteins. Due to the high concentrations of LC in circulation, both of these populations are at risk for developing LC-associated amyloidosis (AL) - a protein misfolding disease characterized by the deposition of LC protein fibrils in organs and tissues, leading to dysfunction and significant morbidity. At present, accurate identification of subjects at risk for developing amyloidosis is not possible, but with the advent of novel, amyloid-targeted therapies, identification of pre-symptomatic individuals is of clinical import. METHODS To address this, a competition assay has been developed to discern LC proteins with enhanced amyloidogenic potential. Numerous factors that may influence the efficacy of the assay have been evaluated to yield optimal conditions. RESULTS Using a panel of nine patient-derived LC, we have demonstrated that amyloid-associated LC inhibited the recruitment of a biotinyl-λ6 variable domain by homologous amyloid-like fibrils significantly more than MM LC (p < .01). CONCLUSION The assay accurately discriminated AL from MM patient populations, suggesting that it may aid in the identification of patients with monoclonal gammopathies who have an increased risk of developing amyloidosis.
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Affiliation(s)
- Emily B Martin
- a Department of Medicine , University of Tennessee Medical Center , Knoxville , TN , USA
| | - Angela D Williams
- a Department of Medicine , University of Tennessee Medical Center , Knoxville , TN , USA
| | - R Eric Heidel
- b Department of Surgery , University of Tennessee Medical Center , Knoxville , TN , USA
| | - James S Foster
- a Department of Medicine , University of Tennessee Medical Center , Knoxville , TN , USA
| | - Ronald H Lands
- a Department of Medicine , University of Tennessee Medical Center , Knoxville , TN , USA
| | - Stephen J Kennel
- a Department of Medicine , University of Tennessee Medical Center , Knoxville , TN , USA.,c Department of Radiology , University of Tennessee Medical Center , Knoxville , TN , USA
| | - Jonathan S Wall
- a Department of Medicine , University of Tennessee Medical Center , Knoxville , TN , USA.,c Department of Radiology , University of Tennessee Medical Center , Knoxville , TN , USA
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23
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Biswas S, Kundu J, Mukherjee SK, Chowdhury PK. Mixed Macromolecular Crowding: A Protein and Solvent Perspective. ACS OMEGA 2018; 3:4316-4330. [PMID: 30023892 PMCID: PMC6044960 DOI: 10.1021/acsomega.7b01864] [Citation(s) in RCA: 37] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/28/2017] [Accepted: 03/16/2018] [Indexed: 06/08/2023]
Abstract
In the living cell, biomolecules perform their respective functions in the presence of not only one type of macromolecules but rather in the presence of various macromolecules with different shapes and sizes. In this study, we have investigated the effects of five single macromolecular crowding agents, Dextran 6, Dextran 40, Dextran 70, Ficoll 70, and PEG 8000 and their binary mixtures on the modulation in the domain separation of human serum albumin using a Förster resonance energy transfer-based approach and the translational mobility of a small fluorescent probe fluorescein isothiocyanate (FITC) using fluorescence correlation spectroscopy (FCS). Our observations suggest that mixed crowding induces greater cooperativity in the domain movement as compared to the components of the mixtures. Thermodynamic analyses of the same provide evidence of crossovers from enthalpy-based interactions to effects dominated by hard-sphere potential. When compared with those obtained for individual crowders, both domain movements and FITC diffusion studies show significant deviations from ideality, with an ideal solution being considered to be that arising from the sum of the contributions of those obtained in the presence of individual crowding agents. Considering the fact that domain movements are local (on the order of a few angstroms) in nature while translational movements span much larger lengthscales, our results imply that the observed deviation from simple additivity exists at several possible levels or lengthscales in such mixtures. Moreover, the nature and the type of deviation not only depend on the identities of the components of the crowder mixtures but are also influenced by the particular face of the serum protein (either the domain I-II or the domain II-III face) that the crowders interact with, thus providing further insights into the possible existence of microheterogeneities in such solutions.
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24
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Inhibition of amyloid fibrillation of lysozyme by bisdemethoxycurcumin and diacetylbisdemethoxycurcumin. Biophys Chem 2018; 235:56-65. [DOI: 10.1016/j.bpc.2018.02.005] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2017] [Revised: 02/07/2018] [Accepted: 02/09/2018] [Indexed: 11/19/2022]
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25
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Siddiqui GA, Naeem A. Aggregation of globular protein as a consequences of macromolecular crowding: A time and concentration dependent study. Int J Biol Macromol 2018; 108:360-366. [DOI: 10.1016/j.ijbiomac.2017.12.001] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2017] [Revised: 11/30/2017] [Accepted: 12/01/2017] [Indexed: 12/11/2022]
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26
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Synthesis of novel muramic acid derivatives and their interaction with lysozyme: Action of lysozyme revisited. J Colloid Interface Sci 2017; 498:395-404. [DOI: 10.1016/j.jcis.2017.03.060] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2017] [Revised: 03/13/2017] [Accepted: 03/13/2017] [Indexed: 12/16/2022]
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27
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Menon S, Sengupta N. Influence of Hyperglycemic Conditions on Self-Association of the Alzheimer's Amyloid β (Aβ 1-42) Peptide. ACS OMEGA 2017; 2:2134-2147. [PMID: 30023655 PMCID: PMC6044820 DOI: 10.1021/acsomega.7b00018] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/09/2017] [Accepted: 05/08/2017] [Indexed: 06/08/2023]
Abstract
Clinical studies have identified a correlation between type-2 diabetes mellitus and cognitive decrements en route to the onset of Alzheimer's disease (AD). Recent studies have established that post-translational modifications of the amyloid β (Aβ) peptide occur under hyperglycemic conditions; particularly, the process of glycation exacerbates its neurotoxicity and accelerates AD progression. In view of the assertion that macromolecular crowding has an altering effect on protein self-assembly, it is crucial to characterize the effects of hyperglycemic conditions via crowding on Aβ self-assembly. Toward this purpose, fully atomistic molecular dynamics simulations were performed to study the effects of glucose crowding on Aβ dimerization, which is the smallest known neurotoxic species. The dimers formed in the glucose-crowded environment were found to have weaker associations as compared to that of those formed in water. Binding free energy calculations show that the reduced binding strength of the dimers can be mainly attributed to the overall weakening of the dispersion interactions correlated with substantial loss of interpeptide contacts in the hydrophobic patches of the Aβ units. Analysis to discern the differential solvation pattern in the glucose-crowded and pure water systems revealed that glucose molecules cluster around the protein, at a distance of 5-7 Å, which traps the water molecules in close association with the protein surface. This preferential exclusion of glucose molecules and resulting hydration of the Aβ peptides has a screening effect on the hydrophobic interactions, which in turn diminishes the binding strength of the resulting dimers. Our results imply that physical effects attributed to crowded hyperglycemic environments are incapable of solely promoting Aβ self-assembly, indicating that further mechanistic studies are required to provide insights into the self-assembly of post-translationally modified Aβ peptides, known to possess aggravated toxicity, under these conditions.
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Affiliation(s)
- Sneha Menon
- Physical
Chemistry Division, CSIR-National Chemical
Laboratory, Dr. Homi
Bhabha Road, Pune 411008, India
- Academy
of Scientific and Innovative Research (AcSIR), Training and Development Complex, CSIR Campus,
CSIR Road, Chennai 600113, India
| | - Neelanjana Sengupta
- Department
of Biological Sciences, Indian Institute
of Science Education and Research (IISER) Kolkata, Mohanpur 741246, West Bengal, India
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28
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Minton AP. Explicit Incorporation of Hard and Soft Protein-Protein Interactions into Models for Crowding Effects in Protein Mixtures. 2. Effects of Varying Hard and Soft Interactions upon Prototypical Chemical Equilibria. J Phys Chem B 2017; 121:5515-5522. [PMID: 28505444 DOI: 10.1021/acs.jpcb.7b02378] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
Previously derived approximate analytical relations for the activity coefficient of each solute in a mixture of up to three spherical solutes in a highly nonideal solution interacting via square well potentials of mean force (Hoppe, T.; Minton, A. P. J Phys Chem B. 2016, 120, 11866-11872) were used to explore the effect of heterogeneity in volume occupancy and intermolecular interactions upon prototypical schemes representing solubility, partitioning, conformational isomerization, and self-association in crowded solutions. Results generally indicate that all of the equilibria explored are exquisitely sensitive to variations in both volume occupancy and intermolecular interaction and have important implications for the design and execution of more detailed simulations of complex media.
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Affiliation(s)
- Allen P Minton
- Laboratory of Biochemistry and Genetics, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, United States Department of Health and Human Welfare , Bethesda, Maryland United States
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29
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Low crowding agent concentration destabilizes against pressure unfolding. Biophys Chem 2017; 231:125-134. [PMID: 28502485 DOI: 10.1016/j.bpc.2017.04.013] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2017] [Revised: 04/28/2017] [Accepted: 04/29/2017] [Indexed: 02/05/2023]
Abstract
The concentration of macromolecules inside a cell is very high, which can affect the behavior of the enzymes, and consequently influence vital biological processes. This is called macromolecular crowding. Since the most important effect of macromolecular crowding is the excluded volume, we performed pressure experiments, where the volume (as conjugate parameter to the pressure) is the crucial factor. We measured the temperature and pressure stability of bovine serum albumin and lysozyme with various concentrations of crowding agents, dextran, Ficoll™ and lysozyme itself. Our most interesting finding is that low concentration of all the studied crowding agents decreases the pressure stability of the proteins. We explain this by the reduced hydration volume change in the crowded environment. Furthermore, we discuss the volumetric parameters and emphasize the difference between the partial volume of the protein and the volume it influences, and their relation to the excluded volume which is responsible for the macromolecular crowding.
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30
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Shahid S, Hassan MI, Islam A, Ahmad F. Size-dependent studies of macromolecular crowding on the thermodynamic stability, structure and functional activity of proteins: in vitro and in silico approaches. Biochim Biophys Acta Gen Subj 2017; 1861:178-197. [DOI: 10.1016/j.bbagen.2016.11.014] [Citation(s) in RCA: 71] [Impact Index Per Article: 10.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2016] [Revised: 11/09/2016] [Accepted: 11/10/2016] [Indexed: 11/27/2022]
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31
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Hoppe T, Minton AP. Incorporation of Hard and Soft Protein-Protein Interactions into Models for Crowding Effects in Binary and Ternary Protein Mixtures. Comparison of Approximate Analytical Solutions with Numerical Simulation. J Phys Chem B 2016; 120:11866-11872. [PMID: 27779417 DOI: 10.1021/acs.jpcb.6b07736] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
In order to better understand how nonspecific interactions between solutes can modulate specific biochemical reactions taking place in complex media, we introduce a simplified model aimed at elucidating general principles. In this model, solutions containing two or three species of interacting globular proteins are modeled as a fluid of spherical particles interacting through square well potentials that qualitatively capture both steric hard core repulsion and longer-ranged attraction or repulsion. The excess chemical potential, or free energy of solvation, of each particle species is calculated as a function of species concentrations, particle radii, and square well interaction range and depth. The results of analytical models incorporating two-body and three-body interactions are compared with the estimates of free energy obtained via Widom insertion into simulated equilibrium square-well fluids. The analytical models agree well with results of numeric simulations carried out for a variety of model parameters and fluid compositions up to a total particle volume fraction of ca. 0.2.
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Affiliation(s)
- Travis Hoppe
- Laboratory of Chemical Physics and ‡Laboratory of Biochemistry and Genetics, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, United States Public Health Service , Bethesda, Maryland 20892, United States
| | - Allen P Minton
- Laboratory of Chemical Physics and ‡Laboratory of Biochemistry and Genetics, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, United States Public Health Service , Bethesda, Maryland 20892, United States
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32
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Rivas G, Minton AP. Macromolecular Crowding In Vitro, In Vivo, and In Between. Trends Biochem Sci 2016; 41:970-981. [PMID: 27669651 DOI: 10.1016/j.tibs.2016.08.013] [Citation(s) in RCA: 308] [Impact Index Per Article: 38.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2016] [Revised: 08/18/2016] [Accepted: 08/22/2016] [Indexed: 10/21/2022]
Abstract
Biochemical processes take place in heterogeneous and highly volume-occupied or crowded environments that can considerably influence the reactivity and distribution of participating macromolecules. We summarize here the thermodynamic consequences of excluded-volume and long-range nonspecific intermolecular interactions for macromolecular reactions in volume-occupied media. In addition, we summarize and compare the information content of studies of crowding in vitro and in vivo. We emphasize the importance of characterizing the behavior not only of labeled tracer macromolecules but also the composition and behavior of unlabeled macromolecules in the immediate vicinity of the tracer. Finally, we propose strategies for extending quantitative analyses of crowding in simple model systems to increasingly complex media up to and including intact cells.
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Affiliation(s)
- Germán Rivas
- Centro de Investigaciones Biológicas, Consejo Superior de Investigaciones Científicas, Madrid, Spain.
| | - Allen P Minton
- Laboratory of Biochemistry and Genetics, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD, USA.
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33
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Barhoum S, Palit S, Yethiraj A. Diffusion NMR studies of macromolecular complex formation, crowding and confinement in soft materials. PROGRESS IN NUCLEAR MAGNETIC RESONANCE SPECTROSCOPY 2016; 94-95:1-10. [PMID: 27247282 DOI: 10.1016/j.pnmrs.2016.01.004] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/18/2015] [Revised: 01/25/2016] [Accepted: 01/28/2016] [Indexed: 06/05/2023]
Abstract
Label-free methods to obtain hydrodynamic size from diffusion measurements are desirable in environments that contain multiple macromolecular species at a high total concentration: one example is the crowded cellular environment. In complex, multi-species macromolecular environments - in this article, we feature aqueous systems involving polymers, surfactants and proteins - the link between dynamics and size is harder to unpack due to macromolecular crowding and confinement. In this review, we demonstrate that the pulsed-field gradient NMR technique, with its spectral separation of different chemical components, is ideal for studying the dynamics of the entire system simultaneously and without labelling, in a wide range of systems. The simultaneous measurement of the dynamics of multiple components allows for internal consistency checks and enables quantitative statements about the link between macromolecular dynamics, size, complex formation and crowding in soft materials.
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Affiliation(s)
- Suliman Barhoum
- Department of Physics and Physical Oceanography, Memorial University, St. John's, Newfoundland and Labrador, Canada
| | - Swomitra Palit
- Department of Physics and Physical Oceanography, Memorial University, St. John's, Newfoundland and Labrador, Canada
| | - Anand Yethiraj
- Department of Physics and Physical Oceanography, Memorial University, St. John's, Newfoundland and Labrador, Canada
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34
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Monterroso B, Reija B, Jiménez M, Zorrilla S, Rivas G. Charged Molecules Modulate the Volume Exclusion Effects Exerted by Crowders on FtsZ Polymerization. PLoS One 2016; 11:e0149060. [PMID: 26870947 PMCID: PMC4752323 DOI: 10.1371/journal.pone.0149060] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2015] [Accepted: 12/28/2015] [Indexed: 01/26/2023] Open
Abstract
We have studied the influence of protein crowders, either combined or individually, on the GTP-induced FtsZ cooperative assembly, crucial for the formation of the dynamic septal ring and, hence, for bacterial division. It was earlier demonstrated that high concentrations of inert polymers like Ficoll 70, used to mimic the crowded cellular interior, favor the assembly of FtsZ into bundles with slow depolymerization. We have found, by fluorescence anisotropy together with light scattering measurements, that the presence of protein crowders increases the tendency of FtsZ to polymerize at micromolar magnesium concentration, being the effect larger with ovomucoid, a negatively charged protein. Neutral polymers and a positively charged protein also diminished the critical concentration of assembly, the extent of the effect being compatible with that expected according to pure volume exclusion models. FtsZ polymerization was also observed to be strongly promoted by a negatively charged polymer, DNA, and by some unrelated polymers like PEGs at concentrations below the crowding regime. The influence of mixed crowders mimicking the heterogeneity of the intracellular environment on the tendency of FtsZ to assemble was also studied and nonadditive effects were found to prevail. Far from exactly reproducing the bacterial cytoplasm environment, this approach serves as a simplified model illustrating how its intrinsically crowded and heterogeneous nature may modulate FtsZ assembly into a functional Z-ring.
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Affiliation(s)
- Begoña Monterroso
- Centro de Investigaciones Biológicas, Consejo Superior de Investigaciones Científicas (CSIC), Madrid, Spain
- * E-mail: (GR); (SZ); (BM)
| | - Belén Reija
- Instituto de Química-Física Rocasolano, Consejo Superior de Investigaciones Científicas (CSIC), Madrid, Spain
| | - Mercedes Jiménez
- Centro de Investigaciones Biológicas, Consejo Superior de Investigaciones Científicas (CSIC), Madrid, Spain
| | - Silvia Zorrilla
- Centro de Investigaciones Biológicas, Consejo Superior de Investigaciones Científicas (CSIC), Madrid, Spain
- Instituto de Química-Física Rocasolano, Consejo Superior de Investigaciones Científicas (CSIC), Madrid, Spain
- * E-mail: (GR); (SZ); (BM)
| | - Germán Rivas
- Centro de Investigaciones Biológicas, Consejo Superior de Investigaciones Científicas (CSIC), Madrid, Spain
- * E-mail: (GR); (SZ); (BM)
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Mohammadi F, Mahmudian A, Moeeni M, Hassani L. Inhibition of amyloid fibrillation of hen egg-white lysozyme by the natural and synthetic curcuminoids. RSC Adv 2016. [DOI: 10.1039/c5ra18992f] [Citation(s) in RCA: 45] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
As one of the strategies for synthesis of novel amyloid inhibitors, chemical modification of the natural curcuminoids framework can be introduced.
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Affiliation(s)
- Fakhrossadat Mohammadi
- Department of Chemistry
- Institute for Advanced Studies in Basic Sciences (IASBS)
- Zanjan 45137-66731
- Iran
| | - Afshin Mahmudian
- Department of Chemistry
- Institute for Advanced Studies in Basic Sciences (IASBS)
- Zanjan 45137-66731
- Iran
| | - Marzieh Moeeni
- Department of Chemistry
- Institute for Advanced Studies in Basic Sciences (IASBS)
- Zanjan 45137-66731
- Iran
| | - Leila Hassani
- Department of Biological Sciences
- Institute for Advanced Studies in Basic Sciences (IASBS)
- Zanjan 45137-66731
- Iran
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36
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Shahid S, Ahmad F, Hassan MI, Islam A. Relationship between protein stability and functional activity in the presence of macromolecular crowding agents alone and in mixture: An insight into stability-activity trade-off. Arch Biochem Biophys 2015; 584:42-50. [PMID: 26325080 DOI: 10.1016/j.abb.2015.08.015] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2015] [Revised: 08/19/2015] [Accepted: 08/23/2015] [Indexed: 12/25/2022]
Abstract
The cellular environment is crowded with different kinds of molecules with varying sizes, shapes and compositions. Most of the experiments studying the nature and behaviour of a protein have been done on the isolated protein in dilute buffer solutions which actually do not imitate the in vivo situation. To understand the consequences of such crowded environment, we investigated the effect of macromolecular crowding on the stability and activity of hen egg white lysozyme. Two crowding agents, dextran 70 and ficoll 70 which have different shapes and composition, have been employed in this study. To mimic the cellular condition from physiological point of view, the effect of mixtures of both the crowding agents has been also studied. The results indicate that owing to volume exclusion, lysozyme is stabilized while its activity decays with the increasing concentration of both the crowders elucidating the hypothesis of stability-activity trade-off. Mixed macromolecular crowding exerts greater effect than the sum of constituent crowding agents (dextran 70 and ficoll 70).
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Affiliation(s)
- Sumra Shahid
- 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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37
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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.
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Crowded milieu prevents fibrillation of hen egg white lysozyme with retention of enzymatic activity. JOURNAL OF PHOTOCHEMISTRY AND PHOTOBIOLOGY B-BIOLOGY 2014; 138:8-16. [DOI: 10.1016/j.jphotobiol.2014.04.021] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/18/2013] [Revised: 04/22/2014] [Accepted: 04/24/2014] [Indexed: 11/18/2022]
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Wawer J, Krakowiak J, Szociński M, Lustig Z, Olszewski M, Szostak K. Inhibition of amyloid fibril formation of hen egg white lysozyme by trimethylamine N-oxide at low pH. Int J Biol Macromol 2014; 70:214-21. [DOI: 10.1016/j.ijbiomac.2014.06.057] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2014] [Revised: 06/20/2014] [Accepted: 06/30/2014] [Indexed: 10/25/2022]
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40
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Ma Q, Hu JY, Chen J, Liang Y. The role of crowded physiological environments in prion and prion-like protein aggregation. Int J Mol Sci 2013; 14:21339-52. [PMID: 24284393 PMCID: PMC3856008 DOI: 10.3390/ijms141121339] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2013] [Revised: 09/24/2013] [Accepted: 09/27/2013] [Indexed: 01/07/2023] Open
Abstract
Prion diseases and prion- like protein misfolding diseases are related to the accumulation of abnormal aggregates of the normal host proteins including prion proteins and Tau protein. These proteins possess self-templating and transmissible characteristics. The crowded physiological environments where the aggregation of these amyloidogenic proteins takes place can be imitated in vitro by the addition of macromolecular crowding agents such as inert polysaccharides. In this review, we summarize the aggregation of prion proteins in crowded physiological environments and discuss the role of macromolecular crowding in prion protein aggregation. We also summarize the aggregation of prion- like proteins including human Tau protein, human α-synuclein, and human copper, zinc superoxide dismutase under macromolecular crowding environments and discuss the role of macromolecular crowding in prion- like protein aggregation. The excluded-volume effects caused by macromolecular crowding could accelerate the aggregation of neurodegenerative disease-associated proteins while inhibiting the aggregation of the proteins that are not neurodegenerative disease-associated.
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Affiliation(s)
- Qian Ma
- State Key Laboratory of Virology, College of Life Sciences, Wuhan University, Wuhan 430072, China.
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41
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Phillip Y, Schreiber G. Formation of protein complexes in crowded environments--from in vitro to in vivo. FEBS Lett 2013; 587:1046-52. [PMID: 23337873 PMCID: PMC7094571 DOI: 10.1016/j.febslet.2013.01.007] [Citation(s) in RCA: 100] [Impact Index Per Article: 9.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2012] [Revised: 12/24/2012] [Accepted: 01/06/2013] [Indexed: 01/17/2023]
Abstract
Traditionally, biochemical studies are performed in dilute homogenous solutions, which are very different from the dense mixture of molecules found in cells. Thus, the physiological relevance of these studies is in question. This recognition motivated scientists to formulate the effect of crowded solutions in general, and excluded volume in particular, on biochemical processes. Using polymers or proteins as crowders, it was shown that while crowding tends to significantly enhance the formation of complexes containing many subunits, dimerizations are only mildly affected. Computer simulations, together with experimental evidence, indicate soft interactions and diffusion as critical factors that operate in a concerted manner with excluded volume to modulate protein binding. Yet, these approaches do not truly mimic the cellular environment. In vivo studies may overcome this shortfall. The few studies conducted thus far suggest that in cells, binding and folding occur at rates close to those determined in dilute solutions. Obtaining quantitative biochemical information on reactions inside living cells is currently a main challenge of the field, as the complexity of the intracellular milieu was what motivated crowding research to begin with.
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Affiliation(s)
- Yael Phillip
- Department of Biological Chemistry, Weizmann Institute of Science, Rehovot 76100, Israel
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42
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Cook NP, Martí AA. Facile methodology for monitoring amyloid-β fibrillization. ACS Chem Neurosci 2012; 3:896-9. [PMID: 23173070 DOI: 10.1021/cn300135n] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2012] [Accepted: 09/12/2012] [Indexed: 01/16/2023] Open
Abstract
Amyloid-β (Aβ) is a peptide fragment that is prone to aggregate into large fibrils under physiological conditions. Many techniques have been developed to quickly monitor the transition from a primarily monomeric peptide into fibrils. Here we propose a novel method for both incubating and monitoring changes in Aβ aggregation by using modified NMR tubes, a microtube thermoshaker, and a fluorescence or UV-vis spectrometer. These NMR tubes are thin and cylindrical, which allows efficient heat transfer and orbital shaking. Our results demonstrate that our technique is both reliable and expedient when tracking Aβ fibrillization using fluorescence or turbidity assays, which presents an alternative for laboratories without specialized equipment for incubating peptide.
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Affiliation(s)
- Nathan P. Cook
- Department
of Chemistry, ‡Department of Bioengineering, and §Smalley Institute for Nanoscale Science and
Technology, Rice University, 6100 South Main Street, Houston, Texas 77005, United States
| | - Angel A. Martí
- Department
of Chemistry, ‡Department of Bioengineering, and §Smalley Institute for Nanoscale Science and
Technology, Rice University, 6100 South Main Street, Houston, Texas 77005, United States
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Lee CF, Bird S, Shaw M, Jean L, Vaux DJ. Combined effects of agitation, macromolecular crowding, and interfaces on amyloidogenesis. J Biol Chem 2012; 287:38006-19. [PMID: 22988239 PMCID: PMC3488071 DOI: 10.1074/jbc.m112.400580] [Citation(s) in RCA: 64] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2012] [Revised: 09/17/2012] [Indexed: 11/06/2022] Open
Abstract
Amyloid formation and accumulation is a hallmark of protein misfolding diseases and is associated with diverse pathologies including type II diabetes and Alzheimer's disease (AD). In vitro, amyloidogenesis is widely studied in conditions that do not simulate the crowded and viscous in vivo environment. A high volume fraction of most biological fluids is occupied by various macromolecules, a phenomenon known as macromolecular crowding. For some amyloid systems (e.g. α-synuclein) and under shaking condition, the excluded volume effect of macromolecular crowding favors aggregation, whereas increased viscosity reduces the kinetics of these reactions. Amyloidogenesis can also be catalyzed by hydrophobic-hydrophilic interfaces, represented by the air-water interface in vitro and diverse heterogeneous interfaces in vivo (e.g. membranes). In this study, we investigated the effects of two different crowding polymers (dextran and Ficoll) and two different experimental conditions (with and without shaking) on the fibrilization of amyloid-β peptide, a major player in AD pathogenesis. Specifically, we demonstrate that, during macromolecular crowding, viscosity dominates over the excluded volume effect only when the system is spatially non homogeneous (i.e. an air-water interface is present). We also show that the surfactant activity of the crowding agents can critically influence the outcome of macromolecular crowding and that the structure of the amyloid species formed may depend on the polymer used. This suggests that, in vivo, the outcome of amyloidogenesis may be affected by both macromolecular crowding and spatial heterogeneity (e.g. membrane turn-over). More generally, our work suggests that any factors causing changes in crowding may be susceptibility factors in AD.
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Affiliation(s)
- Chiu Fan Lee
- the Max Planck Institute for the Physics of Complex Systems, Noethnitzerstr. 38, Dresden 01187, Germany, and
| | - Sarah Bird
- the Medical School, Medical Sciences Office, John Radcliffe Hospital, Oxford University Clinical School, Oxford, OX3 9DU, United Kingdom
| | - Michael Shaw
- From the Sir William Dunn School of Pathology, University of Oxford, Oxford OX1 3RE, United Kingdom
| | - Létitia Jean
- From the Sir William Dunn School of Pathology, University of Oxford, Oxford OX1 3RE, United Kingdom
| | - David J. Vaux
- From the Sir William Dunn School of Pathology, University of Oxford, Oxford OX1 3RE, United Kingdom
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Dannies PS. Prolactin and growth hormone aggregates in secretory granules: the need to understand the structure of the aggregate. Endocr Rev 2012; 33:254-70. [PMID: 22357343 DOI: 10.1210/er.2011-1002] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Abstract
Prolactin and GH form reversible aggregates in the trans-Golgi lumen that become the dense cores of secretory granules. Aggregation is an economical means of sorting, because self-association removes the hormones from other possible pathways. Secretory granules containing different aggregates show different behavior, such as the reduction in stimulated release of granules containing R183H-GH compared with release of those containing wild-type hormone. Aggregates may facilitate localization of membrane proteins necessary for transport and exocytosis of secretory granules, and therefore understanding their properties is important. Three types of self-association have been characterized: dimers of human GH that form with Zn(2+), low-affinity self-association of human prolactin caused by acidic pH and Zn(2+) with macromolecular crowding, and amyloid fibers of prolactin. The best candidate for the form in most granules may be low-affinity self-association because it occurs rapidly at Zn(2+) concentrations that are likely to be in granules and reverses rapidly in neutral pH. Amyloid may form in older granules. Determining differences between aggregates of wild type and those of R183H-GH should help to understand why granules containing the mutant behave differently from those containing wild-type hormone. If reversible aggregation of other hormones, including those that are proteolytically processed, is the crucial act in forming granules, rather than use of a sorting signal, then prohormones should form reversible aggregates in solution in conditions that resemble those of the trans-Golgi lumen, including macromolecular crowding.
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Affiliation(s)
- Priscilla S Dannies
- Department of Pharmacology, Yale University School of Medicine, New Haven, Connecticut 06520-8066, USA.
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45
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Swaminathan R, Ravi VK, Kumar S, Kumar MVS, Chandra N. Lysozyme: a model protein for amyloid research. ADVANCES IN PROTEIN CHEMISTRY AND STRUCTURAL BIOLOGY 2011; 84:63-111. [PMID: 21846563 DOI: 10.1016/b978-0-12-386483-3.00003-3] [Citation(s) in RCA: 187] [Impact Index Per Article: 14.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Ever since lysozyme was discovered by Fleming in 1922, this protein has emerged as a model for investigations on protein structure and function. Over the years, several high-resolution structures have yielded a wealth of structural data on this protein. Extensive studies on folding of lysozyme have shown how different regions of this protein dynamically interact with one another. Data is also available from numerous biotechnological studies wherein lysozyme has been employed as a model protein for recovering active recombinant protein from inclusion bodies using small molecules like l-arginine. A variety of conditions have been developed in vitro to induce fibrillation in hen lysozyme. They include (a) acidic pH at elevated temperature, (b) concentrated solutions of ethanol, (c) moderate concentrations of guanidinium hydrochloride at moderate temperature, and (d) alkaline pH at room temperature. This review aims to bring together similarities and differences in aggregation mechanisms, morphology of aggregates, and related issues that arise using the different conditions mentioned above to improve our understanding. The alkaline pH condition (pH 12.2), discovered and studied extensively in our lab, shall receive special attention. More than a decade ago, it was revealed that mutations in human lysozyme can cause accumulation of large quantities of amyloid in liver, kidney, and other regions of gastrointestinal tract. Understanding the mechanism of lysozyme aggregation will probably have therapeutic implications for the treatment of systemic nonneuropathic amyloidosis. Numerous studies have begun to focus attention on inhibition of lysozyme aggregation using antibody or small molecules. The enzymatic activity of lysozyme presents a convenient handle to quantify the native population of lysozyme in a sample where aggregation has been inhibited. The rich information available on lysozyme coupled with the multiple conditions that have been successful in inducing/inhibiting its aggregation in vitro makes lysozyme an ideal model protein to investigate amyloidogenesis.
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Affiliation(s)
- Rajaram Swaminathan
- Department of Biotechnology, Indian Institute of Technology Guwahati, Guwahati, Assam, India
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46
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Survey of the year 2008: applications of isothermal titration calorimetry. J Mol Recognit 2010; 23:395-413. [DOI: 10.1002/jmr.1025] [Citation(s) in RCA: 53] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
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47
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Kumar S, Ravi VK, Swaminathan R. Suppression of lysozyme aggregation at alkaline pH by tri-N-acetylchitotriose. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2009; 1794:913-20. [DOI: 10.1016/j.bbapap.2009.01.009] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/19/2008] [Revised: 01/07/2009] [Accepted: 01/24/2009] [Indexed: 10/21/2022]
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48
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How do surfactants and DTT affect the size, dynamics, activity and growth of soluble lysozyme aggregates? Biochem J 2009; 415:275-88. [PMID: 18549353 DOI: 10.1042/bj20071499] [Citation(s) in RCA: 66] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
The early intermediates in the protein aggregation pathway, the elusive soluble aggregates, play a pivotal role in growth and maturation of ordered aggregates such as amyloid fibrils. Blocking the growth of soluble oligomers is an effective strategy to inhibit aggregation. To decipher the molecular mechanisms and develop better strategies to arrest aggregation, it is imperative to understand how the size, molecular dynamics, activity and growth kinetics of soluble aggregates are affected when aggregation is inhibited. With this objective, in the present study we have investigated the influence of additives such as SDS, CTAB (cetyltrimethylammonium bromide) and DTT (dithiothreitol) on the slow aggregation of HEWL (hen eggwhite lysozyme) at pH 12.2. For this purpose, techniques such as steady-state and time-resolved fluorescence anisotropy of covalently labelled dansyl probe, gel-filtration chromatography, estimation of free thiol groups, thioflavin T and ANS (8-anilinonaphthalene-1-sulfonic acid) fluorescence, CD and atomic-force microscopy were employed to monitor the soluble oligomers over a period spanning 30 days. The results of the present study reveal that: (i) the spontaneous formation of soluble aggregates is irreversible and abolishes activity; (ii) the initial growth of aggregates (0-24 h) is promoted by a gradual increase in the exposure of hydrophobic surfaces; (iii) subsequently intermolecular disulfide bonds are critical for the assembly and stability of aggregates; (iv) the tight molecular packing inside large aggregates which contributed to slow (approximately 5 ns) and restricted segmental motion of dansyl probe was clearly loosened up in the presence of additives, enabling fast (1-2 ns) and free motion (unlike DTT, the size of lysozyme complexes with surfactants, was large, due to a conglomeration of proteins and surfactants); (v) the aggregates show reduced helical content compared with native lysozyme, except in the presence of SDS; and (vi) DTT was more potent than SDS/CTAB in arresting the growth of aggregates.
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49
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Liang Y. Applications of isothermal titration calorimetry in protein science. Acta Biochim Biophys Sin (Shanghai) 2008; 40:565-76. [PMID: 18604448 DOI: 10.1111/j.1745-7270.2008.00437.x] [Citation(s) in RCA: 67] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
During the past decade, isothermal titration calorimetry (ITC) has developed from a specialist method for understanding molecular interactions and other biological processes within cells to a more robust, widely used method. Nowadays, ITC is used to investigate all types of protein interactions, including protein-protein interactions, protein-DNA/RNA interactions, protein-small molecule interactions and enzyme kinetics; it provides a direct route to the complete thermodynamic characterization of protein interactions. This review concentrates on the new applications of ITC in protein folding and misfolding, its traditional application in protein interactions, and an overview of what can be achieved in the field of protein science using this method and what developments are likely to occur in the near future. Also, this review discusses some new developments of ITC method in protein science, such as the reverse titration of ITC and the displacement method of ITC.
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Affiliation(s)
- Yi Liang
- State Key Laboratory of Virology, College of Life Sciences, Wuhan University, Wuhan 430072, China.
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