1
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Yasuda T, Morita R, Shigeta Y, Harada R. Ribosome Tunnel Environment Drives the Formation of α-Helix during Cotranslational Folding. J Chem Inf Model 2024. [PMID: 39150098 DOI: 10.1021/acs.jcim.4c00901] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/17/2024]
Abstract
Protein conformations in cells are not solely determined by amino acid sequences; they also depend on cellular environments. For instance, the ribosome tunnel induces its specific α-helix formation during cotranslational folding. Owing to the link between these temporally α-helix and biological functions, the mechanism of α-helix formation inside the ribosome tunnel has been previously explored. Consequently, the conformational restrictions of the tunnel were considered one of the driving forces of α-helix formation. Conversely, the ribosomal tunnel environment, including its chemical properties, appears to influence the α-helix formation. However, a comprehensive analysis of the ribosome tunnel environment's impact on the α-helix formation has not been conducted yet due to challenges in experimentally controlling it. Therefore, as a new computational approach, we proposed a ribosome environment-mimicking model (REMM) based on the radius and components of the experimentally determined ribosome tunnel structures. Using REMM, we assessed the impact of the ribosome tunnel environment on α-helix formation. Herein, we employed carbon nanotubes (CNT) as a reference model alongside REMM because CNT reproduce conformational restrictions rather than the ribosome tunnel environment. Quantitatively, the ability to reproduce the α-helix of nascent peptides in the experimental structure was compared between the CNT and REMM using enhanced all-atom molecular dynamics simulations. Consequently, the REMM more accurately reproduced the α-helix of the nascent peptides than the CNT, highlighting the significance of the ribosome tunnel environment in α-helix formation. Additionally, we analyzed the properties of the peptide inside each model to reveal the mechanism of ribosome tunnel-specific α-helix formation. Consequently, we revealed that the chemical diversities of the tunnel are essential for the formation of backbone-to-backbone hydrogen bonds in the peptides. In conclusion, the ribosome tunnel environment, with the diverse chemical properties, drives its specific α-helix formation. By proposing REMM, we newly provide the technical basis for investigating the protein conformations in various cellular environments.
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Affiliation(s)
- Takunori Yasuda
- Doctoral Program in Biology, University of Tsukuba, 1-1-1, Tennodai, Tsukuba, Ibaraki 305-8572, Japan
| | - Rikuri Morita
- Center for Computational Sciences, University of Tsukuba, 1-1-1 Tennodai, Tsukuba, Ibaraki 305-8577, Japan
| | - Yasuteru Shigeta
- Center for Computational Sciences, University of Tsukuba, 1-1-1 Tennodai, Tsukuba, Ibaraki 305-8577, Japan
| | - Ryuhei Harada
- Center for Computational Sciences, University of Tsukuba, 1-1-1 Tennodai, Tsukuba, Ibaraki 305-8577, Japan
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2
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Zhou HX, Kota D, Qin S, Prasad R. Fundamental Aspects of Phase-Separated Biomolecular Condensates. Chem Rev 2024; 124:8550-8595. [PMID: 38885177 PMCID: PMC11260227 DOI: 10.1021/acs.chemrev.4c00138] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/20/2024]
Abstract
Biomolecular condensates, formed through phase separation, are upending our understanding in much of molecular, cell, and developmental biology. There is an urgent need to elucidate the physicochemical foundations of the behaviors and properties of biomolecular condensates. Here we aim to fill this need by writing a comprehensive, critical, and accessible review on the fundamental aspects of phase-separated biomolecular condensates. We introduce the relevant theoretical background, present the theoretical basis for the computation and experimental measurement of condensate properties, and give mechanistic interpretations of condensate behaviors and properties in terms of interactions at the molecular and residue levels.
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Affiliation(s)
- Huan-Xiang Zhou
- Department of Chemistry, University of Illinois Chicago, Chicago, Illinois 60607, USA
- Department of Physics, University of Illinois Chicago, Chicago, Illinois 60607, USA
| | - Divya Kota
- Department of Chemistry, University of Illinois Chicago, Chicago, Illinois 60607, USA
| | - Sanbo Qin
- Department of Chemistry, University of Illinois Chicago, Chicago, Illinois 60607, USA
| | - Ramesh Prasad
- Department of Chemistry, University of Illinois Chicago, Chicago, Illinois 60607, USA
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3
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Wan L, Zhu Y, Zhang W, Mu W. Recent advances in design and application of synthetic membraneless organelles. Biotechnol Adv 2024; 73:108355. [PMID: 38588907 DOI: 10.1016/j.biotechadv.2024.108355] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2023] [Revised: 02/26/2024] [Accepted: 04/05/2024] [Indexed: 04/10/2024]
Abstract
Membraneless organelles (MLOs) formed by liquid-liquid phase separation (LLPS) have been extensively studied due to their spatiotemporal control of biochemical and cellular processes in living cells. These findings have provided valuable insights into the physicochemical principles underlying the formation and functionalization of biomolecular condensates, which paves the way for the development of versatile phase-separating systems capable of addressing a variety of application scenarios. Here, we highlight the potential of constructing synthetic MLOs with programmable and functional properties. Notably, we organize how these synthetic membraneless compartments have been capitalized to manipulate enzymatic activities and metabolic reactions. The aim of this review is to inspire readerships to deeply comprehend the widespread roles of synthetic MLOs in the regulation enzymatic reactions and control of metabolic processes, and to encourage the rational design of controllable and functional membraneless compartments for a broad range of bioengineering applications.
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Affiliation(s)
- Li Wan
- State Key Laboratory of Food Science and Resources, Jiangnan University, Wuxi, Jiangsu 214122, China
| | - Yingying Zhu
- State Key Laboratory of Food Science and Resources, Jiangnan University, Wuxi, Jiangsu 214122, China
| | - Wenli Zhang
- State Key Laboratory of Food Science and Resources, Jiangnan University, Wuxi, Jiangsu 214122, China
| | - Wanmeng Mu
- State Key Laboratory of Food Science and Resources, Jiangnan University, Wuxi, Jiangsu 214122, China; International Joint Laboratory on Food Safety, Jiangnan University, Wuxi, Jiangsu 214122, China.
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4
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Islam M, Shen F, Regmi D, Petersen K, Karim MRU, Du D. Tau liquid-liquid phase separation: At the crossroads of tau physiology and tauopathy. J Cell Physiol 2024; 239:e30853. [PMID: 35980344 PMCID: PMC9938090 DOI: 10.1002/jcp.30853] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2022] [Revised: 07/12/2022] [Accepted: 07/22/2022] [Indexed: 12/14/2022]
Abstract
Abnormal deposition of tau in neurons is a hallmark of Alzheimer's disease and several other neurodegenerative disorders. In the past decades, extensive efforts have been made to explore the mechanistic pathways underlying the development of tauopathies. Recently, the discovery of tau droplet formation by liquid-liquid phase separation (LLPS) has received a great deal of attention. It has been reported that tau condensates have a biological role in promoting and stabilizing microtubule (MT) assembly. Furthermore, it has been hypothesized that the transition of phase-separated tau droplets to a gel-like state and then to fibrils is associated with the pathology of neurodegenerative diseases. In this review, we outline LLPS, the structural disorder that facilitates tau droplet formation, the effects of posttranslational modification of tau on condensate formation, the physiological function of tau droplets, the pathways from droplet to toxic fibrils, and the therapeutic strategies for tauopathies that might evolve from toxic droplets. We expect a deeper understanding of tau LLPS will provide additional insights into tau physiology and tauopathies.
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Affiliation(s)
- Majedul Islam
- Department of Chemistry and Biochemistry, Florida Atlantic University, Boca Raton, Florida 33431, United States
| | - Fengyun Shen
- Department of Chemistry and Biochemistry, Florida Atlantic University, Boca Raton, Florida 33431, United States
| | - Deepika Regmi
- Department of Chemistry and Biochemistry, Florida Atlantic University, Boca Raton, Florida 33431, United States
| | - Katherine Petersen
- Department of Chemistry and Biochemistry, Florida Atlantic University, Boca Raton, Florida 33431, United States
| | - Md Raza Ul Karim
- Department of Chemistry and Biochemistry, Florida Atlantic University, Boca Raton, Florida 33431, United States
| | - Deguo Du
- Department of Chemistry and Biochemistry, Florida Atlantic University, Boca Raton, Florida 33431, United States
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5
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Juković M, Ratkaj I, Kalafatovic D, Bradshaw NJ. Amyloids, amorphous aggregates and assemblies of peptides - Assessing aggregation. Biophys Chem 2024; 308:107202. [PMID: 38382283 DOI: 10.1016/j.bpc.2024.107202] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2023] [Revised: 01/31/2024] [Accepted: 02/14/2024] [Indexed: 02/23/2024]
Abstract
Amyloid and amorphous aggregates represent the two major categories of aggregates associated with diseases, and although exhibiting distinct features, researchers often treat them as equivalent, which demonstrates the need for more thorough characterization. Here, we compare amyloid and amorphous aggregates based on their biochemical properties, kinetics, and morphological features. To further decipher this issue, we propose the use of peptide self-assemblies as minimalistic models for understanding the aggregation process. Peptide building blocks are significantly smaller than proteins that participate in aggregation, however, they make a plausible means to bridge the gap in discerning the aggregation process at the more complex, protein level. Additionally, we explore the potential use of peptide-inspired models to research the liquid-liquid phase separation as a feasible mechanism preceding amyloid formation. Connecting these concepts can help clarify our understanding of aggregation-related disorders and potentially provide novel drug targets to impede and reverse these serious illnesses.
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Affiliation(s)
- Maja Juković
- Faculty of Biotechnology and Drug Development, University of Rijeka, 51000 Rijeka, Croatia
| | - Ivana Ratkaj
- Faculty of Biotechnology and Drug Development, University of Rijeka, 51000 Rijeka, Croatia
| | - Daniela Kalafatovic
- Faculty of Biotechnology and Drug Development, University of Rijeka, 51000 Rijeka, Croatia.
| | - Nicholas J Bradshaw
- Faculty of Biotechnology and Drug Development, University of Rijeka, 51000 Rijeka, Croatia.
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6
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Hu B, Zhang C, Zhu J, Yang J, Zheng Q, Zhang X, Cao J, Han L. Liquid-liquid biopolymers aqueous solution segregative phase separation in food: From fundamentals to applications-A review. Int J Biol Macromol 2024; 265:131044. [PMID: 38518933 DOI: 10.1016/j.ijbiomac.2024.131044] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2023] [Revised: 03/07/2024] [Accepted: 03/19/2024] [Indexed: 03/24/2024]
Abstract
As a result of the spontaneous movement of molecules, liquid-liquid biopolymer segregative phase separation takes place in an aqueous solution. The efficacy of this type of separation can be optimized under conditions where variables such as pH, temperature, and molecular concentrations have minimal impact on its dynamics. Recently, interest in the applications of biopolymers and their segregative phase separation-associated molecular stratification has increased, particularly in the food industry, where these methods permit the purification of specific particles and the embedding of microcapsules. The present review offers a comprehensive examination of the theoretical mechanisms that regulate the liquid-liquid biopolymers aqueous solution segregative phase separation, the factors that may exert an impact on this procedure, and the importance of this particular separation method in the context of food science. These discussion points also address existing difficulties and future possibilities related to the use of segregative phase separation in food applications. This highlights the potential for the design of novel functional foods and the enhancement of food properties.
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Affiliation(s)
- Bing Hu
- College of Life Sciences, Key Laboratory of Biotechnology and Bioresources Utilization, Dalian Minzu University, Ministry of Education, Dalian 116600, China.
| | - Cunzhi Zhang
- College of Life Sciences, Key Laboratory of Biotechnology and Bioresources Utilization, Dalian Minzu University, Ministry of Education, Dalian 116600, China
| | - Junzhe Zhu
- College of Life Sciences, Key Laboratory of Biotechnology and Bioresources Utilization, Dalian Minzu University, Ministry of Education, Dalian 116600, China
| | - Jixin Yang
- Faculty of Social and Life Sciences, Wrexham University, Mold Road, Wrexham LL11 2AW, United Kingdom
| | - Qiuyue Zheng
- College of Life Sciences, Key Laboratory of Biotechnology and Bioresources Utilization, Dalian Minzu University, Ministry of Education, Dalian 116600, China
| | - Xiaobo Zhang
- College of Life Sciences, Key Laboratory of Biotechnology and Bioresources Utilization, Dalian Minzu University, Ministry of Education, Dalian 116600, China
| | - Jijuan Cao
- College of Life Sciences, Key Laboratory of Biotechnology and Bioresources Utilization, Dalian Minzu University, Ministry of Education, Dalian 116600, China
| | - Lingyu Han
- College of Life Sciences, Key Laboratory of Biotechnology and Bioresources Utilization, Dalian Minzu University, Ministry of Education, Dalian 116600, China.
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7
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Thirumalai D, Kumar A, Chakraborty D, Straub JE, Mugnai ML. Conformational fluctuations and phases in fused in sarcoma (FUS) low-complexity domain. Biopolymers 2024; 115:e23558. [PMID: 37399327 PMCID: PMC10831756 DOI: 10.1002/bip.23558] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2023] [Revised: 05/30/2023] [Accepted: 06/15/2023] [Indexed: 07/05/2023]
Abstract
The well-known phenomenon of phase separation in synthetic polymers and proteins has become a major topic in biophysics because it has been invoked as a mechanism of compartment formation in cells, without the need for membranes. Most of the coacervates (or condensates) are composed of Intrinsically Disordered Proteins (IDPs) or regions that are structureless, often in interaction with RNA and DNA. One of the more intriguing IDPs is the 526-residue RNA-binding protein, Fused in Sarcoma (FUS), whose monomer conformations and condensates exhibit unusual behavior that are sensitive to solution conditions. By focussing principally on the N-terminus low-complexity domain (FUS-LC comprising residues 1-214) and other truncations, we rationalize the findings of solid-state NMR experiments, which show that FUS-LC adopts a non-polymorphic fibril structure (core-1) involving residues 39-95, flanked by fuzzy coats on both the N- and C-terminal ends. An alternate structure (core-2), whose free energy is comparable to core-1, emerges only in the truncated construct (residues 110-214). Both core-1 and core-2 fibrils are stabilized by a Tyrosine ladder as well as hydrophilic interactions. The morphologies (gels, fibrils, and glass-like) adopted by FUS seem to vary greatly, depending on the experimental conditions. The effect of phosphorylation is site-specific. Simulations show that phosphorylation of residues within the fibril has a greater destabilization effect than residues that are outside the fibril region, which accords well with experiments. Many of the peculiarities associated with FUS may also be shared by other IDPs, such as TDP43 and hnRNPA2. We outline a number of problems for which there is no clear molecular explanation.
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Affiliation(s)
- D Thirumalai
- Department of Chemistry, The University of Texas at Austin, Austin, Texas, USA
- Department of Physics, The University of Texas at Austin, Austin, Texas, USA
| | - Abhinaw Kumar
- Department of Chemistry, The University of Texas at Austin, Austin, Texas, USA
| | - Debayan Chakraborty
- Department of Chemistry, The University of Texas at Austin, Austin, Texas, USA
| | - John E Straub
- Department of Chemistry, Boston University, Boston, Massachusetts, USA
| | - Mauro L Mugnai
- Institute for Soft Matter Synthesis and Metrology, Georgetown University, Washington, DC, USA
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8
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Zheng H, Zhang H. More than a bystander: RNAs specify multifaceted behaviors of liquid-liquid phase-separated biomolecular condensates. Bioessays 2024; 46:e2300203. [PMID: 38175843 DOI: 10.1002/bies.202300203] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2023] [Revised: 12/09/2023] [Accepted: 12/12/2023] [Indexed: 01/06/2024]
Abstract
Cells contain a myriad of membraneless ribonucleoprotein (RNP) condensates with distinct compositions of proteins and RNAs. RNP condensates participate in different cellular activities, including RNA storage, mRNA translation or decay, stress response, etc. RNP condensates are assembled via liquid-liquid phase separation (LLPS) driven by multivalent interactions. Transition of RNP condensates into bodies with abnormal material properties, such as solid-like amyloid structures, is associated with the pathogenesis of various diseases. In this review, we focus on how RNAs regulate multiple aspects of RNP condensates, such as dynamic assembly and/or disassembly and biophysical properties. RNA properties - including concentration, sequence, length and structure - also determine the phase behaviors of RNP condensates. RNA is also involved in specifying autophagic degradation of RNP condensates. Unraveling the role of RNA in RNPs provides novel insights into pathological accumulation of RNPs in various diseases. This new understanding can potentially be harnessed to develop therapeutic strategies.
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Affiliation(s)
- Hui Zheng
- National Laboratory of Biomacromolecules, New Cornerstone Science Laboratory, Institute of Biophysics, Chinese Academy of Sciences, Beijing, P.R. China
| | - Hong Zhang
- National Laboratory of Biomacromolecules, New Cornerstone Science Laboratory, Institute of Biophysics, Chinese Academy of Sciences, Beijing, P.R. China
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, P.R. China
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9
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Kim J, Qin S, Zhou HX, Rosen MK. Surface Charge Can Modulate Phase Separation of Multidomain Proteins. J Am Chem Soc 2024; 146:3383-3395. [PMID: 38262618 PMCID: PMC10859935 DOI: 10.1021/jacs.3c12789] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2023] [Revised: 12/28/2023] [Accepted: 12/29/2023] [Indexed: 01/25/2024]
Abstract
Phase separation has emerged as an important mechanism explaining the formation of certain biomolecular condensates. Biological phase separation is often driven by the multivalent interactions of modular protein domains. Beyond valency, the physical features of folded domains that promote phase separation are poorly understood. We used a model system─the small ubiquitin modifier (SUMO) and its peptide ligand, the SUMO interaction motif (SIM)─to examine how domain surface charge influences multivalency-driven phase separation. Phase separation of polySUMO and polySIM was altered by pH via a change in the protonation state of SUMO surface histidines. These effects were recapitulated by histidine mutations, which modulated SUMO solubility and polySUMO-polySIM phase separation in parallel and were quantitatively explained by atomistic modeling of weak interactions among proteins in the system. Thus, surface charge can tune the phase separation of multivalent proteins, suggesting a means of controlling phase separation biologically, evolutionarily, and therapeutically.
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Affiliation(s)
- Jonggul Kim
- Department
of Biophysics, University of Texas Southwestern
Medical Center, Dallas, Texas 75390, United States
- Howard
Hughes Medical Institute, Dallas, Texas 75390, United States
| | - Sanbo Qin
- Department
of Chemistry, University of Illinois Chicago, Chicago, Illinois 60607, United States
| | - Huan-Xiang Zhou
- Department
of Chemistry, University of Illinois Chicago, Chicago, Illinois 60607, United States
- Department
of Physics, University of Illinois Chicago, Chicago, Illinois 60607, United States
| | - Michael K. Rosen
- Department
of Biophysics, University of Texas Southwestern
Medical Center, Dallas, Texas 75390, United States
- Howard
Hughes Medical Institute, Dallas, Texas 75390, United States
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10
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Gupta MN, Uversky VN. Biological importance of arginine: A comprehensive review of the roles in structure, disorder, and functionality of peptides and proteins. Int J Biol Macromol 2024; 257:128646. [PMID: 38061507 DOI: 10.1016/j.ijbiomac.2023.128646] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2023] [Revised: 12/02/2023] [Accepted: 12/04/2023] [Indexed: 01/26/2024]
Abstract
Arginine shows Jekyll and Hyde behavior in several respects. It participates in protein folding via ionic and H-bonds and cation-pi interactions; the charge and hydrophobicity of its side chain make it a disorder-promoting amino acid. Its methylation in histones; RNA binding proteins; chaperones regulates several cellular processes. The arginine-centric modifications are important in oncogenesis and as biomarkers in several cardiovascular diseases. The cross-links involving arginine in collagen and cornea are involved in pathogenesis of tissues but have also been useful in tissue engineering and wound-dressing materials. Arginine is a part of active site of several enzymes such as GTPases, peroxidases, and sulfotransferases. Its metabolic importance is obvious as it is involved in production of urea, NO, ornithine and citrulline. It can form unusual functional structures such as molecular tweezers in vitro and sprockets which engage DNA chains as part of histones in vivo. It has been used in design of cell-penetrating peptides as drugs. Arginine has been used as an excipient in both solid and injectable drug formulations; its role in suppressing opalescence due to liquid-liquid phase separation is particularly very promising. It has been known as a suppressor of protein aggregation during protein refolding. It has proved its usefulness in protein bioseparation processes like ion-exchange, hydrophobic and affinity chromatographies. Arginine is an amino acid, whose importance in biological sciences and biotechnology continues to grow in diverse ways.
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Affiliation(s)
- Munishwar Nath Gupta
- Department of Biochemical Engineering and Biotechnology, Indian Institute of Technology, Hauz Khas, New Delhi 110016, India
| | - Vladimir N Uversky
- Department of Molecular Medicine, USF Health Byrd Alzheimer's Research Institute, Morsani College of Medicine, University of South Florida, Tampa, FL 33612, USA.
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11
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Kang WB, Bao L, Zhang K, Guo J, Zhu BC, Tang QY, Ren WT, Zhu G. Multi-scale molecular simulation of random peptide phase separation and its extended-to-compact structure transition driven by hydrophobic interactions. SOFT MATTER 2023; 19:7944-7954. [PMID: 37815389 DOI: 10.1039/d3sm00633f] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/11/2023]
Abstract
Intrinsically disordered proteins (IDPs) often undergo liquid-liquid phase separation (LLPS) and form membraneless organelles or protein condensates. One of the core problems is how do electrostatic repulsion and hydrophobic interactions in peptides regulate the phase separation process? To answer this question, this study uses random peptides composed of positively charged arginine (Arg, R) and hydrophobic isoleucine (Ile, I) as the model systems, and conduct large-scale simulations using all atom and coarse-grained model multi-scale simulation methods. In this article, we investigate the phase separation of different sequences using a coarse-grained model. It is found that the stronger the electrostatic repulsion in the system, the more extended the single-chain structure, and the more likely the system forms a low-density homogeneous phase. In contrast, the stronger the hydrophobic effect of the system, the more compact the single-chain structure, the easier phase separation, and the higher the critical temperature of phase separation. Overall, by taking the random polypeptides composed of two types of amino acid residues as model systems, this study discusses the relationship between the protein sequence and phase behaviour, and provides theoretical insights into the interactions within or between proteins. It is expected to provide essential physical information for the sequence design of functional IDPs, as well as data to support the diagnosis and treatment of the LLPS-associated diseases.
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Affiliation(s)
- Wen Bin Kang
- School of Public Health, Hubei University of Medicine, Shiyan 442000, China.
| | - Lei Bao
- School of Public Health, Hubei University of Medicine, Shiyan 442000, China.
| | - Kai Zhang
- School of Physics, Nanjing University, Nanjing 210093, China
| | - Jia Guo
- School of Public Health, Hubei University of Medicine, Shiyan 442000, China.
| | - Ben Chao Zhu
- School of Public Health, Hubei University of Medicine, Shiyan 442000, China.
| | - Qian-Yuan Tang
- Department of Physics, Hong Kong Baptist University, Kowloon, Hong Kong SAR, China
| | - Wei Tong Ren
- Wenzhou Institute, University of Chinese Academy of Sciences, Wenzhou, China
| | - Gen Zhu
- School of Public Health, Hubei University of Medicine, Shiyan 442000, China.
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12
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Kim N, Kim TH, Kim C, Lee JE, Kang MG, Shin S, Jung M, Kim JS, Mun JY, Rhee HW, Park SY, Shin Y, Yoo JY. Intrinsically disordered region-mediated condensation of IFN-inducible SCOTIN/SHISA-5 inhibits ER-to-Golgi vesicle transport. Dev Cell 2023; 58:1950-1966.e8. [PMID: 37816329 DOI: 10.1016/j.devcel.2023.08.030] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2022] [Revised: 07/27/2023] [Accepted: 08/25/2023] [Indexed: 10/12/2023]
Abstract
Newly synthesized proteins in the endoplasmic reticulum (ER) are sorted by coat protein complex II (COPII) at the ER exit site en route to the Golgi. Under cellular stresses, COPII proteins become targets of regulation to control the transport. Here, we show that the COPII outer coat proteins Sec31 and Sec13 are selectively sequestered into the biomolecular condensate of SCOTIN/SHISA-5, which interferes with COPII vesicle formation and inhibits ER-to-Golgi transport. SCOTIN is an ER transmembrane protein with a cytosolic intrinsically disordered region (IDR), which is required and essential for the formation of condensates. Upon IFN-γ stimulation, which is a cellular condition that induces SCOTIN expression and condensation, ER-to-Golgi transport was inhibited in a SCOTIN-dependent manner. Furthermore, cancer-associated mutations of SCOTIN perturb its ability to form condensates and control transport. Together, we propose that SCOTIN impedes the ER-to-Golgi transport through its ability to form biomolecular condensates at the ER membrane.
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Affiliation(s)
- Nari Kim
- Department of Life Sciences, Pohang University of Science and Technology, Pohang 37673, Republic of Korea.
| | - Tae-Hyeon Kim
- Department of Life Sciences, Pohang University of Science and Technology, Pohang 37673, Republic of Korea
| | - Chaelim Kim
- Interdisciplinary Program in Bioengineering, Seoul National University, Seoul 08826, Republic of Korea
| | - Jee-Eun Lee
- Department of Life Sciences, Pohang University of Science and Technology, Pohang 37673, Republic of Korea
| | - Myeong-Gyun Kang
- Department of Chemistry, Seoul National University, Seoul 08826, Republic of Korea
| | - Sanghee Shin
- School of Biological Sciences, Seoul National University, Seoul 08826, Republic of Korea; Center for RNA Research, Institute for Basic Science (IBS), Seoul 08826, Republic of Korea
| | - Minkyo Jung
- Neural Circuit Research Group, Korea Brain Research Institute, Daegu 41062, Republic of Korea
| | - Jong-Seo Kim
- School of Biological Sciences, Seoul National University, Seoul 08826, Republic of Korea; Center for RNA Research, Institute for Basic Science (IBS), Seoul 08826, Republic of Korea
| | - Ji Young Mun
- Neural Circuit Research Group, Korea Brain Research Institute, Daegu 41062, Republic of Korea
| | - Hyun-Woo Rhee
- Department of Chemistry, Seoul National University, Seoul 08826, Republic of Korea; School of Biological Sciences, Seoul National University, Seoul 08826, Republic of Korea
| | - Seung-Yeol Park
- Department of Life Sciences, Pohang University of Science and Technology, Pohang 37673, Republic of Korea
| | - Yongdae Shin
- Interdisciplinary Program in Bioengineering, Seoul National University, Seoul 08826, Republic of Korea; Department of Mechanical Engineering, Seoul National University, Seoul 08826, Republic of Korea
| | - Joo-Yeon Yoo
- Department of Life Sciences, Pohang University of Science and Technology, Pohang 37673, Republic of Korea.
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13
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Qin S, Zhou HX. Atomistic modeling of liquid-liquid phase equilibrium explains dependence of critical temperature on γ-crystallin sequence. Commun Biol 2023; 6:886. [PMID: 37644195 PMCID: PMC10465548 DOI: 10.1038/s42003-023-05270-7] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2023] [Accepted: 08/22/2023] [Indexed: 08/31/2023] Open
Abstract
Liquid-liquid phase separation of protein solutions has regained heightened attention for its biological importance and pathogenic relevance. Coarse-grained models are limited when explaining residue-level effects on phase equilibrium. Here we report phase diagrams for γ-crystallins using atomistic modeling. The calculations were made possible by combining our FMAP method for computing chemical potentials and Brownian dynamics simulations for configurational sampling of dense protein solutions, yielding the binodal and critic temperature (Tc). We obtain a higher Tc for a known high-Tc γ-crystallin, γF, than for a low-Tc paralog, γB. The difference in Tc is corroborated by a gap in second virial coefficient. Decomposition of inter-protein interactions reveals one amino-acid substitution between γB and γF, from Ser to Trp at position 130, as the major contributor to the difference in Tc. This type of analysis enables us to link phase equilibrium to amino-acid sequence and to design mutations for altering phase equilibrium.
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Affiliation(s)
- Sanbo Qin
- Department of Chemistry, University of Illinois Chicago, Chicago, IL, 60607, USA
| | - Huan-Xiang Zhou
- Department of Chemistry, University of Illinois Chicago, Chicago, IL, 60607, USA.
- Department of Physics, University of Illinois Chicago, Chicago, IL, 60607, USA.
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14
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Rangachari V. Biomolecular condensates - extant relics or evolving microcompartments? Commun Biol 2023; 6:656. [PMID: 37344557 PMCID: PMC10284869 DOI: 10.1038/s42003-023-04963-3] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2023] [Accepted: 05/22/2023] [Indexed: 06/23/2023] Open
Abstract
Unprecedented discoveries during the past decade have unearthed the ubiquitous presence of biomolecular condensates (BCs) in diverse organisms and their involvement in a plethora of biological functions. A predominant number of BCs involve coacervation of RNA and proteins that demix from homogenous solutions by a process of phase separation well described by liquid-liquid phase separation (LLPS), which results in a phase with higher concentration and density from the bulk solution. BCs provide a simple and effective means to achieve reversible spatiotemporal control of cellular processes and adaptation to environmental stimuli in an energy-independent manner. The journey into the past of this phenomenon provides clues to the evolutionary origins of life itself. Here I assemble some current and historic discoveries on LLPS to contemplate whether BCs are extant biological hubs or evolving microcompartments. I conclude that BCs in biology could be extant as a phenomenon but are co-evolving as functionally and compositionally complex microcompartments in cells alongside the membrane-bound organelles.
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Affiliation(s)
- Vijayaraghavan Rangachari
- Department of Chemistry and Biochemistry, School of Mathematics and Natural Sciences and Center for Molecular and Cellular Biosciences, University of Southern Mississippi, Hattiesburg, MS, 39402, USA.
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15
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Thirumalai D, Kumar A, Chakraborty D, Straub JE, Mugnai ML. Conformational Fluctuations and Phases in Fused in Sarcoma (FUS) Low-Complexity Domain. ARXIV 2023:arXiv:2303.04215v2. [PMID: 36945688 PMCID: PMC10029050] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Subscribe] [Scholar Register] [Indexed: 03/23/2023]
Abstract
The well known phenomenon of phase separation in synthetic polymers and proteins has become a major topic in biophysics because it has been invoked as a mechanism of compartment formation in cells, without the need for membranes. Most of the coacervates (or condensates) are composed of Intrinsically Disordered Proteins (IDPs) or regions that are structureless, often in interaction with RNA and DNA. One of the more intriguing IDPs is the 526-residue RNA binding protein, Fused In Sarcoma (FUS), whose monomer conformations and condensates exhibit unusual behavior that are sensitive to solution conditions. By focussing principally on the N-terminus low complexity domain (FUS-LC comprising residues 1-214) and other truncations, we rationalize the findings of solid state NMR experiments, which show that FUS-LC adopts a non-polymorphic fibril (core-1) involving residues 39-95, flanked by fuzzy coats on both the N- and C- terminal ends. An alternate structure (core-2), whose free energy is comparable to core-1, emerges only in the truncated construct (residues 110-214). Both core-1 and core-2 fibrils are stabilized by a Tyrosine ladder as well as hydrophilic interactions. The morphologies (gels, fibrils, and glass-like behavior) adopted by FUS seem to vary greatly, depending on the experimental conditions. The effect of phosphorylation is site specific and affects the stability of the fibril depending on the sites that are phosphorylated. Many of the peculiarities associated with FUS may also be shared by other IDPs, such as TDP43 and hnRNPA2. We outline a number of problems for which there is no clear molecular understanding.
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Affiliation(s)
- D Thirumalai
- Department of Chemistry, The University of Texas at Austin, Austin, TX 78712
- Department of Physics, The University of Texas at Austin, Austin, TX 78712
| | - Abhinaw Kumar
- Department of Chemistry, The University of Texas at Austin, Austin, TX 78712
| | - Debayan Chakraborty
- Department of Chemistry, The University of Texas at Austin, Austin, TX 78712
| | - John E Straub
- Department of Chemistry, Boston University, Boston, MA 78712
| | - Mauro L Mugnai
- Institute of Soft Matter Synthesis and Metrology, Georgetown University, Washington, DC 20057
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16
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Vendruscolo M, Fuxreiter M. Towards sequence-based principles for protein phase separation predictions. Curr Opin Chem Biol 2023; 75:102317. [PMID: 37207400 DOI: 10.1016/j.cbpa.2023.102317] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2023] [Revised: 04/07/2023] [Accepted: 04/11/2023] [Indexed: 05/21/2023]
Abstract
The phenomenon of protein phase separation, which underlies the formation of biomolecular condensates, has been associated with numerous cellular functions. Recent studies indicate that the amino acid sequences of most proteins may harbour not only the code for folding into the native state but also for condensing into the liquid-like droplet state and the solid-like amyloid state. Here we review the current understanding of the principles for sequence-based methods for predicting the propensity of proteins for phase separation. A guiding concept is that entropic contributions are generally more important to stabilise the droplet state than they are for the native and amyloid states. Although estimating these entropic contributions has proven difficult, we describe some progress that has been recently made in this direction. To conclude, we discuss the challenges ahead to extend sequence-based prediction methods of protein phase separation to include quantitative in vivo characterisations of this process.
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Affiliation(s)
- Michele Vendruscolo
- Centre for Misfolding Diseases, Yusuf Hamied Department of Chemistry, University of Cambridge, Cambridge CB2 1EW, UK.
| | - Monika Fuxreiter
- Department of Biomedical Sciences, University of Padova, PD 35131, Italy; Department of Physics and Astronomy, University of Padova, PD 35131, Italy.
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17
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Hagan MF, Mohajerani F. Self-assembly coupled to liquid-liquid phase separation. PLoS Comput Biol 2023; 19:e1010652. [PMID: 37186597 PMCID: PMC10212142 DOI: 10.1371/journal.pcbi.1010652] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2022] [Revised: 05/25/2023] [Accepted: 04/26/2023] [Indexed: 05/17/2023] Open
Abstract
Liquid condensate droplets with distinct compositions of proteins and nucleic acids are widespread in biological cells. While it is known that such droplets, or compartments, can regulate irreversible protein aggregation, their effect on reversible self-assembly remains largely unexplored. In this article, we use kinetic theory and solution thermodynamics to investigate the effect of liquid-liquid phase separation on the reversible self-assembly of structures with well-defined sizes and architectures. We find that, when assembling subunits preferentially partition into liquid compartments, robustness against kinetic traps and maximum achievable assembly rates can be significantly increased. In particular, both the range of solution conditions leading to productive assembly and the corresponding assembly rates can increase by orders of magnitude. We analyze the rate equation predictions using simple scaling estimates to identify effects of liquid-liquid phase separation as a function of relevant control parameters. These results may elucidate self-assembly processes that underlie normal cellular functions or pathogenesis, and suggest strategies for designing efficient bottom-up assembly for nanomaterials applications.
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Affiliation(s)
- Michael F. Hagan
- Martin A. Fisher School of Physics, Brandeis University, Waltham, Massachusetts, United States of America
| | - Farzaneh Mohajerani
- Martin A. Fisher School of Physics, Brandeis University, Waltham, Massachusetts, United States of America
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18
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Qin S, Zhou HX. Atomistic Modeling of Liquid-Liquid Phase Equilibrium Explains Dependence of Critical Temperature on γ-Crystallin Sequence. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.04.25.538329. [PMID: 37162827 PMCID: PMC10168431 DOI: 10.1101/2023.04.25.538329] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/11/2023]
Abstract
Liquid-liquid phase separation of protein solutions has regained heightened attention for its biological importance and pathogenic relevance. Coarse-grained models are limited when explaining residue-level effects on phase equilibrium. Here we report phase diagrams for γ-crystallins using atomistic modeling. The calculations were made possible by combining our FMAP method for computing chemical potentials and Brownian dynamics simulations for configurational sampling of dense protein solutions, yielding the binodal and critic temperature ( T c ). We obtain a higher T c for a known high- T c γ-crystallin, γF, than for a low- T c paralog, γB. The difference in T c is corroborated by a gap in second virial coefficient. Decomposition of inter-protein interactions reveals one amino-acid substitution between γB and γF, from Ser to Trp at position 130, as the major contributor to the difference in T c . This type of analysis enables us to link phase equilibrium to amino-acid sequence and to design mutations for altering phase equilibrium.
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Affiliation(s)
- Sanbo Qin
- Department of Chemistry, University of Illinois Chicago, Chicago, IL 60607, USA
| | - Huan-Xiang Zhou
- Department of Chemistry, University of Illinois Chicago, Chicago, IL 60607, USA
- Department of Physics, University of Illinois Chicago, Chicago, IL 60607, USA
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19
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Whitman BT, Wang Y, Murray CRA, Glover MJN, Owttrim GW. Liquid-Liquid Phase Separation of the DEAD-Box Cyanobacterial RNA Helicase Redox (CrhR) into Dynamic Membraneless Organelles in Synechocystis sp. Strain PCC 6803. Appl Environ Microbiol 2023; 89:e0001523. [PMID: 36920190 PMCID: PMC10132119 DOI: 10.1128/aem.00015-23] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2023] [Accepted: 02/17/2023] [Indexed: 03/16/2023] Open
Abstract
Compartmentalization of macromolecules into discrete non-lipid-bound bodies by liquid-liquid phase separation (LLPS) is a well-characterized regulatory mechanism frequently associated with the cellular stress response in eukaryotes. In contrast, the formation and importance of similar complexes is just becoming evident in bacteria. Here, we identify LLPS as the mechanism by which the DEAD-box RNA helicase, cyanobacterial RNA helicase redox (CrhR), compartmentalizes into dynamic membraneless organelles in a temporal and spatial manner in response to abiotic stress in the cyanobacterium Synechocystis sp. strain PCC 6803. Stress conditions induced CrhR to form a single crescent localized exterior to the thylakoid membrane, indicating that this region is a crucial domain in the cyanobacterial stress response. These crescents rapidly dissipate upon alleviation of the stress conditions. Furthermore, CrhR aggregation was mediated by LLPS in an RNA-dependent reaction. We propose that dynamic CrhR condensation performs crucial roles in RNA metabolism, enabling rapid adaptation of the photosynthetic apparatus to environmental stresses. These results expand our understanding of the role that functional compartmentalization of RNA helicases and thus RNA processing in membraneless organelles by LLPS-mediated protein condensation performs in the bacterial response to environmental stress. IMPORTANCE Oxygen-evolving photosynthetic cyanobacteria evolved ~3 billion years ago, performing fundamental roles in the biogeochemical evolution of the early Earth and continue to perform fundamental roles in nutrient cycling and primary productivity today. The phylum consists of diverse species that flourish in heterogeneous environments. A prime driver for survival is the ability to alter photosynthetic performance in response to the shifting environmental conditions these organisms continuously encounter. This study demonstrated that diverse abiotic stresses elicit dramatic changes in localization and structural organization of the RNA helicase CrhR associated with the photosynthetic thylakoid membrane. These dynamic changes, mediated by a liquid-liquid phase separation (LLPS)-mediated mechanism, reveal a novel mechanism by which cyanobacteria can compartmentalize the activity of ribonucleoprotein complexes in membraneless organelles. The results have significant consequences for understanding bacterial adaptation and survival in response to changing environmental conditions.
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Affiliation(s)
- Brendan T. Whitman
- Department of Biological Sciences, University of Alberta, Edmonton, Alberta, Canada
| | - Yixiong Wang
- Department of Oncology, Cross Cancer Institute, University of Alberta, Edmonton, Alberta, Canada
| | - Cameron R. A. Murray
- Department of Biochemistry, Faculty of Medicine & Dentistry, University of Alberta, Edmonton, Alberta, Canada
| | - Mark J. N. Glover
- Department of Biochemistry, Faculty of Medicine & Dentistry, University of Alberta, Edmonton, Alberta, Canada
| | - George W. Owttrim
- Department of Biological Sciences, University of Alberta, Edmonton, Alberta, Canada
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20
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Galagedera SKK, Dao TP, Enos SE, Chaudhuri A, Schmit JD, Castañeda CA. Decoding optimal ligand design for multicomponent condensates. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.03.13.532222. [PMID: 36993708 PMCID: PMC10054939 DOI: 10.1101/2023.03.13.532222] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/29/2023]
Abstract
Biomolecular condensates form via multivalent interactions among key macromolecules and are regulated through ligand binding and/or post-translational modifications. One such modification is ubiquitination, the covalent addition of ubiquitin (Ub) or polyubiquitin chains to target macromolecules for various cellular processes. Specific interactions between polyubiquitin chains and partner proteins, including hHR23B, NEMO, and UBQLN2, regulate condensate assembly or disassembly. Here, we used a library of designed polyubiquitin hubs and UBQLN2 as model systems for determining the driving forces of ligand-mediated phase transitions. Perturbations to the UBQLN2-binding surface of Ub or deviations from the optimal spacing between Ub units reduce the ability of hubs to modulate UBQLN2 phase behavior. By developing an analytical model that accurately described the effects of different hubs on UBQLN2 phase diagrams, we determined that introduction of Ub to UBQLN2 condensates incurs a significant inclusion energetic penalty. This penalty antagonizes the ability of polyUb hubs to scaffold multiple UBQLN2 molecules and cooperatively amplify phase separation. Importantly, the extent to which polyubiquitin hubs can promote UBQLN2 phase separation are encoded in the spacings between Ub units as found for naturally-occurring chains of different linkages and designed chains of different architectures, thus illustrating how the ubiquitin code regulates functionality via the emergent properties of the condensate. We expect our findings to extend to other condensates necessitating the consideration of ligand properties, including concentration, valency, affinity, and spacing between binding sites in studies and designs of condensates.
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Affiliation(s)
| | - Thuy P. Dao
- Departments of Biology and Chemistry, Syracuse University, Syracuse, NY 13244, USA
| | - Suzanne E. Enos
- Departments of Biology and Chemistry, Syracuse University, Syracuse, NY 13244, USA
| | - Antara Chaudhuri
- Departments of Biology and Chemistry, Syracuse University, Syracuse, NY 13244, USA
| | - Jeremy D. Schmit
- Department of Physics, Kansas State University, Manhattan, KS 66506, USA
| | - Carlos A. Castañeda
- Departments of Biology and Chemistry, Syracuse University, Syracuse, NY 13244, USA
- Interdisciplinary Neuroscience Program, Syracuse University, Syracuse, NY 13244, USA
- BioInspired Institute, Syracuse University, Syracuse, NY 13244, USA
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21
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Ramirez LM, Zweckstetter M. Molecular-level interplay between intrinsically disordered clients and Hsp90. Curr Opin Chem Biol 2023; 74:102304. [PMID: 37068388 DOI: 10.1016/j.cbpa.2023.102304] [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: 01/31/2023] [Revised: 03/13/2023] [Accepted: 03/15/2023] [Indexed: 04/19/2023]
Abstract
Proteostasis is maintained by a network of molecular chaperones, a prominent member of which is the 90-kilodalton heat shock protein Hsp90. The chaperone function of Hsp90 has been extensively reviewed previously, emphasizing its ATPase activity and remodeling of folded client proteins. Experimental evidence implicating Hsp90 in neurodegenerative diseases has bolstered interest in the noncanonical chaperoning of intrinsically disordered protein (IDPs), however the interplay between Hsp90 and its disordered clients remains poorly understood. In this review we describe recent advances that have contributed to our understanding of the intricate mechanisms characterizing Hsp90-mediated chaperoning of the IDPs tau and α-synuclein and survey emerging insights into the modulation of the chaperone-client interplay in the context of neurodegeneration.
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Affiliation(s)
- Lisa Marie Ramirez
- German Center for Neurodegenerative Diseases (DZNE), Von-Siebold-Str. 3a, 37075 Gӧttingen, Germany
| | - Markus Zweckstetter
- German Center for Neurodegenerative Diseases (DZNE), Von-Siebold-Str. 3a, 37075 Gӧttingen, Germany; Department for NMR-based Structural Biology, Max Planck Institute for Multidisciplinary Sciences, Am Fassberg 11, 37077 Gӧttingen, Germany.
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22
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Protein-RNA interactions: from mass spectrometry to drug discovery. Essays Biochem 2023; 67:175-186. [PMID: 36866608 PMCID: PMC10070478 DOI: 10.1042/ebc20220177] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2022] [Revised: 01/25/2023] [Accepted: 01/26/2023] [Indexed: 03/04/2023]
Abstract
Proteins and RNAs are fundamental parts of biological systems, and their interactions affect many essential cellular processes. Therefore, it is crucial to understand at a molecular and at a systems level how proteins and RNAs form complexes and mutually affect their functions. In the present mini-review, we will first provide an overview of different mass spectrometry (MS)-based methods to study the RNA-binding proteome (RBPome), most of which are based on photochemical cross-linking. As we will show, some of these methods are also able to provide higher-resolution information about binding sites, which are important for the structural characterisation of protein-RNA interactions. In addition, classical structural biology techniques such as nuclear magnetic resonance (NMR) spectroscopy and biophysical methods such as electron paramagnetic resonance (EPR) spectroscopy and fluorescence-based methods contribute to a detailed understanding of the interactions between these two classes of biomolecules. We will discuss the relevance of such interactions in the context of the formation of membrane-less organelles (MLOs) by liquid-liquid phase separation (LLPS) processes and their emerging importance as targets for drug discovery.
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23
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Li Y, Chen T, You K, Peng T, Li T. Sequence determinants and solution conditions underlying liquid to solid phase transition. Am J Physiol Cell Physiol 2023; 324:C236-C246. [PMID: 36503242 DOI: 10.1152/ajpcell.00280.2022] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Life consists of numberless functional biomolecules that exist in various states. Besides well-dissolved phases, biomolecules especially proteins and nucleic acids can form liquid droplets through liquid-liquid phase separation (LLPS). Stronger interactions promote a solid-like state of biomolecular condensates, which are also formerly referred to as detergent-insoluble aggregates. Solid-like condensates exist in vivo physiologically and pathologically, and their formation has not been fully understood. Recently, more and more research has proven that liquid to solid phase transition (LST) is an essential way to form solid condensates. In this review, we summarized the regions in the sequence that have different impacts on phase transition and emphasized that the LST is affected by its sequence characteristics. Moreover, increasing evidence unveiled that LST is affected by various solution conditions. We discussed solution conditions like protein concentration, pH, ATP, ions, and small molecules in a solution. Methods have been established to study these solid phase components. Here, we summarized low-throughput experimental techniques and high-throughput omics methods in the study of the LST.
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Affiliation(s)
- Yuxuan Li
- Department of Biomedical Informatics, School of Basic Medical Sciences, Peking University Health Science Center, Beijing, China.,Key Laboratory for Neuroscience, Ministry of Education/National Health Commission of China, Peking University, Beijing, China
| | - Taoyu Chen
- Department of Biomedical Informatics, School of Basic Medical Sciences, Peking University Health Science Center, Beijing, China.,Key Laboratory for Neuroscience, Ministry of Education/National Health Commission of China, Peking University, Beijing, China
| | - Kaiqing You
- Department of Biomedical Informatics, School of Basic Medical Sciences, Peking University Health Science Center, Beijing, China.,Happy Life Technology, Beijing, China
| | - Tao Peng
- Happy Life Technology, Beijing, China
| | - Tingting Li
- Department of Biomedical Informatics, School of Basic Medical Sciences, Peking University Health Science Center, Beijing, China.,Key Laboratory for Neuroscience, Ministry of Education/National Health Commission of China, Peking University, Beijing, China
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24
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Tani I, Oikawa Y, Doi S, Janairo JIB, Kamada R, Sakaguchi K. Ribosomal protein uL30 undergoes phase separation with nucleophosmin and regulates nucleolar formation in the absence of RNA. Biochem Biophys Res Commun 2023; 642:35-40. [PMID: 36543022 DOI: 10.1016/j.bbrc.2022.12.041] [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: 12/02/2022] [Accepted: 12/14/2022] [Indexed: 12/23/2022]
Abstract
The nucleolus is a membrane-less structure that exists in the nucleus of cells and plays a crucial role in ribosome biogenesis. It is known to be formed through liquid-liquid phase separation (LLPS) caused by the interaction of various nucleolar proteins and nucleic acids. Recently, many studies on LLPS with nucleolar proteins in the presence of RNA showed the importance of electrostatic interactions and cation-pi interactions among RNA and intrinsically disordered regions of proteins. However, it is reported that the initiation of nucleolar formation is RNA polymerase I-independent. The mechanism of nucleolar formation in the early stage remains obscure. In this study, we showed for the first time that the ribosomal protein uL30 and a major nucleolar protein, nucleophosmin (NPM) formed liquid droplets in vitro in the absence of RNA. The liquid droplet formation with uL30 and NPM may be derived from the interaction between the basic regions of uL30 and acidic regions of the oligomeric NPM. The knockdown of uL30 in cells significantly reduced the number of nucleoli, while it did not alter the protein level of NPM. The results showed that LLPS and nucleolar formation were affected by changes in uL30 levels. Our results suggest that the protein-protein interaction between nucleolar proteins may play an important role in nucleolar formation in the early stages when the rRNA content is very low.
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Affiliation(s)
- Itsumi Tani
- Department of Chemistry, Faculty of Science, Hokkaido University, Sapporo, 060-0810, Japan
| | - Yui Oikawa
- Department of Chemistry, Faculty of Science, Hokkaido University, Sapporo, 060-0810, Japan
| | - Seiyo Doi
- Department of Chemistry, Faculty of Science, Hokkaido University, Sapporo, 060-0810, Japan
| | - Jose Isagani B Janairo
- Department of Biology, College of Science, De La Salle University, Manila, 0922, Philippines
| | - Rui Kamada
- Department of Chemistry, Faculty of Science, Hokkaido University, Sapporo, 060-0810, Japan
| | - Kazuyasu Sakaguchi
- Department of Chemistry, Faculty of Science, Hokkaido University, Sapporo, 060-0810, Japan.
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25
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Mazarakos K, Qin S, Zhou HX. Calculating Binodals and Interfacial Tension of Phase-Separated Condensates from Molecular Simulations with Finite-Size Corrections. Methods Mol Biol 2023; 2563:1-35. [PMID: 36227466 PMCID: PMC9577455 DOI: 10.1007/978-1-0716-2663-4_1] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
We illustrate three methods for calculating the binodals of phase-separated condensates from molecular simulations. Because molecular simulations can only be carried out for small system sizes, correction for finite sizes may be required for making direct comparison between calculated results and experimental data. We first summarize the three methods and then present detailed implementation of each method on a Lennard-Jones fluid. In the first method, chemical potentials are calculated over a range of particle densities in canonical-ensemble simulations; the densities of the dilute and dense phases at the given temperature are then found by a Maxwell equal-area construction. In Gibbs-ensemble Monte Carlo, the exchange between separated dilute and dense phases is simulated to obtain their densities. Lastly, slab-geometry molecular dynamics simulations model the dilute and dense phases in coexistence and yield not only their densities but also their interfacial tension. The three types of simulations are carried out for a range of system sizes, and the results are scaled to generate the binodals corrected for finite system sizes. Size-corrected interfacial tension is also produced from slab-geometry molecular dynamics simulations.
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Affiliation(s)
| | - Sanbo Qin
- Department of Chemistry, University of Illinois at Chicago, Chicago, IL, USA
| | - Huan-Xiang Zhou
- Department of Physics, University of Illinois at Chicago, Chicago, IL, USA.
- Department of Chemistry, University of Illinois at Chicago, Chicago, IL, USA.
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26
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A mini-review on bio-inspired polymer self-assembly: single-component and interactive polymer systems. Emerg Top Life Sci 2022; 6:593-607. [PMID: 36254846 DOI: 10.1042/etls20220057] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2022] [Revised: 09/17/2022] [Accepted: 09/29/2022] [Indexed: 12/30/2022]
Abstract
Biology demonstrates meticulous ways to control biomaterials self-assemble into ordered and disordered structures to carry out necessary bioprocesses. Empowering the synthetic polymers to self-assemble like biomaterials is a hallmark of polymer physics studies. Unlike protein engineering, polymer science demystifies self-assembly by purposely embedding particular functional groups into the backbone of the polymer while isolating others. The polymer field has now entered an era of advancing materials design by mimicking nature to a very large extend. For example, we can make sequence-specific polymers to study highly ordered mesostructures similar to studying proteins, and use charged polymers to study liquid-liquid phase separation as in membraneless organelles. This mini-review summarizes recent advances in studying self-assembly using bio-inspired strategies on single-component and multi-component systems. Sequence-defined techniques are used to make on-demand hybrid materials to isolate the effects of chirality and chemistry in synthetic block copolymer self-assembly. In the meantime, sequence patterning leads to more hierarchical assemblies comprised of only hydrophobic and hydrophilic comonomers. The second half of the review discusses complex coacervates formed as a result of the associative charge interactions of oppositely charged polyelectrolytes. The tunable phase behavior and viscoelasticity are unique in studying liquid macrophase separation because the slow polymer relaxation comes primarily from charge interactions. Studies of bio-inspired polymer self-assembly significantly impact how we optimize user-defined materials on a molecular level.
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27
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Handa T, Kundu D, Dubey VK. Perspectives on evolutionary and functional importance of intrinsically disordered proteins. Int J Biol Macromol 2022; 224:243-255. [DOI: 10.1016/j.ijbiomac.2022.10.120] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2022] [Revised: 10/08/2022] [Accepted: 10/10/2022] [Indexed: 11/05/2022]
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28
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A novel lncRNA MTAR1 promotes cancer development through IGF2BPs mediated post-transcriptional regulation of c-MYC. Oncogene 2022; 41:4736-4753. [DOI: 10.1038/s41388-022-02464-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2022] [Revised: 08/24/2022] [Accepted: 08/31/2022] [Indexed: 11/09/2022]
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29
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Vazquez DS, Toledo PL, Gianotti AR, Ermácora MR. Protein conformation and biomolecular condensates. Curr Res Struct Biol 2022; 4:285-307. [PMID: 36164646 PMCID: PMC9508354 DOI: 10.1016/j.crstbi.2022.09.004] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2022] [Revised: 09/08/2022] [Accepted: 09/13/2022] [Indexed: 10/27/2022] Open
Abstract
Protein conformation and cell compartmentalization are fundamental concepts and subjects of vast scientific endeavors. In the last two decades, we have witnessed exciting advances that unveiled the conjunction of these concepts. An avalanche of studies highlighted the central role of biomolecular condensates in membraneless subcellular compartmentalization that permits the spatiotemporal organization and regulation of myriads of simultaneous biochemical reactions and macromolecular interactions. These studies have also shown that biomolecular condensation, driven by multivalent intermolecular interactions, is mediated by order-disorder transitions of protein conformation and by protein domain architecture. Conceptually, protein condensation is a distinct level in protein conformational landscape in which collective folding of large collections of molecules takes place. Biomolecular condensates arise by the physical process of phase separation and comprise a variety of bodies ranging from membraneless organelles to liquid condensates to solid-like conglomerates, spanning lengths from mesoscopic clusters (nanometers) to micrometer-sized objects. In this review, we summarize and discuss recent work on the assembly, composition, conformation, material properties, thermodynamics, regulation, and functions of these bodies. We also review the conceptual framework for future studies on the conformational dynamics of condensed proteins in the regulation of cellular processes.
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Affiliation(s)
- Diego S. Vazquez
- Departamento de Ciencia y Tecnología, Universidad Nacional de Quilmes and Grupo de Biología Estructural y Biotecnología, IMBICE, CONICET, Universidad Nacional de Quilmes, Argentina
| | - Pamela L. Toledo
- Departamento de Ciencia y Tecnología, Universidad Nacional de Quilmes and Grupo de Biología Estructural y Biotecnología, IMBICE, CONICET, Universidad Nacional de Quilmes, Argentina
| | - Alejo R. Gianotti
- Departamento de Ciencia y Tecnología, Universidad Nacional de Quilmes and Grupo de Biología Estructural y Biotecnología, IMBICE, CONICET, Universidad Nacional de Quilmes, Argentina
| | - Mario R. Ermácora
- Departamento de Ciencia y Tecnología, Universidad Nacional de Quilmes and Grupo de Biología Estructural y Biotecnología, IMBICE, CONICET, Universidad Nacional de Quilmes, Argentina
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30
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Molecular mechanism for the synchronized electrostatic coacervation and co-aggregation of alpha-synuclein and tau. Nat Commun 2022; 13:4586. [PMID: 35933508 PMCID: PMC9357037 DOI: 10.1038/s41467-022-32350-9] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2022] [Accepted: 07/26/2022] [Indexed: 01/05/2023] Open
Abstract
Amyloid aggregation of α-synuclein (αS) is the hallmark of Parkinson’s disease and other synucleinopathies. Recently, Tau protein, generally associated with Alzheimer’s disease, has been linked to αS pathology and observed to co-localize in αS-rich disease inclusions, although the molecular mechanisms for the co-aggregation of both proteins remain elusive. We report here that αS phase-separates into liquid condensates by electrostatic complex coacervation with positively charged polypeptides such as Tau. Condensates undergo either fast gelation or coalescence followed by slow amyloid aggregation depending on the affinity of αS for the poly-cation and the rate of valence exhaustion of the condensate network. By combining a set of advanced biophysical techniques, we have been able to characterize αS/Tau liquid-liquid phase separation and identified key factors that lead to the formation of hetero-aggregates containing both proteins in the interior of the liquid protein condensates. Here, the authors report that α-synuclein phase-separates into liquid condensates with positively charged polypeptides such as Tau. The condensates undergo different maturation processes, including the formation of α-synuclein/Tau amyloid hetero-aggregates inside the condensates.
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31
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Yao Y, Wang W, Chen C. Mechanisms of phase-separation-mediated cGAS activation revealed by dcFCCS. PNAS NEXUS 2022; 1:pgac109. [PMID: 36741445 PMCID: PMC9896928 DOI: 10.1093/pnasnexus/pgac109] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/07/2022] [Accepted: 07/02/2022] [Indexed: 02/07/2023]
Abstract
Cyclic GMP-AMP synthase (cGAS), as a DNA sensor, plays an important role in cGAS-STING pathway, which further induces expression of type I interferon as the innate immune response. Previous studies reported that liquid-liquid phase separation (LLPS) driven by cGAS and long DNA is essential to promote catalytic activity of cGAS to produce a second messenger, cyclic GMP-AMP (cGAMP). However, the molecular mechanism of LLPS promoting cGAS activity is still unclear. Here, we applied dual-color fluorescence cross-correlation spectroscopy (dcFCCS), a highly sensitive and quantitative method, to characterize phase separation driven by cGAS and DNA from miscible individual molecule to micronscale. Thus, we captured nanoscale condensates formed by cGAS at close-to-physiological concentration and quantified their sizes, molecular compositions and binding affinities within condensates. Our results pinpointed that interactions between DNA and cGAS at DNA binding sites A, B, and C and the dimerization of cGAS are the fundamental molecular basis to fully activate cGAS in vitro. Due to weak binding constants of these sites, endogenous cGAS cannot form stable interactions at these sites, leading to no activity in the absence of LLPS. Phase separation of cGAS and DNA enriches cGAS and DNA by 2 to 3 orders of magnitude to facilitate these interactions among cGAS and DNA and to promote cGAS activity as an on/off switch. Our discoveries not only shed lights on the molecular mechanisms of phase-separation-mediated cGAS activation, but also guided us to engineer a cGAS fusion, which can be activated by 15 bp short DNA without LLPS.
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Affiliation(s)
- Yirong Yao
- School of Life Sciences, Beijing Advanced Innovation Center for Structural Biology, Beijing Frontier Research Center of Biological Structure, Tsinghua University, Beijing, 100084, China
| | - Wenjuan Wang
- School of Life Sciences, Technology Center for Protein Sciences, Tsinghua University, Beijing, 100084, China
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32
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Gupta A, Dey S, Hicks A, Zhou HX. Artificial intelligence guided conformational mining of intrinsically disordered proteins. Commun Biol 2022; 5:610. [PMID: 35725761 PMCID: PMC9209487 DOI: 10.1038/s42003-022-03562-y] [Citation(s) in RCA: 22] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2021] [Accepted: 06/07/2022] [Indexed: 12/29/2022] Open
Abstract
Artificial intelligence recently achieved the breakthrough of predicting the three-dimensional structures of proteins. The next frontier is presented by intrinsically disordered proteins (IDPs), which, representing 30% to 50% of proteomes, readily access vast conformational space. Molecular dynamics (MD) simulations are promising in sampling IDP conformations, but only at extremely high computational cost. Here, we developed generative autoencoders that learn from short MD simulations and generate full conformational ensembles. An encoder represents IDP conformations as vectors in a reduced-dimensional latent space. The mean vector and covariance matrix of the training dataset are calculated to define a multivariate Gaussian distribution, from which vectors are sampled and fed to a decoder to generate new conformations. The ensembles of generated conformations cover those sampled by long MD simulations and are validated by small-angle X-ray scattering profile and NMR chemical shifts. This work illustrates the vast potential of artificial intelligence in conformational mining of IDPs.
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Affiliation(s)
- Aayush Gupta
- grid.185648.60000 0001 2175 0319Department of Chemistry, University of Illinois at Chicago, Chicago, IL 60607 USA
| | - Souvik Dey
- grid.185648.60000 0001 2175 0319Department of Chemistry, University of Illinois at Chicago, Chicago, IL 60607 USA
| | - Alan Hicks
- grid.185648.60000 0001 2175 0319Department of Chemistry, University of Illinois at Chicago, Chicago, IL 60607 USA
| | - Huan-Xiang Zhou
- grid.185648.60000 0001 2175 0319Department of Chemistry, University of Illinois at Chicago, Chicago, IL 60607 USA ,grid.185648.60000 0001 2175 0319Department of Physics, University of Illinois at Chicago, Chicago, IL 60607 USA
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33
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Structure-dependent recruitment and diffusion of guest proteins in liquid droplets of FUS. Sci Rep 2022; 12:7101. [PMID: 35501371 PMCID: PMC9061845 DOI: 10.1038/s41598-022-11177-w] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2022] [Accepted: 04/19/2022] [Indexed: 12/26/2022] Open
Abstract
Liquid droplets of a host protein, formed by liquid–liquid phase separation, recruit guest proteins and provide functional fields. Recruitment into p53 droplets is similar between disordered and folded guest proteins, whereas the diffusion of guest proteins inside droplets depends on their structural types. In this study, to elucidate how the recruitment and diffusion properties of guest proteins are affected by a host protein, we characterized the properties of guest proteins in fused in sarcoma (FUS) droplets using single-molecule fluorescence microscopy in comparison with p53 droplets. Unlike p53 droplets, disordered guest proteins were recruited into FUS droplets more efficiently than folded guest proteins, suggesting physical exclusion of the folded proteins from the small voids of the droplet. The recruitment did not appear to depend on the physical parameters (electrostatic or cation–π) of guests, implying that molecular size exclusion limits intermolecular interaction-assisted uptake. The diffusion of disordered guest proteins was comparable to that of the host FUS, whereas that of folded proteins varied widely, similar to the results for host p53. The scaling exponent of diffusion highlights the molecular sieving of large folded proteins in droplets. Finally, we proposed a molecular recruitment and diffusion model for guest proteins in FUS droplets.
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34
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Mazarakos K, Zhou HX. Multiphase Organization Is a Second Phase Transition Within Multi-Component Biomolecular Condensates. J Chem Phys 2022; 156:191104. [DOI: 10.1063/5.0088004] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
We present a mean-field theoretical model, along with molecular dynamics simulations, to show that the multiphase organization of multi-component condensates is a second phase transition. Whereas the first phase transition that leads to the separation of condensates from the bulk phase is driven by overall attraction among the macromolecular components, the second phase transition can be driven by the disparity in strength between self and cross-species attraction. At a fixed level of disparity in interaction strengths, both of the phase transitions can be observed by decreasing temperature, leading first to the separation of condensates from the bulk phase and then to component demixing inside condensates. The existence of a critical temperature for demixing and predicted binodals are verified by molecular dynamics simulations of model mixtures.
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Affiliation(s)
| | - Huan-Xiang Zhou
- Department of Chemistry and Department of Physics, University of Illinois at Chicago, United States of America
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35
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Antifeeva IA, Fonin AV, Fefilova AS, Stepanenko OV, Povarova OI, Silonov SA, Kuznetsova IM, Uversky VN, Turoverov KK. Liquid-liquid phase separation as an organizing principle of intracellular space: overview of the evolution of the cell compartmentalization concept. Cell Mol Life Sci 2022; 79:251. [PMID: 35445278 PMCID: PMC11073196 DOI: 10.1007/s00018-022-04276-4] [Citation(s) in RCA: 30] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2021] [Revised: 03/24/2022] [Accepted: 03/27/2022] [Indexed: 12/14/2022]
Abstract
At the turn of the twenty-first century, fundamental changes took place in the understanding of the structure and function of proteins and then in the appreciation of the intracellular space organization. A rather mechanistic model of the organization of living matter, where the function of proteins is determined by their rigid globular structure, and the intracellular processes occur in rigidly determined compartments, was replaced by an idea that highly dynamic and multifunctional "soft matter" lies at the heart of all living things. According this "new view", the most important role in the spatio-temporal organization of the intracellular space is played by liquid-liquid phase transitions of biopolymers. These self-organizing cellular compartments are open dynamic systems existing at the edge of chaos. They are characterized by the exceptional structural and compositional dynamics, and their multicomponent nature and polyfunctionality provide means for the finely tuned regulation of various intracellular processes. Changes in the external conditions can cause a disruption of the biogenesis of these cellular bodies leading to the irreversible aggregation of their constituent proteins, followed by the transition to a gel-like state and the emergence of amyloid fibrils. This work represents a historical overview of changes in our understanding of the intracellular space compartmentalization. It also reflects methodological breakthroughs that led to a change in paradigms in this area of science and discusses modern ideas about the organization of the intracellular space. It is emphasized here that the membrane-less organelles have to combine a certain resistance to the changes in their environment and, at the same time, show high sensitivity to the external signals, which ensures the normal functioning of the cell.
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Affiliation(s)
- Iuliia A Antifeeva
- Laboratory of Structural Dynamics, Stability and Folding of Proteins, Institute of Cytology, Russian Academy of Sciences, Tikhoretsky Av., 4, St. Petersburg, 194064, Russia
| | - Alexander V Fonin
- Laboratory of Structural Dynamics, Stability and Folding of Proteins, Institute of Cytology, Russian Academy of Sciences, Tikhoretsky Av., 4, St. Petersburg, 194064, Russia
| | - Anna S Fefilova
- Laboratory of Structural Dynamics, Stability and Folding of Proteins, Institute of Cytology, Russian Academy of Sciences, Tikhoretsky Av., 4, St. Petersburg, 194064, Russia
| | - Olesya V Stepanenko
- Laboratory of Structural Dynamics, Stability and Folding of Proteins, Institute of Cytology, Russian Academy of Sciences, Tikhoretsky Av., 4, St. Petersburg, 194064, Russia
| | - Olga I Povarova
- Laboratory of Structural Dynamics, Stability and Folding of Proteins, Institute of Cytology, Russian Academy of Sciences, Tikhoretsky Av., 4, St. Petersburg, 194064, Russia
| | - Sergey A Silonov
- Laboratory of Structural Dynamics, Stability and Folding of Proteins, Institute of Cytology, Russian Academy of Sciences, Tikhoretsky Av., 4, St. Petersburg, 194064, Russia
| | - Irina M Kuznetsova
- Laboratory of Structural Dynamics, Stability and Folding of Proteins, Institute of Cytology, Russian Academy of Sciences, Tikhoretsky Av., 4, St. Petersburg, 194064, Russia
| | - Vladimir N Uversky
- Department of Molecular Medicine and USF Health Byrd Alzheimer's Research Institute, Morsani College of Medicine, University of South Florida, 12901 Bruce B. Downs Blvd. MDC07, Tampa, FL, 33612, USA.
| | - Konstantin K Turoverov
- Laboratory of Structural Dynamics, Stability and Folding of Proteins, Institute of Cytology, Russian Academy of Sciences, Tikhoretsky Av., 4, St. Petersburg, 194064, Russia.
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36
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Abstract
Continuously renewing the proteome, translation is exquisitely controlled by a number of dedicated factors that interact with the ribosome. The RNA helicase DDX3 belonging to the DEAD box family has emerged as one of the critical regulators of translation, the failure of which is frequently observed in a wide range of proliferative, degenerative, and infectious diseases in humans. DDX3 unwinds double-stranded RNA molecules with coupled ATP hydrolysis and thereby remodels complex RNA structures present in various protein-coding and noncoding RNAs. By interacting with specific features on messenger RNAs (mRNAs) and 18S ribosomal RNA (rRNA), DDX3 facilitates translation, while repressing it under certain conditions. We review recent findings underlying these properties of DDX3 in diverse modes of translation, such as cap-dependent and cap-independent translation initiation, usage of upstream open reading frames, and stress-induced ribonucleoprotein granule formation. We further discuss how disease-associated DDX3 variants alter the translation landscape in the cell.
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Affiliation(s)
- Joon Tae Park
- Division of Life Sciences, Incheon National University, Incheon 22012, Korea
| | - Sekyung Oh
- Department of Medical Science, Catholic Kwandong University College of Medicine, Incheon 22711, Korea
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37
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Abstract
Although long noncoding RNAs (lncRNAs) are generally expressed at low levels, emerging evidence has revealed that many play important roles in gene regulation by a variety of mechanisms as they engage with proteins. Given that the abundance of proteins often greatly exceeds that of their interacting lncRNAs, quantification of the relative abundance, or even the exact stoichiometry in some cases, within lncRNA-protein complexes is helpful for understanding of the mechanism(s) of action of lncRNAs. We discuss methods used to examine lncRNA and protein expression at the single cell, subcellular, and suborganelle levels, the average and local lncRNA concentration in cells, as well as how lncRNAs can modulate the functions of their interacting proteins even at a low stoichiometric concentration.
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Affiliation(s)
- Man Wu
- State Key Laboratory of Molecular Biology, Shanghai Key Laboratory of Molecular Andrology, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai 200031, China
| | - Liang-Zhong Yang
- State Key Laboratory of Molecular Biology, Shanghai Key Laboratory of Molecular Andrology, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai 200031, China
| | - Ling-Ling Chen
- State Key Laboratory of Molecular Biology, Shanghai Key Laboratory of Molecular Andrology, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai 200031, China
- School of Life Science and Technology, ShanghaiTech University, Shanghai 201210, China
- School of Life Science, Hangzhou Institute for Advanced Study, University of Chinese Academy of Sciences, Hangzhou 310024, China
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38
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Samanta N, Ribeiro SS, Becker M, Laborie E, Pollak R, Timr S, Sterpone F, Ebbinghaus S. Sequestration of Proteins in Stress Granules Relies on the In-Cell but Not the In Vitro Folding Stability. J Am Chem Soc 2021; 143:19909-19918. [PMID: 34788540 DOI: 10.1021/jacs.1c09589] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
Stress granules (SGs) are among the most studied membraneless organelles that form upon heat stress (HS) to sequester unfolded, misfolded, or aggregated protein, supporting protein quality control (PQC) clearance. The folding states that are primarily associated with SGs, as well as the function of the phase separated environment in adjusting the energy landscapes, remain unknown. Here, we investigate the association of superoxide dismutase 1 (SOD1) proteins with different folding stabilities and aggregation propensities with condensates in cells, in vitro and by simulation. We find that irrespective of aggregation the folding stability determines the association of SOD1 with SGs in cells. In vitro and in silico experiments however suggest that the increased flexibility of the unfolded state constitutes only a minor driving force to associate with the dynamic biomolecular network of the condensate. Specific protein-protein interactions in the cytoplasm in comparison to SGs determine the partitioning of folding states between the respective phases during HS.
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Affiliation(s)
- Nirnay Samanta
- Institute of Physical and Theoretical Chemistry, TU Braunschweig, Rebenring 56, D-38106 Braunschweig, Germany
| | - Sara S Ribeiro
- Institute of Physical and Theoretical Chemistry, TU Braunschweig, Rebenring 56, D-38106 Braunschweig, Germany
| | - Mailin Becker
- Institute of Physical and Theoretical Chemistry, TU Braunschweig, Rebenring 56, D-38106 Braunschweig, Germany
| | - Emeline Laborie
- CNRS Laboratoire de Biochimie Théorique, Institut de Biologie Physico-Chimique, Université Paris Denis Diderot, Sorbonne Paris Cité, PSL Research University, 13 rue Pierre et Marie Curie, Paris 75005, France
| | - Roland Pollak
- Institute of Physical and Theoretical Chemistry, TU Braunschweig, Rebenring 56, D-38106 Braunschweig, Germany
| | - Stepan Timr
- CNRS Laboratoire de Biochimie Théorique, Institut de Biologie Physico-Chimique, Université Paris Denis Diderot, Sorbonne Paris Cité, PSL Research University, 13 rue Pierre et Marie Curie, Paris 75005, France.,J. Heyrovský Institute of Physical Chemistry, Czech Academy of Sciences, Dolejskova 2155/3, Prague 8 182 23, Czech Republic
| | - Fabio Sterpone
- CNRS Laboratoire de Biochimie Théorique, Institut de Biologie Physico-Chimique, Université Paris Denis Diderot, Sorbonne Paris Cité, PSL Research University, 13 rue Pierre et Marie Curie, Paris 75005, France
| | - Simon Ebbinghaus
- Institute of Physical and Theoretical Chemistry, TU Braunschweig, Rebenring 56, D-38106 Braunschweig, Germany
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39
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Starvation-induced proteasome assemblies in the nucleus link amino acid supply to apoptosis. Nat Commun 2021; 12:6984. [PMID: 34848715 PMCID: PMC8633328 DOI: 10.1038/s41467-021-27306-4] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2019] [Accepted: 11/09/2021] [Indexed: 11/15/2022] Open
Abstract
Eukaryotic cells have evolved highly orchestrated protein catabolic machineries responsible for the timely and selective disposal of proteins and organelles, thereby ensuring amino acid recycling. However, how protein degradation is coordinated with amino acid supply and protein synthesis has remained largely elusive. Here we show that the mammalian proteasome undergoes liquid-liquid phase separation in the nucleus upon amino acid deprivation. We termed these proteasome condensates SIPAN (Starvation-Induced Proteasome Assemblies in the Nucleus) and show that these are a common response of mammalian cells to amino acid deprivation. SIPAN undergo fusion events, rapidly exchange proteasome particles with the surrounding milieu and quickly dissolve following amino acid replenishment. We further show that: (i) SIPAN contain K48-conjugated ubiquitin, (ii) proteasome inhibition accelerates SIPAN formation, (iii) deubiquitinase inhibition prevents SIPAN resolution and (iv) RAD23B proteasome shuttling factor is required for SIPAN formation. Finally, SIPAN formation is associated with decreased cell survival and p53-mediated apoptosis, which might contribute to tissue fitness in diverse pathophysiological conditions.
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40
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Lyonnais S, Sadiq SK, Lorca-Oró C, Dufau L, Nieto-Marquez S, Escribà T, Gabrielli N, Tan X, Ouizougun-Oubari M, Okoronkwo J, Reboud-Ravaux M, Gatell JM, Marquet R, Paillart JC, Meyerhans A, Tisné C, Gorelick RJ, Mirambeau G. The HIV-1 Nucleocapsid Regulates Its Own Condensation by Phase-Separated Activity-Enhancing Sequestration of the Viral Protease during Maturation. Viruses 2021; 13:v13112312. [PMID: 34835118 PMCID: PMC8625067 DOI: 10.3390/v13112312] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2021] [Revised: 11/09/2021] [Accepted: 11/11/2021] [Indexed: 02/07/2023] Open
Abstract
A growing number of studies indicate that mRNAs and long ncRNAs can affect protein populations by assembling dynamic ribonucleoprotein (RNP) granules. These phase-separated molecular ‘sponges’, stabilized by quinary (transient and weak) interactions, control proteins involved in numerous biological functions. Retroviruses such as HIV-1 form by self-assembly when their genomic RNA (gRNA) traps Gag and GagPol polyprotein precursors. Infectivity requires extracellular budding of the particle followed by maturation, an ordered processing of ∼2400 Gag and ∼120 GagPol by the viral protease (PR). This leads to a condensed gRNA-NCp7 nucleocapsid and a CAp24-self-assembled capsid surrounding the RNP. The choreography by which all of these components dynamically interact during virus maturation is one of the missing milestones to fully depict the HIV life cycle. Here, we describe how HIV-1 has evolved a dynamic RNP granule with successive weak–strong–moderate quinary NC-gRNA networks during the sequential processing of the GagNC domain. We also reveal two palindromic RNA-binding triads on NC, KxxFxxQ and QxxFxxK, that provide quinary NC-gRNA interactions. Consequently, the nucleocapsid complex appears properly aggregated for capsid reassembly and reverse transcription, mandatory processes for viral infectivity. We show that PR is sequestered within this RNP and drives its maturation/condensation within minutes, this process being most effective at the end of budding. We anticipate such findings will stimulate further investigations of quinary interactions and emergent mechanisms in crowded environments throughout the wide and growing array of RNP granules.
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Affiliation(s)
- Sébastien Lyonnais
- Infectious Disease & AIDS Research Unit, Institut d’Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Villaroel 170, 08036 Barcelona, Spain; (C.L.-O.); (S.N.-M.); (T.E.); (N.G.); (X.T.); (M.O.-O.); (J.O.); (J.M.G.)
- Centre d’Etudes des Maladies Infectieuses et Pharmacologie Anti-Infectieuse (CEMIPAI), CNRS UAR 3725, Université de Montpellier, 1919 Route de Mende, CEDEX 05, 34293 Montpellier, France
- Correspondence: (S.L.); (S.K.S.); (G.M.)
| | - S. Kashif Sadiq
- Infection Biology Laboratory, Department of Experimental and Health Sciences (DCEXS), Universitat Pompeu Fabra, Carrer Doctor Aiguader 88, 08003 Barcelona, Spain;
- Molecular and Cellular Modeling Group, Heidelberg Institute for Theoretical Studies (HITS), Schloss-Wolfsbrunnenweg 35, 69118 Heidelberg, Germany
- Genome Biology Unit, European Molecular Biology Laboratory, Meyerhofstrasse 1, 69117 Heidelberg, Germany
- Correspondence: (S.L.); (S.K.S.); (G.M.)
| | - Cristina Lorca-Oró
- Infectious Disease & AIDS Research Unit, Institut d’Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Villaroel 170, 08036 Barcelona, Spain; (C.L.-O.); (S.N.-M.); (T.E.); (N.G.); (X.T.); (M.O.-O.); (J.O.); (J.M.G.)
| | - Laure Dufau
- Biological Adaptation and Ageing (B2A), CNRS UMR 8256 & INSERM ERL U1164, Institut de Biologie Paris-Seine (IBPS), Faculté des Sciences et d’Ingénierie (FSI), Sorbonne Université, 7 Quai St Bernard, CEDEX 05, 75252 Paris, France; (L.D.); (M.R.-R.)
| | - Sara Nieto-Marquez
- Infectious Disease & AIDS Research Unit, Institut d’Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Villaroel 170, 08036 Barcelona, Spain; (C.L.-O.); (S.N.-M.); (T.E.); (N.G.); (X.T.); (M.O.-O.); (J.O.); (J.M.G.)
| | - Tuixent Escribà
- Infectious Disease & AIDS Research Unit, Institut d’Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Villaroel 170, 08036 Barcelona, Spain; (C.L.-O.); (S.N.-M.); (T.E.); (N.G.); (X.T.); (M.O.-O.); (J.O.); (J.M.G.)
| | - Natalia Gabrielli
- Infectious Disease & AIDS Research Unit, Institut d’Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Villaroel 170, 08036 Barcelona, Spain; (C.L.-O.); (S.N.-M.); (T.E.); (N.G.); (X.T.); (M.O.-O.); (J.O.); (J.M.G.)
| | - Xiao Tan
- Infectious Disease & AIDS Research Unit, Institut d’Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Villaroel 170, 08036 Barcelona, Spain; (C.L.-O.); (S.N.-M.); (T.E.); (N.G.); (X.T.); (M.O.-O.); (J.O.); (J.M.G.)
- Biological Adaptation and Ageing (B2A), CNRS UMR 8256 & INSERM ERL U1164, Institut de Biologie Paris-Seine (IBPS), Faculté des Sciences et d’Ingénierie (FSI), Sorbonne Université, 7 Quai St Bernard, CEDEX 05, 75252 Paris, France; (L.D.); (M.R.-R.)
| | - Mohamed Ouizougun-Oubari
- Infectious Disease & AIDS Research Unit, Institut d’Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Villaroel 170, 08036 Barcelona, Spain; (C.L.-O.); (S.N.-M.); (T.E.); (N.G.); (X.T.); (M.O.-O.); (J.O.); (J.M.G.)
| | - Josephine Okoronkwo
- Infectious Disease & AIDS Research Unit, Institut d’Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Villaroel 170, 08036 Barcelona, Spain; (C.L.-O.); (S.N.-M.); (T.E.); (N.G.); (X.T.); (M.O.-O.); (J.O.); (J.M.G.)
| | - Michèle Reboud-Ravaux
- Biological Adaptation and Ageing (B2A), CNRS UMR 8256 & INSERM ERL U1164, Institut de Biologie Paris-Seine (IBPS), Faculté des Sciences et d’Ingénierie (FSI), Sorbonne Université, 7 Quai St Bernard, CEDEX 05, 75252 Paris, France; (L.D.); (M.R.-R.)
| | - José Maria Gatell
- Infectious Disease & AIDS Research Unit, Institut d’Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Villaroel 170, 08036 Barcelona, Spain; (C.L.-O.); (S.N.-M.); (T.E.); (N.G.); (X.T.); (M.O.-O.); (J.O.); (J.M.G.)
- Facultat de Medicina y Ciencias de la Salud, Universitat de Barcelona, Carrer de Casanova 143, 08036 Barcelona, Spain
| | - Roland Marquet
- Architecture et Réactivité de l’ARN, CNRS UPR 9002, Université de Strasbourg, 2 Allée Conrad Roentgen, 67000 Strasbourg, France; (R.M.); (J.-C.P.)
| | - Jean-Christophe Paillart
- Architecture et Réactivité de l’ARN, CNRS UPR 9002, Université de Strasbourg, 2 Allée Conrad Roentgen, 67000 Strasbourg, France; (R.M.); (J.-C.P.)
| | - Andreas Meyerhans
- Infection Biology Laboratory, Department of Experimental and Health Sciences (DCEXS), Universitat Pompeu Fabra, Carrer Doctor Aiguader 88, 08003 Barcelona, Spain;
- Institució Catalana de Recerca i Estudis Avançats (ICREA), Passeig de Lluís Companys 23, 08010 Barcelona, Spain
| | - Carine Tisné
- Expression Génétique Microbienne, CNRS UMR 8261, Institut de Biologie Physico-Chimique (IBPC), Université de Paris, 13 Rue Pierre et Marie Curie, 75005 Paris, France;
| | - Robert J. Gorelick
- AIDS and Cancer Virus Program, Leidos Biomedical Research, Inc., Frederick National Laboratory for Cancer Research, Frederick, MD 21701, USA;
| | - Gilles Mirambeau
- Infectious Disease & AIDS Research Unit, Institut d’Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Villaroel 170, 08036 Barcelona, Spain; (C.L.-O.); (S.N.-M.); (T.E.); (N.G.); (X.T.); (M.O.-O.); (J.O.); (J.M.G.)
- Biologie Intégrative des Organismes Marins (BIOM), CNRS UMR 7232, Observatoire Océanologique de Banyuls (OOB), Faculté des Sciences et d’Ingénierie (FSI), Sorbonne Université, 1 Avenue Pierre Fabre, 66650 Banyuls-sur-Mer, France
- Correspondence: (S.L.); (S.K.S.); (G.M.)
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41
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Smirnova EV, Rakitina TV, Ziganshin RH, Arapidi GP, Saratov GA, Kudriaeva AA, Belogurov AA. Comprehensive Atlas of the Myelin Basic Protein Interaction Landscape. Biomolecules 2021; 11:1628. [PMID: 34827627 PMCID: PMC8615356 DOI: 10.3390/biom11111628] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2021] [Revised: 10/27/2021] [Accepted: 10/29/2021] [Indexed: 12/22/2022] Open
Abstract
Intrinsically disordered myelin basic protein (MBP) is one of the key autoantigens in autoimmune neurodegeneration and multiple sclerosis particularly. MBP is highly positively charged and lacks distinct structure in solution and therefore its intracellular partners are still mostly enigmatic. Here we used combination of formaldehyde-induced cross-linking followed by immunoprecipitation and liquid chromatography-tandem mass spectrometry (LC-MS/MS) to elucidate the interaction network of MBP in mammalian cells and provide the list of potential MBP interacting proteins. Our data suggest that the largest group of MBP-interacting proteins belongs to cellular proteins involved in the protein translation machinery, as well as in the spatial and temporal regulation of translation. MBP interacts with core ribosomal proteins, RNA helicase Ddx28 and RNA-binding proteins STAU1, TDP-43, ADAR-1 and hnRNP A0, which are involved in various stages of RNA biogenesis and processing, including specific maintaining MBP-coding mRNA. Among MBP partners we identified CTNND1, which has previously been shown to be necessary for myelinating Schwann cells for cell-cell interactions and the formation of a normal myelin sheath. MBP binds proteins MAGEB2/D2 associated with neurotrophin receptor p75NTR, involved in pathways that promote neuronal survival and neuronal death. Finally, we observed that MBP interacts with RNF40-a component of heterotetrameric Rnf40/Rnf20 E3 ligase complex, recruited by Egr2, which is the central transcriptional regulator of peripheral myelination. Concluding, our data suggest that MBP may be more actively involved in myelination not only as a main building block but also as a self-regulating element.
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Affiliation(s)
- Evgeniya V. Smirnova
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, 117997 Moscow, Russia; (E.V.S.); (T.V.R.); (R.H.Z.); (G.P.A.); (G.A.S.); (A.A.K.)
| | - Tatiana V. Rakitina
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, 117997 Moscow, Russia; (E.V.S.); (T.V.R.); (R.H.Z.); (G.P.A.); (G.A.S.); (A.A.K.)
| | - Rustam H. Ziganshin
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, 117997 Moscow, Russia; (E.V.S.); (T.V.R.); (R.H.Z.); (G.P.A.); (G.A.S.); (A.A.K.)
| | - Georgij P. Arapidi
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, 117997 Moscow, Russia; (E.V.S.); (T.V.R.); (R.H.Z.); (G.P.A.); (G.A.S.); (A.A.K.)
- Federal Research and Clinical Center of Physical-Chemical Medicine of Federal Medical Biological Agency, 119435 Moscow, Russia
- Moscow Institute of Physics and Technology, National Research University, 141701 Dolgoprudny, Moscow Region, Russia
| | - George A. Saratov
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, 117997 Moscow, Russia; (E.V.S.); (T.V.R.); (R.H.Z.); (G.P.A.); (G.A.S.); (A.A.K.)
- Moscow Institute of Physics and Technology, National Research University, 141701 Dolgoprudny, Moscow Region, Russia
| | - Anna A. Kudriaeva
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, 117997 Moscow, Russia; (E.V.S.); (T.V.R.); (R.H.Z.); (G.P.A.); (G.A.S.); (A.A.K.)
| | - Alexey A. Belogurov
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, 117997 Moscow, Russia; (E.V.S.); (T.V.R.); (R.H.Z.); (G.P.A.); (G.A.S.); (A.A.K.)
- Department of Fundamental Medicine, Lomonosov Moscow State University, 117192 Moscow, Russia
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42
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Kershaw CJ, Nelson MG, Lui J, Bates CP, Jennings MD, Hubbard SJ, Ashe MP, Grant CM. Integrated multi-omics reveals common properties underlying stress granule and P-body formation. RNA Biol 2021; 18:655-673. [PMID: 34672913 PMCID: PMC8782181 DOI: 10.1080/15476286.2021.1976986] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022] Open
Abstract
Non-membrane-bound compartments such as P-bodies (PBs) and stress granules (SGs) play important roles in the regulation of gene expression following environmental stresses. We have systematically and quantitatively determined the protein and mRNA composition of PBs and SGs formed before and after nutrient stress. We find that high molecular weight (HMW) complexes exist prior to glucose depletion that we propose may act as seeds for further condensation of proteins forming mature PBs and SGs. We identify an enrichment of proteins with low complexity and RNA binding domains, as well as long, structured mRNAs that are poorly translated following nutrient stress. Many proteins and mRNAs are shared between PBs and SGs including several multivalent RNA binding proteins that promote condensate interactions during liquid-liquid phase separation. We uncover numerous common protein and RNA components across PBs and SGs that support a complex interaction profile during the maturation of these biological condensates. These interaction networks represent a tuneable response to stress, highlighting previously unrecognized condensate heterogeneity. These studies therefore provide an integrated and quantitative understanding of the dynamic nature of key biological condensates.
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Affiliation(s)
- Christopher J Kershaw
- University of Manchester School of Biological Science, The University of Manchester Faculty of Biology Medicine and Health, Manchester, UK
| | - Michael G Nelson
- University of Manchester School of Biological Science, The University of Manchester Faculty of Biology Medicine and Health, Manchester, UK
| | - Jennifer Lui
- University of Manchester School of Biological Science, The University of Manchester Faculty of Biology Medicine and Health, Manchester, UK
| | - Christian P Bates
- University of Manchester School of Biological Science, The University of Manchester Faculty of Biology Medicine and Health, Manchester, UK
| | - Martin D Jennings
- University of Manchester School of Biological Science, The University of Manchester Faculty of Biology Medicine and Health, Manchester, UK
| | - Simon J Hubbard
- University of Manchester School of Biological Science, The University of Manchester Faculty of Biology Medicine and Health, Manchester, UK
| | - Mark P Ashe
- University of Manchester School of Biological Science, The University of Manchester Faculty of Biology Medicine and Health, Manchester, UK
| | - Chris M Grant
- University of Manchester School of Biological Science, The University of Manchester Faculty of Biology Medicine and Health, Manchester, UK
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43
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Nassar R, Dignon GL, Razban RM, Dill KA. The Protein Folding Problem: The Role of Theory. J Mol Biol 2021; 433:167126. [PMID: 34224747 PMCID: PMC8547331 DOI: 10.1016/j.jmb.2021.167126] [Citation(s) in RCA: 41] [Impact Index Per Article: 13.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2021] [Revised: 06/21/2021] [Accepted: 06/26/2021] [Indexed: 10/20/2022]
Abstract
The protein folding problem was first articulated as question of how order arose from disorder in proteins: How did the various native structures of proteins arise from interatomic driving forces encoded within their amino acid sequences, and how did they fold so fast? These matters have now been largely resolved by theory and statistical mechanics combined with experiments. There are general principles. Chain randomness is overcome by solvation-based codes. And in the needle-in-a-haystack metaphor, native states are found efficiently because protein haystacks (conformational ensembles) are funnel-shaped. Order-disorder theory has now grown to encompass a large swath of protein physical science across biology.
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Affiliation(s)
- Roy Nassar
- Laufer Center for Physical and Quantitative Biology, Stony Brook University, Stony Brook, NY, USA; Department of Chemistry, Stony Brook University, Stony Brook, NY, USA
| | - Gregory L Dignon
- Laufer Center for Physical and Quantitative Biology, Stony Brook University, Stony Brook, NY, USA
| | - Rostam M Razban
- Laufer Center for Physical and Quantitative Biology, Stony Brook University, Stony Brook, NY, USA
| | - Ken A Dill
- Laufer Center for Physical and Quantitative Biology, Stony Brook University, Stony Brook, NY, USA; Department of Chemistry, Stony Brook University, Stony Brook, NY, USA; Department of Physics and Astronomy, Stony Brook University, Stony Brook, NY, USA.
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44
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Kamagata K, Iwaki N, Hazra MK, Kanbayashi S, Banerjee T, Chiba R, Sakomoto S, Gaudon V, Castaing B, Takahashi H, Kimura M, Oikawa H, Takahashi S, Levy Y. Molecular principles of recruitment and dynamics of guest proteins in liquid droplets. Sci Rep 2021; 11:19323. [PMID: 34588591 PMCID: PMC8481498 DOI: 10.1038/s41598-021-98955-0] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2021] [Accepted: 09/16/2021] [Indexed: 11/10/2022] Open
Abstract
Despite the continuous discovery of host and guest proteins in membraneless organelles, complex host–guest interactions hinder the understanding of the molecular grammar governing liquid–liquid phase separation. In this study, we characterized the localization and dynamic properties of guest proteins in liquid droplets using single-molecule fluorescence microscopy. Eighteen guest proteins of different sizes, structures, and oligomeric states were examined in host p53 liquid droplets. Recruitment did not significantly depend on the structural properties of the guest proteins, but was moderately correlated with their length, total charge, and number of R and Y residues. In contrast, the diffusion of disordered guest proteins was comparable to that of host p53, whereas that of folded proteins varied widely. Molecular dynamics simulations suggest that folded proteins diffuse within the voids of the liquid droplet while interacting weakly with neighboring host proteins, whereas disordered proteins adapt their structures to form tight interactions with the host proteins. Our study provides insights into the key molecular principles of the localization and dynamics of guest proteins in liquid droplets.
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Affiliation(s)
- Kiyoto Kamagata
- Institute of Multidisciplinary Research for Advanced Materials, Tohoku University, Katahira 2-1-1, Aoba-ku, Sendai, 980-8577, Japan. .,Department of Chemistry, Graduate School of Science, Tohoku University, Sendai, 980-8578, Japan. .,Graduate School of Life Sciences, Tohoku University, Katahira 2-1-1, Aoba-ku, Sendai, 980-8577, Japan.
| | - Nanako Iwaki
- Institute of Multidisciplinary Research for Advanced Materials, Tohoku University, Katahira 2-1-1, Aoba-ku, Sendai, 980-8577, Japan.,Department of Chemistry, Graduate School of Science, Tohoku University, Sendai, 980-8578, Japan
| | - Milan Kumar Hazra
- Department of Structural Biology, Weizmann Institute of Science, 76100, Rehovot, Israel
| | - Saori Kanbayashi
- Institute of Multidisciplinary Research for Advanced Materials, Tohoku University, Katahira 2-1-1, Aoba-ku, Sendai, 980-8577, Japan
| | - Trishit Banerjee
- Institute of Multidisciplinary Research for Advanced Materials, Tohoku University, Katahira 2-1-1, Aoba-ku, Sendai, 980-8577, Japan.,Department of Chemistry, Graduate School of Science, Tohoku University, Sendai, 980-8578, Japan
| | - Rika Chiba
- Institute of Multidisciplinary Research for Advanced Materials, Tohoku University, Katahira 2-1-1, Aoba-ku, Sendai, 980-8577, Japan.,Graduate School of Life Sciences, Tohoku University, Katahira 2-1-1, Aoba-ku, Sendai, 980-8577, Japan
| | - Seiji Sakomoto
- Department of Synthetic Chemistry and Biological Chemistry, Graduate School of Engineering, Kyoto University, Katsura, Nishikyo-ku, Kyoto, 615-8510, Japan
| | - Virginie Gaudon
- Centre de Biophysique Moléculaire, CNRS, UPR4301, rue Charles Sadron, 45072, Orléans, France
| | - Bertrand Castaing
- Centre de Biophysique Moléculaire, CNRS, UPR4301, rue Charles Sadron, 45072, Orléans, France
| | - Hiroto Takahashi
- Institute of Multidisciplinary Research for Advanced Materials, Tohoku University, Katahira 2-1-1, Aoba-ku, Sendai, 980-8577, Japan
| | - Michiko Kimura
- Institute of Multidisciplinary Research for Advanced Materials, Tohoku University, Katahira 2-1-1, Aoba-ku, Sendai, 980-8577, Japan.,Graduate School of Life Sciences, Tohoku University, Katahira 2-1-1, Aoba-ku, Sendai, 980-8577, Japan
| | - Hiroyuki Oikawa
- Institute of Multidisciplinary Research for Advanced Materials, Tohoku University, Katahira 2-1-1, Aoba-ku, Sendai, 980-8577, Japan.,Department of Chemistry, Graduate School of Science, Tohoku University, Sendai, 980-8578, Japan.,Graduate School of Life Sciences, Tohoku University, Katahira 2-1-1, Aoba-ku, Sendai, 980-8577, Japan
| | - Satoshi Takahashi
- Institute of Multidisciplinary Research for Advanced Materials, Tohoku University, Katahira 2-1-1, Aoba-ku, Sendai, 980-8577, Japan.,Department of Chemistry, Graduate School of Science, Tohoku University, Sendai, 980-8578, Japan.,Graduate School of Life Sciences, Tohoku University, Katahira 2-1-1, Aoba-ku, Sendai, 980-8577, Japan
| | - Yaakov Levy
- Department of Structural Biology, Weizmann Institute of Science, 76100, Rehovot, Israel
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45
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Rana U, Brangwynne CP, Panagiotopoulos AZ. Phase separation vs aggregation behavior for model disordered proteins. J Chem Phys 2021; 155:125101. [PMID: 34598580 DOI: 10.1063/5.0060046] [Citation(s) in RCA: 33] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
Liquid-liquid phase separation (LLPS) is widely utilized by the cell to organize and regulate various biochemical processes. Although the LLPS of proteins is known to occur in a sequence-dependent manner, it is unclear how sequence properties dictate the nature of the phase transition and thereby influence condensed phase morphology. In this work, we have utilized grand canonical Monte Carlo simulations for a simple coarse-grained model of disordered proteins to systematically investigate how sequence distribution, sticker fraction, and chain length impact the formation of finite-size aggregates, which can preempt macroscopic phase separation for some sequences. We demonstrate that a normalized sequence charge decoration (SCD) parameter establishes a "soft" predictive criterion for distinguishing when a model protein undergoes macroscopic phase separation vs finite aggregation. Additionally, we find that this order parameter is strongly correlated with the critical density for phase separation, highlighting an unambiguous connection between sequence distribution and condensed phase density. Results obtained from an analysis of the order parameter reveal that at sufficiently long chain lengths, the vast majority of sequences are likely to phase separate. Our results suggest that classical LLPS should be the primary phase transition for disordered proteins when short-ranged attractive interactions dominate and suggest a possible reason behind recent findings of widespread phase separation throughout living cells.
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Affiliation(s)
- Ushnish Rana
- Department of Chemical and Biological Engineering, Princeton University, Princeton, New Jersey 08544, USA
| | - Clifford P Brangwynne
- Department of Chemical and Biological Engineering, Princeton University, Princeton, New Jersey 08544, USA
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46
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Yoneda M, Nakagawa T, Hattori N, Ito T. The nucleolus from a liquid droplet perspective. J Biochem 2021; 170:153-162. [PMID: 34358306 DOI: 10.1093/jb/mvab090] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2021] [Accepted: 07/27/2021] [Indexed: 11/14/2022] Open
Abstract
The nucleolus is a membrane-less organelle sequestered from the nucleus by liquid droplet formation through a liquid-liquid phase separation (LLPS). It plays important roles in cell homeostasis through its internal thermodynamic changes. Reversible nucleolar transitions between coalescence and dispersion are dependent on the concentrations, conformations, and interactions of its molecular liquid droplet-forming components, including DNA, RNA, and protein. The liquid droplet-like properties of the nucleolus enable its diverse dynamic roles. The liquid droplet formation mechanism, by which the nucleolus is sequestered from the nucleoplasm despite the absence of a membrane, explains a number of complex nucleolar functions.
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Affiliation(s)
- Mitsuhiro Yoneda
- Department of Biochemistry, Nagasaki University School of Medicine, Nagasaki, 852-8523, JAPAN.,Nagasaki University Graduate School of Biomedical Sciences, Nagasaki, 852-8523, JAPAN
| | - Takeya Nakagawa
- Department of Biochemistry, Nagasaki University School of Medicine, Nagasaki, 852-8523, JAPAN.,Nagasaki University Graduate School of Biomedical Sciences, Nagasaki, 852-8523, JAPAN
| | - Naoko Hattori
- Department of Biochemistry, Nagasaki University School of Medicine, Nagasaki, 852-8523, JAPAN.,Nagasaki University Graduate School of Biomedical Sciences, Nagasaki, 852-8523, JAPAN
| | - Takashi Ito
- Department of Biochemistry, Nagasaki University School of Medicine, Nagasaki, 852-8523, JAPAN.,Nagasaki University Graduate School of Biomedical Sciences, Nagasaki, 852-8523, JAPAN
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47
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Dinic J, Marciel AB, Tirrell MV. Polyampholyte physics: Liquid–liquid phase separation and biological condensates. Curr Opin Colloid Interface Sci 2021. [DOI: 10.1016/j.cocis.2021.101457] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
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48
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Dolnik O, Gerresheim GK, Biedenkopf N. New Perspectives on the Biogenesis of Viral Inclusion Bodies in Negative-Sense RNA Virus Infections. Cells 2021; 10:cells10061460. [PMID: 34200781 PMCID: PMC8230417 DOI: 10.3390/cells10061460] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2021] [Revised: 06/06/2021] [Accepted: 06/08/2021] [Indexed: 12/13/2022] Open
Abstract
Infections by negative strand RNA viruses (NSVs) induce the formation of viral inclusion bodies (IBs) in the host cell that segregate viral as well as cellular proteins to enable efficient viral replication. The induction of those membrane-less viral compartments leads inevitably to structural remodeling of the cellular architecture. Recent studies suggested that viral IBs have properties of biomolecular condensates (or liquid organelles), as have previously been shown for other membrane-less cellular compartments like stress granules or P-bodies. Biomolecular condensates are highly dynamic structures formed by liquid-liquid phase separation (LLPS). Key drivers for LLPS in cells are multivalent protein:protein and protein:RNA interactions leading to specialized areas in the cell that recruit molecules with similar properties, while other non-similar molecules are excluded. These typical features of cellular biomolecular condensates are also a common characteristic in the biogenesis of viral inclusion bodies. Viral IBs are predominantly induced by the expression of the viral nucleoprotein (N, NP) and phosphoprotein (P); both are characterized by a special protein architecture containing multiple disordered regions and RNA-binding domains that contribute to different protein functions. P keeps N soluble after expression to allow a concerted binding of N to the viral RNA. This results in the encapsidation of the viral genome by N, while P acts additionally as a cofactor for the viral polymerase, enabling viral transcription and replication. Here, we will review the formation and function of those viral inclusion bodies upon infection with NSVs with respect to their nature as biomolecular condensates.
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49
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Zheng T, Galagedera SKK, Castañeda CA. Previously uncharacterized interactions between the folded and intrinsically disordered domains impart asymmetric effects on UBQLN2 phase separation. Protein Sci 2021; 30:1467-1481. [PMID: 34029402 DOI: 10.1002/pro.4128] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2021] [Revised: 05/20/2021] [Accepted: 05/21/2021] [Indexed: 02/06/2023]
Abstract
Shuttle protein UBQLN2 functions in protein quality control (PQC) by binding to proteasomal receptors and ubiquitinated substrates via its N-terminal ubiquitin-like (UBL) and C-terminal ubiquitin-associated (UBA) domains, respectively. Between these two folded domains are low-complexity STI1-I and STI1-II regions, connected by disordered linkers. The STI1 regions bind other components, such as HSP70, that are important to the PQC functions of UBQLN2. We recently determined that the STI1-II region enables UBQLN2 to undergo liquid-liquid phase separation (LLPS) to form liquid droplets in vitro and biomolecular condensates in cells. However, how the interplay between the folded (UBL/UBA) domains and the intrinsically disordered regions mediates phase separation is largely unknown. Using engineered domain deletion constructs, we found that removing the UBA domain inhibits UBQLN2 LLPS while removing the UBL domain enhances LLPS, suggesting that UBA and UBL domains contribute asymmetrically in modulating UBQLN2 LLPS. To explain these differential effects, we interrogated the interactions that involve the UBA and UBL domains across the entire UBQLN2 molecule using nuclear magnetic resonance spectroscopy. To our surprise, aside from well-studied canonical UBL:UBA interactions, there also exist moderate interactions between the UBL and several disordered regions, including STI1-I and residues 555-570, the latter of which is a known contributor to UBQLN2 LLPS. Our findings are essential for the understanding of both the molecular driving forces of UBQLN2 LLPS and the effects of ligand binding to UBL, UBA, or disordered regions on the phase behavior and physiological functions of UBQLN2.
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Affiliation(s)
- Tongyin Zheng
- Department of Chemistry, Syracuse University, Syracuse, New York, USA
| | | | - Carlos A Castañeda
- Departments of Biology and Chemistry, Syracuse University, Syracuse, New York, USA.,Interdisciplinary Neuroscience Program, Syracuse University, Syracuse, New York, USA.,BioInspired Institute, Syracuse University, Syracuse, New York, USA
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50
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Prabhu VM. Interfacial tension in polyelectrolyte systems exhibiting associative liquid–liquid phase separation. Curr Opin Colloid Interface Sci 2021. [DOI: 10.1016/j.cocis.2021.101422] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
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