1
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Li HY, Zhang B, Wang ZY. Conformational and static properties of tagged chains in solvents: effect of chain connectivity in solvent molecules. SOFT MATTER 2024; 20:3073-3081. [PMID: 38265776 DOI: 10.1039/d3sm01473h] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/25/2024]
Abstract
Polymer chains immersed in different solvent molecules exhibit diverse properties due to multiple spatiotemporal scales and complex interactions. Using molecular dynamics simulations, we study the conformational and static properties of tagged chains in different solvent molecules. Two types of solvent molecules were examined: one type consisted of chain molecules connected by bonds, while the other type consisted of individual bead molecules without any bonds. The only difference between the two solvent molecules lies in the chain connectivity. Our results show a compression of the tagged chains with the addition of bead or chain molecules. Chain molecule confinement induces a stronger compression compared to bead molecule confinement. In chain solvent molecules, the tagged chain's radius of gyration reached a minimum at a monomer volume fraction of ∼0.3. Notably, the probability distributions of chain size remain unchanged at different solvent densities, irrespective of whether the solvent consists of beads or polymers. Furthermore, as solvent density increases, a crossover from a unimodal to a bimodal distribution of bond angles is observed, indicating the presence of both compressed and expanded regions within the chain. The effective monomer-solvent interaction is obtained by calculating the partial radial distribution function and the potential of the mean force. In chain solvents, the correlation hole effect results in a reduced number of nearest neighbors around tagged monomers compared to bead solvents. The calculation of pore size distribution reveals that the solvent nonhomogeneity induced by chain connectivity leads to a broader distribution of pore sizes and larger pore dimensions at low volume fractions. These findings provide a deeper understanding of the conformational behavior of polymer chains in different solvent environments.
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Affiliation(s)
- Hong-Yao Li
- School of Physical Science and Technology, Southwest University, Chongqing 400715, China.
- Chongqing Key Laboratory of Micro-Nano Structure Optoelectronics, Chongqing 400715, China
| | - Bokai Zhang
- School of Physical Science and Technology, Southwest University, Chongqing 400715, China.
- Chongqing Key Laboratory of Micro-Nano Structure Optoelectronics, Chongqing 400715, China
| | - Zhi-Yong Wang
- School of Physical Science and Technology, Southwest University, Chongqing 400715, China.
- Chongqing Key Laboratory of Micro-Nano Structure Optoelectronics, Chongqing 400715, China
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2
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Monterroso B, Margolin W, Boersma AJ, Rivas G, Poolman B, Zorrilla S. Macromolecular Crowding, Phase Separation, and Homeostasis in the Orchestration of Bacterial Cellular Functions. Chem Rev 2024; 124:1899-1949. [PMID: 38331392 PMCID: PMC10906006 DOI: 10.1021/acs.chemrev.3c00622] [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: 08/31/2023] [Revised: 12/01/2023] [Accepted: 01/10/2024] [Indexed: 02/10/2024]
Abstract
Macromolecular crowding affects the activity of proteins and functional macromolecular complexes in all cells, including bacteria. Crowding, together with physicochemical parameters such as pH, ionic strength, and the energy status, influences the structure of the cytoplasm and thereby indirectly macromolecular function. Notably, crowding also promotes the formation of biomolecular condensates by phase separation, initially identified in eukaryotic cells but more recently discovered to play key functions in bacteria. Bacterial cells require a variety of mechanisms to maintain physicochemical homeostasis, in particular in environments with fluctuating conditions, and the formation of biomolecular condensates is emerging as one such mechanism. In this work, we connect physicochemical homeostasis and macromolecular crowding with the formation and function of biomolecular condensates in the bacterial cell and compare the supramolecular structures found in bacteria with those of eukaryotic cells. We focus on the effects of crowding and phase separation on the control of bacterial chromosome replication, segregation, and cell division, and we discuss the contribution of biomolecular condensates to bacterial cell fitness and adaptation to environmental stress.
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Affiliation(s)
- Begoña Monterroso
- Department
of Structural and Chemical Biology, Centro de Investigaciones Biológicas
Margarita Salas, Consejo Superior de Investigaciones
Científicas (CSIC), 28040 Madrid, Spain
| | - William Margolin
- Department
of Microbiology and Molecular Genetics, McGovern Medical School, UTHealth-Houston, Houston, Texas 77030, United States
| | - Arnold J. Boersma
- Cellular
Protein Chemistry, Bijvoet Centre for Biomolecular Research, Faculty
of Science, Utrecht University, Padualaan 8, 3584 CH Utrecht, The Netherlands
| | - Germán Rivas
- Department
of Structural and Chemical Biology, Centro de Investigaciones Biológicas
Margarita Salas, Consejo Superior de Investigaciones
Científicas (CSIC), 28040 Madrid, Spain
| | - Bert Poolman
- Department
of Biochemistry, University of Groningen, Nijenborgh 4, 9747 AG Groningen, The Netherlands
| | - Silvia Zorrilla
- Department
of Structural and Chemical Biology, Centro de Investigaciones Biológicas
Margarita Salas, Consejo Superior de Investigaciones
Científicas (CSIC), 28040 Madrid, Spain
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3
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Yu M, Ye R, Zeng T, Tan L, Zhao Z, Gao W, Chen X, Lian Z, Ma Y, Li A, Hu J. Constructing an Ultra-Rapid Nanoconfinement-Enhanced Fluorescence Clinical Detection Platform by Using Machine Learning and Tunable DNA Xerogel "Probe". Anal Chem 2023; 95:15690-15699. [PMID: 37830461 DOI: 10.1021/acs.analchem.3c02955] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/14/2023]
Abstract
Low mass transfer efficiency and unavoidable matrix effects seriously limit the development of rapid and accurate determination of biosensing systems. Herein, we have successfully constructed an ultra-rapid nanoconfinement-enhanced fluorescence clinical detection platform based on machine learning (ML) and DNA xerogel "probe", which was performed by detecting neutrophil gelatinase-associated lipocalin (NGAL, protein biomarker of acute kidney injury). By regulating pore sizes of the xerogels, the transfer of NGAL in xerogels can approximate that in homogeneous solution. Due to electrostatic attraction of the pore entrances, NGAL rapidly enriches on the surface and inside the xerogels. The reaction rate of NGAL and aptamer cross-linked in xerogels is also accelerated because of the nanoconfinement effect-induced increasing reactant concentration and the enhanced affinity constant KD between reactants, which can be promoted by ∼667-fold than that in bulk solution, thus achieving ultra-rapid detection (ca. 5 min) of human urine. The platform could realize one-step detection without sample pretreatments due to the antiligand exchange effect on the surface of N-doped carbon quantum dots (N-CQDs) in xerogels, in which ligand exchange between -COOH and underlying interfering ions in urine will be inhibited due to higher adsorption energy of -COOH on the N-CQD surface relative to the interfering ions. Based on the ML-extended program, the real-time analysis of the urine fluorescence spectra can be completed within 2 s. Interestingly, by changing DNA, aptamer sequences, or xerogel fluorescence intensities, the detection platform can be customized for targeted diseases.
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Affiliation(s)
- Meng Yu
- School of Chemistry and Chemical Engineering, Key Lab of Fuel Cell Technology of Guangdong Province, South China University of Technology, Guangzhou 510641, China
- Division of Nephrology, Nanfang Hospital, National Clinical Research Center for Kidney Disease, State Key Laboratory of Organ Failure Research, Guangdong Provincial Institute of Nephrology, Guangdong Provincial Key Laboratory of Renal Failure Research, Southern Medical University, Guangzhou 510515, China
| | - Rongkai Ye
- School of Chemistry and Chemical Engineering, Key Lab of Fuel Cell Technology of Guangdong Province, South China University of Technology, Guangzhou 510641, China
| | - Tao Zeng
- Division of Nephrology, Nanfang Hospital, National Clinical Research Center for Kidney Disease, State Key Laboratory of Organ Failure Research, Guangdong Provincial Institute of Nephrology, Guangdong Provincial Key Laboratory of Renal Failure Research, Southern Medical University, Guangzhou 510515, China
| | - Li Tan
- School of Chemistry and Chemical Engineering, Key Lab of Fuel Cell Technology of Guangdong Province, South China University of Technology, Guangzhou 510641, China
| | - Ziyu Zhao
- School of Chemistry and Chemical Engineering, Key Lab of Fuel Cell Technology of Guangdong Province, South China University of Technology, Guangzhou 510641, China
| | - Wenjing Gao
- School of Chemistry and Chemical Engineering, Key Lab of Fuel Cell Technology of Guangdong Province, South China University of Technology, Guangzhou 510641, China
| | - Xin Chen
- School of Chemistry and Chemical Engineering, Key Lab of Fuel Cell Technology of Guangdong Province, South China University of Technology, Guangzhou 510641, China
| | - Ziqi Lian
- School of Chemistry and Chemical Engineering, Key Lab of Fuel Cell Technology of Guangdong Province, South China University of Technology, Guangzhou 510641, China
| | - Ying Ma
- School of Chemistry and Chemical Engineering, Key Lab of Fuel Cell Technology of Guangdong Province, South China University of Technology, Guangzhou 510641, China
| | - Aiqing Li
- Division of Nephrology, Nanfang Hospital, National Clinical Research Center for Kidney Disease, State Key Laboratory of Organ Failure Research, Guangdong Provincial Institute of Nephrology, Guangdong Provincial Key Laboratory of Renal Failure Research, Southern Medical University, Guangzhou 510515, China
| | - Jianqiang Hu
- School of Chemistry and Chemical Engineering, Key Lab of Fuel Cell Technology of Guangdong Province, South China University of Technology, Guangzhou 510641, China
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4
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Skóra T, Janssen M, Carlson A, Kondrat S. Crowding-Regulated Binding of Divalent Biomolecules. PHYSICAL REVIEW LETTERS 2023; 130:258401. [PMID: 37418731 DOI: 10.1103/physrevlett.130.258401] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/06/2022] [Accepted: 05/08/2023] [Indexed: 07/09/2023]
Abstract
Macromolecular crowding affects biophysical processes as diverse as diffusion, gene expression, cell growth, and senescence. Yet, there is no comprehensive understanding of how crowding affects reactions, particularly multivalent binding. Herein, we use scaled particle theory and develop a molecular simulation method to investigate the binding of monovalent to divalent biomolecules. We find that crowding can increase or reduce cooperativity-the extent to which the binding of a second molecule is enhanced after binding a first molecule-by orders of magnitude, depending on the sizes of the involved molecular complexes. Cooperativity generally increases when a divalent molecule swells and then shrinks upon binding two ligands. Our calculations also reveal that, in some cases, crowding enables binding that does not occur otherwise. As an immunological example, we consider immunoglobulin G-antigen binding and show that crowding enhances its cooperativity in bulk but reduces it when an immunoglobulin G binds antigens on a surface.
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Affiliation(s)
- Tomasz Skóra
- Institute of Physical Chemistry, Polish Academy of Sciences, 01-224 Warsaw, Poland
- Scientific Computing and Imaging Institute, University of Utah, Salt Lake City, Utah 84112, USA
| | - Mathijs Janssen
- Department of Mathematics, Mechanics Division, University of Oslo, N-0851 Oslo, Norway
- Centre for Cancer Cell Reprogramming, Faculty of Medicine, University of Oslo, Montebello, N-0379 Oslo, Norway
- Norwegian University of Life Sciences, Faculty of Science and Technology, Pb 5003, 1433 Ås, Norway
| | - Andreas Carlson
- Department of Mathematics, Mechanics Division, University of Oslo, N-0851 Oslo, Norway
| | - Svyatoslav Kondrat
- Institute of Physical Chemistry, Polish Academy of Sciences, 01-224 Warsaw, Poland
- Institute for Computational Physics, University of Stuttgart, Stuttgart 70569, Germany
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5
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Zong W, Shao X, Li J, Chai Y, Hu X, Zhang X. Synthetic Intracellular Environments: From Basic Science to Applications. Anal Chem 2023; 95:535-549. [PMID: 36625127 DOI: 10.1021/acs.analchem.2c04199] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
Affiliation(s)
- Wei Zong
- College of Chemistry and Chemical Engineering, Qiqihar University, No. 42 Wenhua Street, Qiqihar161006, China
| | - Xiaotong Shao
- College of Chemistry and Chemical Engineering, Qiqihar University, No. 42 Wenhua Street, Qiqihar161006, China
| | - Jinlong Li
- College of Chemistry and Chemical Engineering, Qiqihar University, No. 42 Wenhua Street, Qiqihar161006, China.,Heilongjiang Provincial Key Laboratory of Catalytic Synthesis for Fine Chemicals, Qiqihar University, Qiqihar161006, China
| | - Yunhe Chai
- College of Chemistry and Chemical Engineering, Qiqihar University, No. 42 Wenhua Street, Qiqihar161006, China
| | - Xinyu Hu
- Key Laboratory of Micro-Nano Optoelectronic Devices (Wenzhou), College of Electrical and Electronic Engineering, Wenzhou University, Wenzhou325035, China
| | - Xunan Zhang
- College of Chemistry and Chemical Engineering, Qiqihar University, No. 42 Wenhua Street, Qiqihar161006, China
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6
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Oliveira RJD. Coordinate-Dependent Drift-Diffusion Reveals the Kinetic Intermediate Traps of Top7-Based Proteins. J Phys Chem B 2022; 126:10854-10869. [PMID: 36519977 DOI: 10.1021/acs.jpcb.2c07031] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
The computer-designed Top7 served as a scaffold to produce immunoreactive proteins by grafting of the 2F5 HIV-1 antibody epitope (Top7-2F5) followed by biotinylation (Top7-2F5-biotin). The resulting nonimmunoglobulin affinity proteins were effective in inducing and detecting the HIV-1 antibody. However, the grafted Top7-2F5 design led to protein aggregation, as opposed to the soluble biotinylated Top7-2F5-biotin. The structure-based model predicted that the thermodynamic cooperativity of Top7 increases after grafting and biotin-labeling, reducing their intermediate state populations. In this work, the folding kinetic traps that might contribute to the aggregation propensity are investigated by the diffusion theory. Since the engineered proteins have similar sequence and structural homology, they served as protein models to study the kinetic intermediate traps that were uncovered by characterizing the position-dependent drift-velocity (v(Q)) and the diffusion (D(Q)) coefficients. These coordinate-dependent coefficients were taken into account to obtain the folding and transition path times over the free energy transition states containing the intermediate kinetic traps. This analysis may be useful to predict the aggregated kinetic traps of scaffold-epitope proteins that might compose novel diagnostic and therapeutic platforms.
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Affiliation(s)
- Ronaldo Junio de Oliveira
- Laboratório de Biofísica Teórica, Departamento de Física, Instituto de Ciências Exatas, Naturais e Educação, Universidade Federal do Triângulo Mineiro, Uberaba, MG38064-200, Brazil
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7
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Słyk E, Skóra T, Kondrat S. How macromolecules softness affects diffusion under crowding. SOFT MATTER 2022; 18:5366-5370. [PMID: 35833511 DOI: 10.1039/d2sm00357k] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
Diffusion in a macromolecularly crowded environment is essential for many intracellular processes, from metabolism and catalysis to gene transcription and translation. So far, theoretical and experimental work has focused on anomalous subdiffusion, and the effects of interactions, shapes, and composition, while the compactness or softness of macromolecules has received less attention. Herein, we use Brownian dynamics simulations to study how the softness of crowders affects macromolecular diffusion. We find that in most cases, soft crowders slow down the diffusion less effectively than hard crowders like Ficoll. For instance, at a 30% occupied volume fraction, the diffusion in Ficoll70 is about 20% slower than in soft crowders of the same size. However, our simulations indicate that elongated macromolecules, such as double-stranded DNA pieces, can diffuse comparably or even faster in hard crowders. We relate these effects to the volume excluded by soft and hard crowders to different tracers. Our results show that the softness and shape of macromolecules are crucial factors determining diffusion under crowding, relevant to diverse intracellular environments.
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Affiliation(s)
- Edyta Słyk
- Institute of Physical Chemistry, Polish Academy of Sciences, 01-224 Warsaw, Poland.
- Department of Theoretical Chemistry, Institute of Chemical Sciences, Faculty of Chemistry, Maria Curie-Skłodowska University in Lublin, 20-031 Lublin, Poland
| | - Tomasz Skóra
- Institute of Physical Chemistry, Polish Academy of Sciences, 01-224 Warsaw, Poland.
| | - Svyatoslav Kondrat
- Institute of Physical Chemistry, Polish Academy of Sciences, 01-224 Warsaw, Poland.
- Max-Planck-Institut für Intelligente Systeme, Heisenbergstraße 3, 70569 Stuttgart, Germany
- IV. Institut für Theoretische Physik, Universität Stuttgart, Pfaffenwaldring 57, 70569 Stuttgart, Germany
- Institut für Computerphysik, Universität Stuttgart, Allmandring 3, 70569 Stuttgart, Germany
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8
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Freitas FC, Maldonado M, Oliveira Junior AB, Onuchic JN, Oliveira RJD. Biotin-painted proteins have thermodynamic stability switched by kinetic folding routes. J Chem Phys 2022; 156:195101. [PMID: 35597640 DOI: 10.1063/5.0083875] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023] Open
Abstract
Biotin-labeled proteins are widely used as tools to study protein-protein interactions and proximity in living cells. Proteomic methods broadly employ proximity-labeling technologies based on protein biotinylation in order to investigate the transient encounters of biomolecules in subcellular compartments. Biotinylation is a post-translation modification in which the biotin molecule is attached to lysine or tyrosine residues. So far, biotin-based technologies proved to be effective instruments as affinity and proximity tags. However, the influence of biotinylation on aspects such as folding, binding, mobility, thermodynamic stability, and kinetics needs to be investigated. Here, we selected two proteins [biotin carboxyl carrier protein (BCCP) and FKBP3] to test the influence of biotinylation on thermodynamic and kinetic properties. Apo (without biotin) and holo (biotinylated) protein structures were used separately to generate all-atom structure-based model simulations in a wide range of temperatures. Holo BCCP contains one biotinylation site, and FKBP3 was modeled with up to 23 biotinylated lysines. The two proteins had their estimated thermodynamic stability changed by altering their energy landscape. In all cases, after comparison between the apo and holo simulations, differences were observed on the free-energy profiles and folding routes. Energetic barriers were altered with the density of states clearly showing changes in the transition state. This study suggests that analysis of large-scale datasets of biotinylation-based proximity experiments might consider possible alterations in thermostability and folding mechanisms imposed by the attached biotins.
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Affiliation(s)
- Frederico Campos Freitas
- Laboratório de Biofísica Teórica, Departamento de Física, Instituto de Ciências Exatas, Naturais e Educação, Universidade Federal do Triângulo Mineiro, Uberaba, MG 38064-200, Brazil
| | - Michelli Maldonado
- Departamento de Matemática, Instituto de Ciências Exatas, Naturais e Educação, Universidade Federal do Triângulo Mineiro, Uberaba, MG 38064-200, Brazil
| | - Antonio Bento Oliveira Junior
- Center for Theoretical Biological Physics, Rice University, BioScience Research Collaborative, 6566 Main St., Houston, Texas 77030, USA
| | - José Nelson Onuchic
- Center for Theoretical Biological Physics, Rice University, BioScience Research Collaborative, 6566 Main St., Houston, Texas 77030, USA
| | - Ronaldo Junio de Oliveira
- Laboratório de Biofísica Teórica, Departamento de Física, Instituto de Ciências Exatas, Naturais e Educação, Universidade Federal do Triângulo Mineiro, Uberaba, MG 38064-200, Brazil
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9
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Liu F, Yang Y, Wan X, Gao H, Wang Y, Lu J, Xu LP, Wang S. Space-Confinment-Enhanced Fluorescence Detection of DNA on Hydrogel Particles Array. ACS NANO 2022; 16:6266-6273. [PMID: 35385247 DOI: 10.1021/acsnano.2c00157] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
Fluorescent biosensors have been widely applied in DNA detection because of their reliability and reproducibility. However, low kinetics in DNA hybridization often brings out long test terms, thus restricting their practical use. Here, we demonstrate unexpected fast DNA fluorescence detection on the confined surface of hydrogel particles. When the pore size and surface charge of hydrogel particles are tailored, DNA molecules can be confined in the outer water layer of hydrogel particles. We fabricated a fluorescence-on DNA sensor based on the hydrogel particle array by utilizing the fluorescence quenching property of graphene oxide and its different adsorption behaviors toward single-strand DNA or double-strand DNA. Benefiting from the confinement effect of hydrogel particle surface and the enrichment effect of water evaporation, the DNA-recognition time was descreased significantly from 3000 s to less than 10 s under the target concentration of 400 nM. Moreover, rapid detection can be achieved at concentrations between 50 and 400 nM. The study provides another insight to fabricate fast biosensors and shows great potential in DNA diagnostics, gene analysis, and liquid biopsy.
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Affiliation(s)
- Fei Liu
- Beijing Key Laboratory for Bioengineering and Sensing Technology, School of Chemistry and Biological Engineering, University of Science and Technology Beijing, Beijing 100083, China
| | - Yuemeng Yang
- Beijing Key Laboratory for Bioengineering and Sensing Technology, School of Chemistry and Biological Engineering, University of Science and Technology Beijing, Beijing 100083, China
| | - Xizi Wan
- CAS Key Laboratory of Bio-inspired Materials and Interfacial Science, Technical Institute of Physics and Chemistry, Chinese Academy of Sciences, Beijing 100190, China
| | - Hongxiao Gao
- Beijing Key Laboratory for Bioengineering and Sensing Technology, School of Chemistry and Biological Engineering, University of Science and Technology Beijing, Beijing 100083, China
| | - Yulu Wang
- Beijing Key Laboratory for Bioengineering and Sensing Technology, School of Chemistry and Biological Engineering, University of Science and Technology Beijing, Beijing 100083, China
| | - Jingwei Lu
- Beijing Key Laboratory for Bioengineering and Sensing Technology, School of Chemistry and Biological Engineering, University of Science and Technology Beijing, Beijing 100083, China
| | - Li-Ping Xu
- Beijing Key Laboratory for Bioengineering and Sensing Technology, School of Chemistry and Biological Engineering, University of Science and Technology Beijing, Beijing 100083, China
| | - Shutao Wang
- CAS Key Laboratory of Bio-inspired Materials and Interfacial Science, Technical Institute of Physics and Chemistry, Chinese Academy of Sciences, Beijing 100190, China
- University of Chinese Academy of Sciences, Beijing 100049, China
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10
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Punia B, Chaudhury S. Influence of Nonspecific Interactions between Proteins and In Vivo Cytoplasmic Crowders in Facilitated Diffusion of Proteins: Theoretical Insights. J Phys Chem B 2022; 126:3037-3047. [PMID: 35438996 DOI: 10.1021/acs.jpcb.2c01021] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The binding of proteins to their respective specific sites on the DNA through facilitated diffusion serves as the initial step of various important biological processes. While this search process has been thoroughly investigated via in vitro studies, the cellular environment is complex and may interfere with the protein's search dynamics. The cytosol is heavily crowded, which can potentially modify the search by nonspecifically interacting with the protein that has been mostly overlooked. In this work, we probe the target search dynamics in the presence of explicit crowding agents that have an affinity toward the protein. We theoretically investigate the role of such protein-crowder associations in the target search process using a discrete-state stochastic framework that allows for the analytical description of dynamic properties. It is found that stronger nonspecific associations between the crowder and proteins can accelerate the facilitated diffusion of proteins in comparison with a purely inert, rather weakly interacting cellular environment. This effect depends on how strong these associations are, the spatial positions of the target with respect to the crowders, and the size of the crowded region. Our theoretical results are also tested with Monte Carlo computer simulations. Our predictions are in qualitative agreement with existing experimental observations and computational studies.
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Affiliation(s)
- Bhawakshi Punia
- Department of Chemistry, Indian Institute of Science Education and Research, Dr. Homi Bhabha Road, Pune 411008, Maharashtra, India
| | - Srabanti Chaudhury
- Department of Chemistry, Indian Institute of Science Education and Research, Dr. Homi Bhabha Road, Pune 411008, Maharashtra, India
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11
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Kondrat S, von Lieres E. Mechanisms and Effects of Substrate Channelling in Enzymatic Cascades. Methods Mol Biol 2022; 2487:27-50. [PMID: 35687228 DOI: 10.1007/978-1-0716-2269-8_3] [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] [Indexed: 06/15/2023]
Abstract
Substrate or metabolite channelling is a transfer of intermediates produced by one enzyme to the sequential enzyme of a reaction cascade or metabolic pathway, without releasing them entirely into bulk. Despite an enormous effort and more than three decades of research, substrate channelling remains the subject of continuing debates and active investigation. Herein, we review the benefits and mechanisms of substrate channelling in vivo and in vitro. We discuss critically the effects that substrate channelling can have on enzymatic cascades, including speeding up or slowing down reaction cascades and protecting intermediates from sequestration and enzymes' surroundings from toxic or otherwise detrimental intermediates. We also discuss how macromolecular crowding affects substrate channelling and point out the galore of open questions.
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Affiliation(s)
- Svyatoslav Kondrat
- Institute of Physical Chemistry, Polish Academy of Sciences, Warsaw, Poland.
- Max-Planck-Institut für Intelligente Systeme, Stuttgart, Germany.
- IV. Institut für Theoretische Physik, Universität Stuttgart, Stuttgart, Germany.
| | - Eric von Lieres
- Forschungszentrum Jülich, IBG-1: Biotechnology, Jülich, Germany
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12
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Skóra T, Popescu MN, Kondrat S. Conformation-changing enzymes and macromolecular crowding. Phys Chem Chem Phys 2021; 23:9065-9069. [PMID: 33885078 DOI: 10.1039/d0cp06631a] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Abstract
We study how crowding affects the activity and catalysis-enhanced diffusion of enzymes and passive tracers by employing a fluctuating-dumbbell model of conformation-changing enzymes. Our Brownian dynamics simulations reveal that the diffusion of enzymes depends qualitatively on the type of crowding. If only enzymes are present in the system, the catalysis-induced enhancement of the enzyme diffusion - somewhat counter-intuitively - increases with crowding, while it decreases if crowding is due to inert particles. For the tracers, the diffusion enhancement increases with increasing the enzyme concentration. We also show how the enzyme activity is reduced by crowding and propose a simple expression to describe this reduction. Our results highlight subtle effects at play concerning enzymatic activity and macromolecular transport in crowded systems, such as, e.g., the interior of living cells.
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Affiliation(s)
- Tomasz Skóra
- Institute of Physical Chemistry, Polish Academy of Sciences, 01-224 Warsaw, Poland.
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13
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Wilcox XE, Chung CB, Slade KM. Macromolecular crowding effects on the kinetics of opposing reactions catalyzed by alcohol dehydrogenase. Biochem Biophys Rep 2021; 26:100956. [PMID: 33665382 PMCID: PMC7905371 DOI: 10.1016/j.bbrep.2021.100956] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2020] [Revised: 01/03/2021] [Accepted: 02/09/2021] [Indexed: 12/01/2022] Open
Abstract
In order to better understand how the complex, densely packed, heterogeneous milieu of a cell influences enzyme kinetics, we exposed opposing reactions catalyzed by yeast alcohol dehydrogenase (YADH) to both synthetic and protein crowders ranging from 10 to 550 kDa. The results reveal that the effects from macromolecular crowding depend on the direction of the reaction. The presence of the synthetic polymers, Ficoll and dextran, decrease Vmax and Km for ethanol oxidation. In contrast, these crowders have little effect or even increase these kinetic parameters for acetaldehyde reduction. This increase in Vmax is likely due to excluded volume effects, which are partially counteracted by viscosity hindering release of the NAD+ product. Macromolecular crowding is further complicated by the presence of a depletion layer in solutions of dextran larger than YADH, which diminishes the hindrance from viscosity. The disparate effects from 25 g/L dextran or glucose compared to 25 g/L Ficoll or sucrose reveals that soft interactions must also be considered. Data from binary mixtures of glucose, dextran, and Ficoll support this “tuning” of opposing factors. While macromolecular crowding was originally proposed to influence proteins mainly through excluded volume effects, this work compliments the growing body of evidence revealing that other factors, such as preferential hydration, chemical interactions, and the presence of a depletion layer also contribute to the overall effect of crowding. Yeast alcohol dehydrogenase reduction of acetaldehyde is enhanced by crowding. Crowding effects on YADH kinetics depend on the direction of the reaction. Crowders like dextran can be used as a tool to elucidate enzyme mechanism. Excluded volume optimizes YADH hydride transfer; viscosity hinders product release. The presence of a depletion layer with large crowders mitigates their effects.
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Affiliation(s)
- Xander E Wilcox
- Department of Chemistry, University of California at Davis, CA, 95616, USA
| | - Charmaine B Chung
- Department of Chemistry, Hobart and William Smith Colleges, 300 Pulteney St, Geneva, NY, 14456, USA
| | - Kristin M Slade
- Department of Chemistry, Hobart and William Smith Colleges, 300 Pulteney St, Geneva, NY, 14456, USA
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14
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Vibhute MA, Schaap MH, Maas RJM, Nelissen FHT, Spruijt E, Heus HA, Hansen MMK, Huck WTS. Transcription and Translation in Cytomimetic Protocells Perform Most Efficiently at Distinct Macromolecular Crowding Conditions. ACS Synth Biol 2020; 9:2797-2807. [PMID: 32976714 PMCID: PMC7573978 DOI: 10.1021/acssynbio.0c00330] [Citation(s) in RCA: 34] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
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The formation of
cytomimetic protocells that capture the physicochemical
aspects of living cells is an important goal in bottom-up synthetic
biology. Here, we recreated the crowded cytoplasm in liposome-based
protocells and studied the kinetics of cell-free gene expression in
these crowded containers. We found that diffusion of key components
is affected not only by macromolecular crowding but also by enzymatic
activity in the protocell. Surprisingly, size-dependent diffusion
in crowded conditions yielded two distinct maxima for protein synthesis,
reflecting the differential impact of crowding on transcription and
translation. Our experimental data show, for the first time, that
macromolecular crowding induces a switch from reaction to diffusion
control and that this switch depends on the sizes of the macromolecules
involved. These results highlight the need to control the physical
environment in the design of synthetic cells.
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Affiliation(s)
- Mahesh A. Vibhute
- Radboud University, Institute for Molecules and Materials, Heyendaalseweg 135, 6525 AJ Nijmegen, The Netherlands
| | - Mark H. Schaap
- Radboud University, Institute for Molecules and Materials, Heyendaalseweg 135, 6525 AJ Nijmegen, The Netherlands
| | - Roel J. M. Maas
- Radboud University, Institute for Molecules and Materials, Heyendaalseweg 135, 6525 AJ Nijmegen, The Netherlands
| | - Frank H. T. Nelissen
- Radboud University, Institute for Molecules and Materials, Heyendaalseweg 135, 6525 AJ Nijmegen, The Netherlands
| | - Evan Spruijt
- Radboud University, Institute for Molecules and Materials, Heyendaalseweg 135, 6525 AJ Nijmegen, The Netherlands
| | - Hans A. Heus
- Radboud University, Institute for Molecules and Materials, Heyendaalseweg 135, 6525 AJ Nijmegen, The Netherlands
| | - Maike M. K. Hansen
- Radboud University, Institute for Molecules and Materials, Heyendaalseweg 135, 6525 AJ Nijmegen, The Netherlands
| | - Wilhelm T. S. Huck
- Radboud University, Institute for Molecules and Materials, Heyendaalseweg 135, 6525 AJ Nijmegen, The Netherlands
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15
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Skóra T, Vaghefikia F, Fitter J, Kondrat S. Macromolecular Crowding: How Shape and Interactions Affect Diffusion. J Phys Chem B 2020; 124:7537-7543. [PMID: 32790396 DOI: 10.1021/acs.jpcb.0c04846] [Citation(s) in RCA: 40] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
Abstract
A significant fraction of the cell volume is occupied by various proteins, polysaccharides, nucleic acids, etc., which considerably reduces the mobility of macromolecules. Theoretical and experimental work so far have mainly focused on the dependence of the mobility on the occupied volume, while the effect of a macromolecular shape received less attention. Herein, using fluorescence correlation spectroscopy (FCS) and Brownian dynamics (BD) simulations, we report on a dramatic slowdown of tracer diffusion by cylindrically shaped double-stranded (ds) DNAs (16 nm in length). We find, for instance, that the translational diffusion coefficient of a streptavidin tracer is reduced by about 60% for a volume fraction of dsDNA as low as just 5%. For comparison, for a spherical crowder (Ficoll70) the slowdown is only 10% at the same volume fraction and 60% reduction occurs at a volume fraction as high as 35%. BD simulations reveal that this reduction can be attributed to a larger volume excluded to a tracer by dsDNA particles, as compared with spherical Ficoll70 at the same volume fraction, and to the differences in the tracer-crowder attractive interactions. In addition, we find using BD simulations that rotational diffusion of dsDNA is less affected by the crowder shape than its translational motion. Our results show that diffusion in crowded systems is determined not merely by the occupied volume fraction, but that the shape and interactions can determine diffusion, which is relevant to the diverse intracellular environments inside living cells.
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Affiliation(s)
- Tomasz Skóra
- Department of Complex Systems, Institute of Physical Chemistry, Polish Academy of Sciences, Kasprzaka 44/52, 01-224 Warsaw, Poland
| | - Farzaneh Vaghefikia
- I. Physikalisches Institut (IA), AG Biophysik, RWTH Aachen University, 52074 Aachen, Germany
| | - Jörg Fitter
- I. Physikalisches Institut (IA), AG Biophysik, RWTH Aachen University, 52074 Aachen, Germany.,Institut für Biologische Informationsprozesse (IBI-6), Forschungszentrum Jülich, 52425 Jülich, Germany
| | - Svyatoslav Kondrat
- Department of Complex Systems, Institute of Physical Chemistry, Polish Academy of Sciences, Kasprzaka 44/52, 01-224 Warsaw, Poland.,Max-Planck-Institut für Intelligente Systeme, Heisenbergstraße 3, 70569 Stuttgart, Germany.,Institut für Theoretische Physik IV, Universität Stuttgart, Pfaffenwaldring 57, 70569 Stuttgart, Germany
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16
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Chen A, Zhang B, Zhao N. A comparative study of semi-flexible linear and ring polymer conformational change in an anisotropic environment. Phys Chem Chem Phys 2020; 22:9137-9147. [PMID: 32301953 DOI: 10.1039/c9cp07018d] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
We adopt a Langevin-dynamics based simulation to systematically study the conformational change of a semi-flexible probed polymer in a rod crowding environment. Two topologically different probed polymer types, linear and ring polymers, are specifically considered. Our results unravel the significance of the interplay of probed polymer's semi-flexibility and crowding anisotropy. Firstly, both ring and linear polymers show a non-trivial dimensional change including nonmonotonicity and collapse-swelling crossover as their stiffness increases. Secondly, we modulate rod crowder length to investigate the anisotropic effect. We reveal that the formation of an ordered parallel arrangement of the environment can effectively lead to a remarkable stretching effect on the probed polymer. The coupling between the crowding anisotropy-induced stretching and the polymer stiffness can account for the unusual swelling behavior. Lastly, nonmonotonic swelling and shape change of the ring polymer are analyzed. We find out that the ring polymer is subject to most pronounced swelling at robust stiffness. Moreover, the maximum prolate shape is also observed at the same robust location.
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Affiliation(s)
- Anpu Chen
- College of Chemistry, Sichuan University, Chengdu 610064, China.
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17
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Dey P, Bhattacherjee A. Structural Basis of Enhanced Facilitated Diffusion of DNA-Binding Protein in Crowded Cellular Milieu. Biophys J 2020; 118:505-517. [PMID: 31862109 PMCID: PMC6976804 DOI: 10.1016/j.bpj.2019.11.3388] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2019] [Revised: 11/03/2019] [Accepted: 11/18/2019] [Indexed: 02/06/2023] Open
Abstract
Although the fast association between DNA-binding proteins (DBPs) and DNA is explained by a facilitated diffusion mechanism, in which DBPs adopt a weighted combination of three-dimensional diffusion and one-dimensional (1D) sliding and hopping modes of transportation, the role of cellular environment that contains many nonspecifically interacting proteins and other biomolecules is mostly overlooked. By performing large-scale computational simulations with an appropriately tuned model of protein and DNA in the presence of nonspecifically interacting bulk and DNA-bound crowders (genomic crowders), we demonstrate the structural basis of the enhanced facilitated diffusion of DBPs inside a crowded cellular milieu through, to our knowledge, novel 1D scanning mechanisms. In this one-dimensional scanning mode, the protein can float along the DNA under the influence of nonspecific interactions of bulk crowder molecules. The search mode is distinctly different compared to usual 1D sliding and hopping dynamics in which protein diffusion is regulated by the DNA electrostatics. In contrast, the presence of genomic crowders expedites the target search process by transporting the protein over DNA segments through the formation of a transient protein-crowder bridged complex. By analyzing the ruggedness of the associated potential energy landscape, we underpin the molecular origin of the kinetic advantages of these search modes and show that they successfully explain the experimentally observed acceleration of facilitated diffusion of DBPs by molecular crowding agents and crowder-concentration-dependent enzymatic activity of transcription factors. Our findings provide crucial insights into gene regulation kinetics inside the crowded cellular milieu.
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Affiliation(s)
- Pinki Dey
- School of Computational and Integrative Sciences, Jawaharlal Nehru University, New Delhi, India
| | - Arnab Bhattacherjee
- School of Computational and Integrative Sciences, Jawaharlal Nehru University, New Delhi, India.
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18
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Makuch K, Hołyst R, Kalwarczyk T, Garstecki P, Brady JF. Diffusion and flow in complex liquids. SOFT MATTER 2020; 16:114-124. [PMID: 31702751 DOI: 10.1039/c9sm01119f] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
Thermal motion of particles and molecules in liquids underlies many chemical and biological processes. Liquids, especially in biology, are complex due to structure at multiple relevant length scales. While diffusion in homogeneous simple liquids is well understood through the Stokes-Einstein relation, this equation fails completely in describing diffusion in complex media. Modeling, understanding, engineering and controlling processes at the nanoscale, most importantly inside living cells, requires a theoretical framework for the description of viscous response to allow predictions of diffusion rates in complex fluids. Here we use a general framework with the viscosity η(k) described by a function of wave vector in reciprocal space. We introduce a formulation that allows one to relate the rotational and translational diffusion coefficients and determine the viscosity η(k) directly from experiments. We apply our theory to provide a database for rotational diffusion coefficients of proteins/protein complexes in the bacterium E. coli. We also provide a database for the diffusion coefficient of proteins sliding along major grooves of DNA in E. coli. These parameters allow predictions of rate constants for association of proteins. In addition to constituting a theoretical framework for description of diffusion of probes and viscosity in complex fluids, the formulation that we propose should decrease substantially the cost of numerical simulations of transport in complex media by replacing the simulation of individual crowding particles with a continuous medium characterized by a wave-length dependent viscosity η(k).
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Affiliation(s)
- Karol Makuch
- Institute of Physical Chemistry, Polish Academy of Sciences, Kasprzaka 44/52, 01-224 Warsaw, Poland. and Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, CA 91125, USA
| | - Robert Hołyst
- Institute of Physical Chemistry, Polish Academy of Sciences, Kasprzaka 44/52, 01-224 Warsaw, Poland.
| | - Tomasz Kalwarczyk
- Institute of Physical Chemistry, Polish Academy of Sciences, Kasprzaka 44/52, 01-224 Warsaw, Poland.
| | - Piotr Garstecki
- Institute of Physical Chemistry, Polish Academy of Sciences, Kasprzaka 44/52, 01-224 Warsaw, Poland.
| | - John F Brady
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, CA 91125, USA
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19
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Dey P, Bhattacherjee A. Mechanism of Facilitated Diffusion of DNA Repair Proteins in Crowded Environment: Case Study with Human Uracil DNA Glycosylase. J Phys Chem B 2019; 123:10354-10364. [DOI: 10.1021/acs.jpcb.9b07342] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]
Affiliation(s)
- Pinki Dey
- School of Computational and Integrative Sciences, Jawaharlal Nehru University, New Delhi, India 110067
| | - Arnab Bhattacherjee
- School of Computational and Integrative Sciences, Jawaharlal Nehru University, New Delhi, India 110067
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20
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Qing J, Chen A, Zhao N. Quantifying the protein-protein association rate in polymer solutions: crowding-induced diffusion and energy modifications. Phys Chem Chem Phys 2019; 20:27937-27948. [PMID: 30379153 DOI: 10.1039/c8cp05203d] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
A theoretical framework is developed to study protein-protein association in polymer solutions under diffusion-limited conditions. Starting from the basal association rate, two fundamental aspects concerning macromolecular crowding are particularly taken into account. One is the effect of microviscosity on protein diffusion. The length-scale dependent relations of translational and rotational diffusion coefficients are incorporated. Another is relevant to the crowding-induced effective interaction between the pair of proteins. The resultant energy modifications to the basal association rate are properly introduced, following an instructive classification with increasing crowder size: repulsive interaction dominant, repulsive and attractive interactions competitive, and attractive interaction prevailing. With specific energy modification terms, we are able to investigate the deviations of the association rate from the Stokes-Einstein (SE) behavior (i.e., the linear relationship with respect to the reciprocal of macroviscosity) in a quantitative manner. Our theory is applied to study the association of TEM1-β-lactamase (TEM) and the β-lactamase inhibitor protein (BLIP) in polyethylene glycol (PEG) solutions, with varying concentration and polymerization. We explicitly evaluate the relative association rate constant as a function of the solution macroviscosity. The theoretical results demonstrate very good agreement with the experimental data. Moreover, the complicated non-trivial deviations, either positive (slower than SE) or negative (faster than SE), are systematically rationalized. The precise role of energy modifications and the microviscosity effect on diffusion, in particular on rotational diffusion, are clearly unraveled.
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Affiliation(s)
- Jing Qing
- College of Chemistry, Sichuan University, Chengdu 610064, China.
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21
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Polovnikov KE, Nechaev S, Tamm MV. Many-body contacts in fractal polymer chains and fractional Brownian trajectories. Phys Rev E 2019; 99:032501. [PMID: 30999417 DOI: 10.1103/physreve.99.032501] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2019] [Indexed: 01/25/2023]
Abstract
We calculate the probabilities that a trajectory of a fractional Brownian motion with arbitrary fractal dimension d_{f} visits the same spot n≥3 times, at given moments t_{1},...,t_{n}, and obtain a determinant expression for these probabilities in terms of a displacement-displacement covariance matrix. Except for the standard Brownian trajectories with d_{f}=2, the resulting many-body contact probabilities cannot be factorized into a product of single-loop contributions. Within a Gaussian network model of a self-interacting polymer chain, which we suggested recently [K. Polovnikov et al., Soft Matter 14, 6561 (2018)1744-683X10.1039/C8SM00785C], the probabilities we calculate here can be interpreted as probabilities of multibody contacts in a fractal polymer conformation with the same fractal dimension d_{f}. This Gaussian approach, which implies a mapping from fractional Brownian motion trajectories to polymer conformations, can be used as a semiquantitative model of polymer chains in topologically stabilized conformations, e.g., in melts of unconcatenated rings or in the chromatin fiber, which is the material medium containing genetic information. The model presented here can be used, therefore, as a benchmark for interpretation of the data of many-body contacts in genomes, which we expect to be available soon in, e.g., Hi-C experiments.
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Affiliation(s)
- K E Polovnikov
- Skolkovo Institute of Science and Technology, 143026 Skolkovo, Russia.,Faculty of Physics, Lomonosov Moscow State University, 119992 Moscow, Russia
| | - S Nechaev
- Interdisciplinary Scientific Center Poncelet (ISCP), 119002, Moscow, Russia.,Lebedev Physical Institute RAS, 119991, Moscow, Russia
| | - M V Tamm
- Faculty of Physics, Lomonosov Moscow State University, 119992 Moscow, Russia.,Department of Applied Mathematics, MIEM, National Research University Higher School of Economics, 101000, Moscow, Russia
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22
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Ali Al-Radhawi M, Del Vecchio D, Sontag ED. Multi-modality in gene regulatory networks with slow promoter kinetics. PLoS Comput Biol 2019; 15:e1006784. [PMID: 30779734 PMCID: PMC6396950 DOI: 10.1371/journal.pcbi.1006784] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2018] [Revised: 03/01/2019] [Accepted: 01/14/2019] [Indexed: 12/27/2022] Open
Abstract
Phenotypical variability in the absence of genetic variation often reflects complex energetic landscapes associated with underlying gene regulatory networks (GRNs). In this view, different phenotypes are associated with alternative states of complex nonlinear systems: stable attractors in deterministic models or modes of stationary distributions in stochastic descriptions. We provide theoretical and practical characterizations of these landscapes, specifically focusing on stochastic Slow Promoter Kinetics (SPK), a time scale relevant when transcription factor binding and unbinding are affected by epigenetic processes like DNA methylation and chromatin remodeling. In this case, largely unexplored except for numerical simulations, adiabatic approximations of promoter kinetics are not appropriate. In contrast to the existing literature, we provide rigorous analytic characterizations of multiple modes. A general formal approach gives insight into the influence of parameters and the prediction of how changes in GRN wiring, for example through mutations or artificial interventions, impact the possible number, location, and likelihood of alternative states. We adapt tools from the mathematical field of singular perturbation theory to represent stationary distributions of Chemical Master Equations for GRNs as mixtures of Poisson distributions and obtain explicit formulas for the locations and probabilities of metastable states as a function of the parameters describing the system. As illustrations, the theory is used to tease out the role of cooperative binding in stochastic models in comparison to deterministic models, and applications are given to various model systems, such as toggle switches in isolation or in communicating populations, a synthetic oscillator, and a trans-differentiation network.
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Affiliation(s)
- M. Ali Al-Radhawi
- Departments of Electrical and Computer Engineering and of Bioengineering, Northeastern University, Boston, Massachusetts, United States of America
| | - Domitilla Del Vecchio
- Department of Mechanical Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts, United States of America
| | - Eduardo D. Sontag
- Departments of Electrical and Computer Engineering and of Bioengineering, Northeastern University, Boston, Massachusetts, United States of America
- Laboratory of Systems Pharmacology, Harvard Medical School, Boston, Massachusetts, United States of America
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23
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Nakano SI, Yamaguchi D, Sugimoto N. Thermal stability and conformation of DNA and proteins under the confined condition in the matrix of hydrogels. Mol Biol Rep 2018; 45:403-411. [PMID: 29626318 DOI: 10.1007/s11033-018-4174-z] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2017] [Accepted: 03/24/2018] [Indexed: 01/15/2023]
Abstract
Spatially confined environments are seen in biological systems and in the fields of biotechnology and nanotechnology. The confinement restricts the conformational space of polymeric molecules and increasing the degree of molecular crowding. Here, we developed preparation methods for agarose and polyacrylamide gels applicable to UV spectroscopy that can evaluate the confinement effects on DNA and protein structures. Measurements of UV absorbance and CD spectra showed no significant effect of the confinement in the porous media of agarose gels on the base-pair stability of DNA polynucleotides [poly(dA)/poly(dT)] and oligonucleotides (hairpin, duplex, and triplex structures). On the other hand, a highly confined environment created by polyacrylamide gels at high concentrations increased the stability of polynucleotides while leaving that of oligonucleotides unaffected. The changes in the base-pair stability of the polynucleotides were accompanied by the perturbation of the helical conformation. The polyacrylamide gels prepared in this study were also used for the studies on proteins (lysozyme, bovine serum albumin, and myoglobin). The effects on the proteins were different from the effects on DNA structures, suggesting different nature of interactions within the gel. The experimental methods and results are useful to understand the physical properties of nucleic acids and proteins under confined conditions.
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Affiliation(s)
- Shu-Ichi Nakano
- Department of Nanobiochemistry, Faculty of Frontiers of Innovative Research in Science and Technology (FIRST), Konan University, 7-1-20, Minatojima-minamimachi, Chuo-ku, Kobe, 650-0047, Japan.
| | - Daisuke Yamaguchi
- Department of Nanobiochemistry, Faculty of Frontiers of Innovative Research in Science and Technology (FIRST), Konan University, 7-1-20, Minatojima-minamimachi, Chuo-ku, Kobe, 650-0047, Japan
| | - Naoki Sugimoto
- Department of Nanobiochemistry, Faculty of Frontiers of Innovative Research in Science and Technology (FIRST), Konan University, 7-1-20, Minatojima-minamimachi, Chuo-ku, Kobe, 650-0047, Japan.,Frontier Institute for Biomolecular Engineering Research (FIBER), Konan University, 7-1-20, Minatojima-minamimachi, Chuo-ku, Kobe, 650-0047, Japan
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24
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Krepel D, Levy Y. Intersegmental transfer of proteins between DNA regions in the presence of crowding. Phys Chem Chem Phys 2018; 19:30562-30569. [PMID: 29115315 DOI: 10.1039/c7cp05251k] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Intersegmental transfer that involves direct relocation of a DNA-binding protein from one nonspecific DNA site to another was previously shown to contribute to speeding up the identification of the DNA target site. This mechanism is promoted when the protein is composed of at least two domains that have different DNA binding affinities and thus show a degree of mobility. In this study, we investigate the effect of particle crowding on the ability of a multi-domain protein to perform intersegmental transfer. We show that although crowding conditions often favor 1D diffusion of proteins along DNA over 3D diffusion, relocation of one of the tethered domains to initiate intersegmental transfer is possible even under crowding conditions. The tendency to perform intersegmental transfer by a multi-domain protein under crowding conditions is much higher for larger crowding particles than smaller ones and can be even greater than under no-crowding conditions. We report that the asymmetry of the two domains is even magnified by the crowders. The observations that crowding supports intersegmental transfer serve as another example that in vivo complexity does not necessarily slow down DNA search kinetics by proteins.
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Affiliation(s)
- Dana Krepel
- Department of Structural Biology, Weizmann Institute of Science, Rehovot 76100, Israel.
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25
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Role of Macromolecular Crowding on the Intracellular Diffusion of DNA Binding Proteins. Sci Rep 2018; 8:844. [PMID: 29339733 PMCID: PMC5770392 DOI: 10.1038/s41598-017-18933-3] [Citation(s) in RCA: 31] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2017] [Accepted: 12/20/2017] [Indexed: 11/08/2022] Open
Abstract
Recent experiments suggest that cellular crowding facilitates the target search dynamics of proteins on DNA, the mechanism of which is not yet known. By using large scale computer simulations, we show that two competing factors, namely the width of the depletion layer that separates the crowder cloud from the DNA molecule and the degree of protein-crowder crosstalk, act in harmony to affect the target search dynamics of proteins. The impacts vary from nonspecific to specific target search regime. During a nonspecific search, dynamics of a protein is only minimally affected, whereas, a significantly different behaviour is observed when the protein starts forming a specific protein-DNA complex. We also find that the severity of impacts largely depends upon physiological crowder concentration and deviation from it leads to attenuation in the binding kinetics. Based on extensive kinetic study and binding energy landscape analysis, we further present a comprehensive molecular description of the search process that allows us to interpret the experimental findings.
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26
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Benny P, Raghunath M. Making microenvironments: A look into incorporating macromolecular crowding into in vitro experiments, to generate biomimetic microenvironments which are capable of directing cell function for tissue engineering applications. J Tissue Eng 2017; 8:2041731417730467. [PMID: 29051808 PMCID: PMC5638150 DOI: 10.1177/2041731417730467] [Citation(s) in RCA: 30] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2017] [Accepted: 08/09/2017] [Indexed: 01/07/2023] Open
Abstract
Biomimetic microenvironments are key components to successful cell culture and tissue engineering in vitro. One of the most accurate biomimetic microenvironments is that made by the cells themselves. Cell-made microenvironments are most similar to the in vivo state as they are cell-specific and produced by the actual cells which reside in that specific microenvironment. However, cell-made microenvironments have been challenging to re-create in vitro due to the lack of extracellular matrix composition, volume and complexity which are required. By applying macromolecular crowding to current cell culture protocols, cell-made microenvironments, or cell-derived matrices, can be generated at significant rates in vitro. In this review, we will examine the causes and effects of macromolecular crowding and how it has been applied in several in vitro systems including tissue engineering.
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Affiliation(s)
- Paula Benny
- Department of Biochemistry, National University of Singapore, Singapore
| | - Michael Raghunath
- Department of Biochemistry, National University of Singapore, Singapore.,Institute of Chemistry and Biotechnology, Zurich University of Applied Sciences, Wädenswil, Switzerland
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27
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Chow E, Skolnick J. DNA Internal Motion Likely Accelerates Protein Target Search in a Packed Nucleoid. Biophys J 2017; 112:2261-2270. [PMID: 28591599 DOI: 10.1016/j.bpj.2017.04.049] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2016] [Revised: 04/17/2017] [Accepted: 04/28/2017] [Indexed: 12/18/2022] Open
Abstract
Transcription factors must diffuse through densely packed and coiled DNA to find their binding sites. Using a coarse-grained model of DNA and lac repressor (LacI) in the Escherichia coli nucleoid, simulations were performed to examine how LacI diffuses in such a space. Despite the canonical picture of LacI diffusing rather freely, in reality the DNA is densely packed, is not rigid but highly mobile, and the dynamics of DNA dictates to a great extent the LacI motion. A possibly better picture of unbound LacI motion is that of gated diffusion, where DNA confines LacI in a cage, but LacI can move between cages when hindering DNA strands move out of the way. Three-dimensional diffusion constants for unbound LacI computed from simulations closely match those for unbound LacI in vivo reported in the literature. The internal motions of DNA appear to be governed by strong internal forces arising from being crowded into the small space of the nucleoid. A consequence of the DNA internal motion is that protein target search may be accelerated.
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Affiliation(s)
- Edmond Chow
- School of Computational Science and Engineering, Georgia Institute of Technology, Atlanta, Georgia.
| | - Jeffrey Skolnick
- Center for the Study of Systems Biology, School of Biosciences, Georgia Institute of Technology, Atlanta, Georgia
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28
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Nakano SI, Sugimoto N. Model studies of the effects of intracellular crowding on nucleic acid interactions. MOLECULAR BIOSYSTEMS 2017; 13:32-41. [PMID: 27819369 DOI: 10.1039/c6mb00654j] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Molecular interactions and reactions in living cells occur with high concentrations of background molecules and ions. Many research studies have shown that intracellular molecules have characteristics different from those obtained using simple aqueous solutions. To better understand the behavior of biomolecules in intracellular environments, biophysical experiments were conducted under cell-mimicking conditions in a test tube. It has been shown that the molecular environments at the physiological level of macromolecular crowding, spatial confinement, water activity and dielectric constant, have significant effects on the interactions of DNA and RNA for hybridization, higher-order folding, and catalytic activity. The experimental approaches using in vitro model systems are useful to reveal the origin of the environmental effects and to bridge the gap between the behaviors of nucleic acids in vitro and in vivo. This paper highlights the model experiments used to evaluate the influences of intracellular environment on nucleic acid interactions.
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Affiliation(s)
- Shu-Ichi Nakano
- Department of Nanobiochemistry, Faculty of Frontiers of Innovative Research in Science and Technology (FIRST), Konan University, 7-1-20, Minatojima-minamimachi, Chuo-ku, Kobe, 650-0047, Japan.
| | - Naoki Sugimoto
- Frontier Institute for Biomolecular Engineering Research (FIBER), Konan University, 7-1-20, Minatojima-minamimachi, Chuo-ku, Kobe, 650-0047, Japan. and Graduate School of Frontiers of Innovative Research in Science and Technology (FIRST), Konan University, 7-1-20, Minatojima-minamimachi, Chuo-ku, Kobe, 650-0047, Japan
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29
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Rotella C, Doni G, Bosco A, Castronovo M, De Vita A, Casalis L, Pavan GM, Parisse P. Site accessibility tailors DNA cleavage by restriction enzymes in DNA confined monolayers. NANOSCALE 2017; 9:6399-6405. [PMID: 28453019 DOI: 10.1039/c7nr00966f] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Density-tunable nanografted monolayers (NAMs) of short oligonucleotide sequences on gold surfaces show novel properties that make them suitable for advanced biosensing applications, and in particular to study the effects of crowding and confinement on biomolecular interactions. Here, combining atomic force microscopy nanolithography, topography measurements and coarse-grained molecular dynamics simulations, we investigated restriction enzyme reaction mechanisms within confined DNA brushes highlighting the role played by the DNA sequence conformation and restriction site position along the chain, respectively, in determining the accessibility of the enzyme, and its consequent cleavage efficiency.
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Affiliation(s)
- Chiara Rotella
- Elettra Sincrotrone Trieste, s.s. 14 km 163.5 in Area Science Park, Trieste, Italy.
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Lin Q, Zhou Z, Luo W, Fang M, Li M, Li H. Screening of Proximal and Interacting Proteins in Rice Protoplasts by Proximity-Dependent Biotinylation. FRONTIERS IN PLANT SCIENCE 2017; 8:749. [PMID: 28553299 PMCID: PMC5427108 DOI: 10.3389/fpls.2017.00749] [Citation(s) in RCA: 44] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/22/2016] [Accepted: 04/21/2017] [Indexed: 05/20/2023]
Abstract
Proximity-dependent biotin identification (BioID), which detects physiologically relevant proteins based on the proximity-dependent biotinylation process, has been successfully used in different organisms. In this report, we established the BioID system in rice protoplasts. Biotin ligase BirAG was obtained by removing a cryptic intron site in the BirA∗ gene when expressed in rice protoplasts. We found that protein biotinylation in rice protoplasts increased with increased expression levels of BirAG. The biotinylation effects can also be achieved by exogenous supplementation of high concentrations of biotin and long incubation time with protoplasts. By using this system, multiple proteins were identified that associated with and/or were proximate to OsFD2 in vivo. Our results suggest that BioID is a useful and generally applicable method to screen for both interacting and neighboring proteins in their native cellular environment in plant cell.
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Affiliation(s)
- Qiupeng Lin
- Guangdong Provincial Key Lab of Biotechnology for Plant Development, South China Normal UniversityGuangzhou, China
| | - Zejiao Zhou
- Guangdong Provincial Key Lab of Biotechnology for Plant Development, South China Normal UniversityGuangzhou, China
| | - Wanbin Luo
- Guangdong Provincial Key Lab of Biotechnology for Plant Development, South China Normal UniversityGuangzhou, China
| | - Maichun Fang
- Key Laboratory of Plant Resources Conservation and Sustainable Utilization, South China Botanical Garden, Chinese Academy of SciencesGuangzhou, China
- Guangdong Provincial Key Laboratory of Applied Botany, South China Botanical Garden, Chinese Academy of SciencesGuangzhou, China
| | - Meiru Li
- Key Laboratory of Plant Resources Conservation and Sustainable Utilization, South China Botanical Garden, Chinese Academy of SciencesGuangzhou, China
- Guangdong Provincial Key Laboratory of Applied Botany, South China Botanical Garden, Chinese Academy of SciencesGuangzhou, China
- *Correspondence: Meiru Li, Hongqing Li,
| | - Hongqing Li
- Guangdong Provincial Key Lab of Biotechnology for Plant Development, South China Normal UniversityGuangzhou, China
- *Correspondence: Meiru Li, Hongqing Li,
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31
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Krepel D, Gomez D, Klumpp S, Levy Y. Mechanism of Facilitated Diffusion during a DNA Search in Crowded Environments. J Phys Chem B 2016; 120:11113-11122. [DOI: 10.1021/acs.jpcb.6b07813] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Affiliation(s)
- Dana Krepel
- Department
of Structural Biology, Weizmann Institute of Science, Rehovot 76100, Israel
| | - David Gomez
- Max Planck Institute of Colloids and Interfaces, Science Park Golm, 14424 Potsdam, Germany
| | - Stefan Klumpp
- Max Planck Institute of Colloids and Interfaces, Science Park Golm, 14424 Potsdam, Germany
- Institute
for Nonlinear Dynamics, Georg-August University Göttingen, Friedrich-Hund-Platz
1, 37077 Göttingen, Germany
| | - Yaakov Levy
- Department
of Structural Biology, Weizmann Institute of Science, Rehovot 76100, Israel
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32
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Thoring L, Wüstenhagen DA, Borowiak M, Stech M, Sonnabend A, Kubick S. Cell-Free Systems Based on CHO Cell Lysates: Optimization Strategies, Synthesis of "Difficult-to-Express" Proteins and Future Perspectives. PLoS One 2016; 11:e0163670. [PMID: 27684475 PMCID: PMC5042383 DOI: 10.1371/journal.pone.0163670] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2016] [Accepted: 09/11/2016] [Indexed: 11/18/2022] Open
Abstract
Nowadays, biotechnological processes play a pivotal role in target protein production. In this context, Chinese Hamster Ovary (CHO) cells are one of the most prominent cell lines for the expression of recombinant proteins and revealed as a safe host for nearly 40 years. Nevertheless, the major bottleneck of common in vivo protein expression platforms becomes obvious when looking at the production of so called “difficult-to-express” proteins. This class of proteins comprises in particular several ion channels and multipass membrane proteins as well as cytotoxic proteins. To enhance the production of “difficult-to-express” proteins, alternative technologies were developed, mainly based on translationally active cell lysates. These so called “cell-free” protein synthesis systems enable an efficient production of different classes of proteins. Eukaryotic cell-free systems harboring endogenous microsomal structures for the synthesis of functional membrane proteins and posttranslationally modified proteins are of particular interest for future applications. Therefore, we present current developments in cell-free protein synthesis based on translationally active CHO cell extracts, underlining the high potential of this platform. We present novel results highlighting the optimization of protein yields, the synthesis of various “difficult-to-express” proteins and the cotranslational incorporation of non-standard amino acids, which was exemplarily demonstrated by residue specific labeling of the glycoprotein Erythropoietin and the multimeric membrane protein KCSA.
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Affiliation(s)
- Lena Thoring
- Department of Cell-free and Cell-based Bioproduction, Branch Bioanalysis and Bioprocesses, Fraunhofer-Institute for Cell Therapy and Immunology (IZI-BB), Potsdam-Golm, Germany
- Institute for Biotechnology, Technical University of Berlin (TUB), Gustav-Meyer-Allee 25, 13355, Berlin
| | - Doreen A. Wüstenhagen
- Department of Cell-free and Cell-based Bioproduction, Branch Bioanalysis and Bioprocesses, Fraunhofer-Institute for Cell Therapy and Immunology (IZI-BB), Potsdam-Golm, Germany
| | - Maria Borowiak
- Department of Cell-free and Cell-based Bioproduction, Branch Bioanalysis and Bioprocesses, Fraunhofer-Institute for Cell Therapy and Immunology (IZI-BB), Potsdam-Golm, Germany
| | - Marlitt Stech
- Department of Cell-free and Cell-based Bioproduction, Branch Bioanalysis and Bioprocesses, Fraunhofer-Institute for Cell Therapy and Immunology (IZI-BB), Potsdam-Golm, Germany
| | - Andrei Sonnabend
- Department of Cell-free and Cell-based Bioproduction, Branch Bioanalysis and Bioprocesses, Fraunhofer-Institute for Cell Therapy and Immunology (IZI-BB), Potsdam-Golm, Germany
- Institute for Biotechnology, Technical University of Berlin (TUB), Gustav-Meyer-Allee 25, 13355, Berlin
| | - Stefan Kubick
- Department of Cell-free and Cell-based Bioproduction, Branch Bioanalysis and Bioprocesses, Fraunhofer-Institute for Cell Therapy and Immunology (IZI-BB), Potsdam-Golm, Germany
- * E-mail:
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Sun L, Tabaka M, Hou S, Li L, Burdzy K, Aksimentiev A, Maffeo C, Zhang X, Holyst R. The Hinge Region Strengthens the Nonspecific Interaction between Lac-Repressor and DNA: A Computer Simulation Study. PLoS One 2016; 11:e0152002. [PMID: 27008630 PMCID: PMC4805274 DOI: 10.1371/journal.pone.0152002] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2015] [Accepted: 03/06/2016] [Indexed: 11/30/2022] Open
Abstract
LacI is commonly used as a model to study the protein-DNA interaction and gene regulation. The headpiece of the lac-repressor (LacI) protein is an ideal system for investigation of nonspecific binding of the whole LacI protein to DNA. The hinge region of the headpiece has been known to play a key role in the specific binding of LacI to DNA, whereas its role in nonspecific binding process has not been elucidated. Here, we report the results of explicit solvent molecular dynamics simulation and continuum electrostatic calculations suggesting that the hinge region strengthens the nonspecific interaction, accounting for up to 50% of the micro-dissociation free energy of LacI from DNA. Consequently, the rate of microscopic dissociation of LacI from DNA is reduced by 2~3 orders of magnitude in the absence of the hinge region. We find the hinge region makes an important contribution to the electrostatic energy, the salt dependence of electrostatic energy, and the number of salt ions excluded from binding of the LacI-DNA complex.
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Affiliation(s)
- Lili Sun
- Institute of Physical Chemistry PAS, Kasprzaka 44/52, 01–224, Warsaw, Poland
| | - Marcin Tabaka
- Institute of Physical Chemistry PAS, Kasprzaka 44/52, 01–224, Warsaw, Poland
| | - Sen Hou
- Institute of Physical Chemistry PAS, Kasprzaka 44/52, 01–224, Warsaw, Poland
| | - Lin Li
- Computational Biophysics and Bioinformatics, Department of Physics, Clemson University, Clemson, South Carolina, 29634, United States of America
| | - Krzysztof Burdzy
- Department of Mathematics, University of Washington, Seattle, Washington, 98195–4350, United States of America
| | - Aleksei Aksimentiev
- Department of Physics, University of Illinois, Urbana, Illinois, 61801, United States of America
| | - Christopher Maffeo
- Department of Physics, University of Illinois, Urbana, Illinois, 61801, United States of America
| | - Xuzhu Zhang
- Institute of Physical Chemistry PAS, Kasprzaka 44/52, 01–224, Warsaw, Poland
| | - Robert Holyst
- Institute of Physical Chemistry PAS, Kasprzaka 44/52, 01–224, Warsaw, Poland
- * E-mail:
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Sun L, Tabaka M, Hou S, Li L, Burdzy K, Aksimentiev A, Maffeo C, Zhang X, Holyst R. The Hinge Region Strengthens the Nonspecific Interaction between Lac-Repressor and DNA: A Computer Simulation Study. PLoS One 2016; 11:e0152002. [PMID: 27008630 DOI: 10.1371/joumal.pone.0152002] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2015] [Accepted: 03/06/2016] [Indexed: 05/27/2023] Open
Abstract
LacI is commonly used as a model to study the protein-DNA interaction and gene regulation. The headpiece of the lac-repressor (LacI) protein is an ideal system for investigation of nonspecific binding of the whole LacI protein to DNA. The hinge region of the headpiece has been known to play a key role in the specific binding of LacI to DNA, whereas its role in nonspecific binding process has not been elucidated. Here, we report the results of explicit solvent molecular dynamics simulation and continuum electrostatic calculations suggesting that the hinge region strengthens the nonspecific interaction, accounting for up to 50% of the micro-dissociation free energy of LacI from DNA. Consequently, the rate of microscopic dissociation of LacI from DNA is reduced by 2~3 orders of magnitude in the absence of the hinge region. We find the hinge region makes an important contribution to the electrostatic energy, the salt dependence of electrostatic energy, and the number of salt ions excluded from binding of the LacI-DNA complex.
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Affiliation(s)
- Lili Sun
- Institute of Physical Chemistry PAS, Kasprzaka 44/52, 01-224, Warsaw, Poland
| | - Marcin Tabaka
- Institute of Physical Chemistry PAS, Kasprzaka 44/52, 01-224, Warsaw, Poland
| | - Sen Hou
- Institute of Physical Chemistry PAS, Kasprzaka 44/52, 01-224, Warsaw, Poland
| | - Lin Li
- Computational Biophysics and Bioinformatics, Department of Physics, Clemson University, Clemson, South Carolina, 29634, United States of America
| | - Krzysztof Burdzy
- Department of Mathematics, University of Washington, Seattle, Washington, 98195-4350, United States of America
| | - Aleksei Aksimentiev
- Department of Physics, University of Illinois, Urbana, Illinois, 61801, United States of America
| | - Christopher Maffeo
- Department of Physics, University of Illinois, Urbana, Illinois, 61801, United States of America
| | - Xuzhu Zhang
- Institute of Physical Chemistry PAS, Kasprzaka 44/52, 01-224, Warsaw, Poland
| | - Robert Holyst
- Institute of Physical Chemistry PAS, Kasprzaka 44/52, 01-224, Warsaw, Poland
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Single-molecule motions and interactions in live cells reveal target search dynamics in mismatch repair. Proc Natl Acad Sci U S A 2015; 112:E6898-906. [PMID: 26575623 DOI: 10.1073/pnas.1507386112] [Citation(s) in RCA: 58] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
MutS is responsible for initiating the correction of DNA replication errors. To understand how MutS searches for and identifies rare base-pair mismatches, we characterized the dynamic movement of MutS and the replisome in real time using superresolution microscopy and single-molecule tracking in living cells. We report that MutS dynamics are heterogeneous in cells, with one MutS population exploring the nucleoid rapidly, while another MutS population moves to and transiently dwells at the replisome region, even in the absence of appreciable mismatch formation. Analysis of MutS motion shows that the speed of MutS is correlated with its separation distance from the replisome and that MutS motion slows when it enters the replisome region. We also show that mismatch detection increases MutS speed, supporting the model for MutS sliding clamp formation after mismatch recognition. Using variants of MutS and the replication processivity clamp to impair mismatch repair, we find that MutS dynamically moves to and from the replisome before mismatch binding to scan for errors. Furthermore, a block to DNA synthesis shows that MutS is only capable of binding mismatches near the replisome. It is well-established that MutS engages in an ATPase cycle, which is necessary for signaling downstream events. We show that a variant of MutS with a nucleotide binding defect is no longer capable of dynamic movement to and from the replisome, showing that proper nucleotide binding is critical for MutS to localize to the replisome in vivo. Our results provide mechanistic insight into the trafficking and movement of MutS in live cells as it searches for mismatches.
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37
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Mondal A, Bhattacherjee A. Searching target sites on DNA by proteins: Role of DNA dynamics under confinement. Nucleic Acids Res 2015; 43:9176-86. [PMID: 26400158 PMCID: PMC4627088 DOI: 10.1093/nar/gkv931] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2015] [Revised: 08/15/2015] [Accepted: 09/07/2015] [Indexed: 02/07/2023] Open
Abstract
DNA-binding proteins (DBPs) rapidly search and specifically bind to their target sites on genomic DNA in order to trigger many cellular regulatory processes. It has been suggested that the facilitation of search dynamics is achieved by combining 3D diffusion with one-dimensional sliding and hopping dynamics of interacting proteins. Although, recent studies have advanced the knowledge of molecular determinants that affect one-dimensional search efficiency, the role of DNA molecule is poorly understood. In this study, by using coarse-grained simulations, we propose that dynamics of DNA molecule and its degree of confinement due to cellular crowding concertedly regulate its groove geometry and modulate the inter-communication with DBPs. Under weak confinement, DNA dynamics promotes many short, rotation-decoupled sliding events interspersed by hopping dynamics. While this results in faster 1D diffusion, associated probability of missing targets by jumping over them increases. In contrast, strong confinement favours rotation-coupled sliding to locate targets but lacks structural flexibility to achieve desired specificity. By testing under physiological crowding, our study provides a plausible mechanism on how DNA molecule may help in maintaining an optimal balance between fast hopping and rotation-coupled sliding dynamics, to locate target sites rapidly and form specific complexes precisely.
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Affiliation(s)
- Anupam Mondal
- Center for Computational Biology, Indraprastha Institute of Information Technology (IIIT) Delhi, New Delhi-110020, India
| | - Arnab Bhattacherjee
- Center for Computational Biology, Indraprastha Institute of Information Technology (IIIT) Delhi, New Delhi-110020, India
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38
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Rees JS, Li XW, Perrett S, Lilley KS, Jackson AP. Protein Neighbors and Proximity Proteomics. Mol Cell Proteomics 2015; 14:2848-56. [PMID: 26355100 PMCID: PMC4638030 DOI: 10.1074/mcp.r115.052902] [Citation(s) in RCA: 88] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2015] [Indexed: 12/31/2022] Open
Abstract
Within cells, proteins can co-assemble into functionally integrated and spatially restricted multicomponent complexes. Often, the affinities between individual proteins are relatively weak, and proteins within such clusters may interact only indirectly with many of their other protein neighbors. This makes proteomic characterization difficult using methods such as immunoprecipitation or cross-linking. Recently, several groups have described the use of enzyme-catalyzed proximity labeling reagents that covalently tag the neighbors of a targeted protein with a small molecule such as fluorescein or biotin. The modified proteins can then be isolated by standard pulldown methods and identified by mass spectrometry. Here we will describe the techniques as well as their similarities and differences. We discuss their applications both to study protein assemblies and to provide a new way for characterizing organelle proteomes. We stress the importance of proteomic quantitation and independent target validation in such experiments. Furthermore, we suggest that there are biophysical and cell-biological principles that dictate the appropriateness of enzyme-catalyzed proximity labeling methods to address particular biological questions of interest.
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Affiliation(s)
- Johanna S Rees
- From the ‡Department of Biochemistry, University of Cambridge, Tennis Court Road, Cambridge, United Kingdom CB2 1QW, the §Cambridge Centre for Proteomics, University of Cambridge, Tennis Court Road, Cambridge, United Kingdom CB2 1QR, and
| | - Xue-Wen Li
- the ‖National Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, 15 Datun Road, Beijing 100101, China
| | - Sarah Perrett
- the ‖National Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, 15 Datun Road, Beijing 100101, China
| | - Kathryn S Lilley
- the §Cambridge Centre for Proteomics, University of Cambridge, Tennis Court Road, Cambridge, United Kingdom CB2 1QR, and
| | - Antony P Jackson
- From the ‡Department of Biochemistry, University of Cambridge, Tennis Court Road, Cambridge, United Kingdom CB2 1QW,
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39
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Kalwarczyk T, Sozanski K, Ochab-Marcinek A, Szymanski J, Tabaka M, Hou S, Holyst R. Motion of nanoprobes in complex liquids within the framework of the length-scale dependent viscosity model. Adv Colloid Interface Sci 2015; 223:55-63. [PMID: 26189602 DOI: 10.1016/j.cis.2015.06.007] [Citation(s) in RCA: 56] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2015] [Revised: 06/27/2015] [Accepted: 06/27/2015] [Indexed: 01/12/2023]
Abstract
This paper deals with the recent phenomenological model of the motion of nanoscopic objects (colloidal particles, proteins, nanoparticles, molecules) in complex liquids. We analysed motion in polymer, micellar, colloidal and protein solutions and the cytoplasm of living cells using the length-scale dependent viscosity model. Viscosity monotonically approaches macroscopic viscosity as the size of the object increases and thus gives a single, coherent picture of motion at the nano and macro scale. The model includes interparticle interactions (solvent-solute), temperature and the internal structure of a complex liquid. The depletion layer ubiquitously occurring in complex liquids is also incorporated into the model. We also discuss the biological aspects of crowding in terms of the length-scale dependent viscosity model.
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Affiliation(s)
- Tomasz Kalwarczyk
- Institute of Physical Chemistry of the Polish Academy of Sciences, Kasprzaka 44/52, 01-224 Warsaw, Poland.
| | - Krzysztof Sozanski
- Institute of Physical Chemistry of the Polish Academy of Sciences, Kasprzaka 44/52, 01-224 Warsaw, Poland
| | - Anna Ochab-Marcinek
- Institute of Physical Chemistry of the Polish Academy of Sciences, Kasprzaka 44/52, 01-224 Warsaw, Poland
| | - Jedrzej Szymanski
- Nencki Institute of Experimental Biology of the Polish Academy of Sciences, 3 Pasteur Street, 02-093 Warsaw, Poland
| | - Marcin Tabaka
- Institute of Physical Chemistry of the Polish Academy of Sciences, Kasprzaka 44/52, 01-224 Warsaw, Poland
| | - Sen Hou
- Institute of Physical Chemistry of the Polish Academy of Sciences, Kasprzaka 44/52, 01-224 Warsaw, Poland; State Key Laboratory of Medicinal Chemical Biology, Nankai University, China
| | - Robert Holyst
- Institute of Physical Chemistry of the Polish Academy of Sciences, Kasprzaka 44/52, 01-224 Warsaw, Poland.
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Kang H, Toan NM, Hyeon C, Thirumalai D. Unexpected Swelling of Stiff DNA in a Polydisperse Crowded Environment. J Am Chem Soc 2015; 137:10970-8. [PMID: 26267166 DOI: 10.1021/jacs.5b04531] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
We investigate the conformations of DNA-like stiff chains, characterized by contour length (L) and persistence length (lp), in a variety of crowded environments containing monodisperse soft spherical (SS) and spherocylindrical (SC) particles, a mixture of SS and SC, and a milieu mimicking the composition of proteins in the Escherichia coli cytoplasm. The stiff chain, whose size modestly increases in SS crowders up to ϕ ≈ 0.1, is considerably more compact at low volume fractions (ϕ ≤ 0.2) in monodisperse SC particles than in a medium containing SS particles. A 1:1 mixture of SS and SC crowders induces greater chain compaction than the pure SS or SC crowders at the same ϕ, with the effect being highly nonadditive. We also discover a counterintuitive result that the polydisperse crowding environment, mimicking the composition of a cell lysate, swells the DNA-like polymer, which is in stark contrast to the size reduction of flexible polymers in the same milieu. Trapping of the stiff chain in a fluctuating tube-like environment created by large-sized crowders explains the dramatic increase in size and persistence length of the stiff chain. In the polydisperse medium, mimicking the cellular environment, the size of the DNA (or related RNA) is determined by L/lp. At low L/lp, the size of the polymer is unaffected, whereas there is a dramatic swelling at an intermediate value of L/lp. We use these results to provide insights into recent experiments on crowding effects on RNA and also make testable predictions.
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Affiliation(s)
| | | | | | - D Thirumalai
- Korea Institute for Advanced Study , Seoul 130-722, Korea
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41
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Tabaka M, Burdzy K, Hołyst R. Method for the analysis of contribution of sliding and hopping to a facilitated diffusion of DNA-binding protein: Application to in vivo data. PHYSICAL REVIEW. E, STATISTICAL, NONLINEAR, AND SOFT MATTER PHYSICS 2015; 92:022721. [PMID: 26382446 DOI: 10.1103/physreve.92.022721] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/11/2015] [Indexed: 06/05/2023]
Abstract
DNA-binding protein searches for its target, a specific site on DNA, by means of diffusion. The search process consists of many recurrent steps of one-dimensional diffusion (sliding) along the DNA chain and three-dimensional diffusion (hopping) after dissociation of a protein from the DNA chain. Here we propose a computational method that allows extracting the contribution of sliding and hopping to the search process in vivo from the measurements of the kinetics of the target search by the lac repressor in Escherichia coli [P. Hammar et al., Science 336, 1595 (2012)]. The method combines lattice Monte Carlo simulations with the Brownian excursion theory and includes explicitly steric constraints for hopping due to the helical structure of DNA. The simulation results including all experimental data reveal that the in vivo target search is dominated by sliding. The short-range hopping to the same base pair interrupts one-dimensional sliding while long-range hopping does not contribute significantly to the kinetics of the search of the target in vivo.
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Affiliation(s)
- Marcin Tabaka
- Institute of Physical Chemistry, Polish Academy of Sciences, Kasprzaka 44/52, 01-224 Warsaw, Poland
| | - Krzysztof Burdzy
- Department of Mathematics, University of Washington, Box 354350, Seattle, Washington 98195, USA
| | - Robert Hołyst
- Institute of Physical Chemistry, Polish Academy of Sciences, Kasprzaka 44/52, 01-224 Warsaw, Poland
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42
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Real sequence effects on the search dynamics of transcription factors on DNA. Sci Rep 2015; 5:10072. [PMID: 26154484 PMCID: PMC5507490 DOI: 10.1038/srep10072] [Citation(s) in RCA: 45] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2015] [Accepted: 03/30/2015] [Indexed: 11/15/2022] Open
Abstract
Recent experiments show that transcription factors (TFs) indeed use the facilitated diffusion mechanism to locate their target sequences on DNA in living bacteria cells: TFs alternate between sliding motion along DNA and relocation events through the cytoplasm. From simulations and theoretical analysis we study the TF-sliding motion for a large section of the DNA-sequence of a common E. coli strain, based on the two-state TF-model with a fast-sliding search state and a recognition state enabling target detection. For the probability to detect the target before dissociating from DNA the TF-search times self-consistently depend heavily on whether or not an auxiliary operator (an accessible sequence similar to the main operator) is present in the genome section. Importantly, within our model the extent to which the interconversion rates between search and recognition states depend on the underlying nucleotide sequence is varied. A moderate dependence maximises the capability to distinguish between the main operator and similar sequences. Moreover, these auxiliary operators serve as starting points for DNA looping with the main operator, yielding a spectrum of target detection times spanning several orders of magnitude. Auxiliary operators are shown to act as funnels facilitating target detection by TFs.
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43
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Mahmutovic A, Berg OG, Elf J. What matters for lac repressor search in vivo--sliding, hopping, intersegment transfer, crowding on DNA or recognition? Nucleic Acids Res 2015; 43:3454-64. [PMID: 25779051 PMCID: PMC4402528 DOI: 10.1093/nar/gkv207] [Citation(s) in RCA: 40] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2015] [Accepted: 02/28/2015] [Indexed: 01/04/2023] Open
Abstract
We have investigated which aspects of transcription factor DNA interactions are most important to account for the recent in vivo search time measurements for the dimeric lac repressor. We find the best agreement for a sliding model where non-specific binding to DNA is improbable at first contact and the sliding LacI protein binds at high probability when reaching the specific Osym operator. We also find that the contribution of hopping to the overall search speed is negligible although physically unavoidable. The parameters that give the best fit reveal sliding distances, including hopping, close to what has been proposed in the past, i.e. ∼40 bp, but with an unexpectedly high 1D diffusion constant on non-specific DNA sequences. Including a mechanism of inter-segment transfer between distant DNA segments does not bring down the 1D diffusion to the expected fraction of the in vitro value. This suggests a mechanism where transcription factors can slide less hindered in vivo than what is given by a simple viscosity scaling argument or that a modification of the model is needed. For example, the estimated diffusion rate constant would be consistent with the expectation if parts of the chromosome, away from the operator site, were inaccessible for searching.
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Affiliation(s)
- Anel Mahmutovic
- Department of Cell and Molecular Biology, Science for Life Laboratory, Uppsala University, 75124 Uppsala, Sweden
| | - Otto G Berg
- Department of Cell and Molecular Biology, Science for Life Laboratory, Uppsala University, 75124 Uppsala, Sweden
| | - Johan Elf
- Department of Cell and Molecular Biology, Science for Life Laboratory, Uppsala University, 75124 Uppsala, Sweden
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Potapov I, Zhurov B, Volkov E. Multi-stable dynamics of the non-adiabatic repressilator. J R Soc Interface 2015; 12:20141315. [PMID: 25631570 PMCID: PMC4345497 DOI: 10.1098/rsif.2014.1315] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2014] [Accepted: 01/02/2015] [Indexed: 11/12/2022] Open
Abstract
The assumption of the fast binding of transcription factors (TFs) to promoters is a typical point in studies of synthetic genetic circuits functioning in bacteria. Although the assumption is effective for simplifying the models, it becomes questionable in the light of in vivo measurements of the times TF spends searching for its cognate DNA sites. We investigated the dynamics of the full idealized model of the paradigmatic genetic oscillator, the repressilator, using deterministic mathematical modelling and stochastic simulations. We found (using experimentally approved parameter values) that decreases in the TF binding rate changes the type of transition between steady state and oscillation. As a result, this gives rise to the hysteresis region in the parameter space, where both the steady state and the oscillation coexist. We further show that the hysteresis is persistent over a considerable range of the parameter values, but the presence of the oscillations is limited by the low rate of TF dimer degradation. Finally, the stochastic simulation of the model confirms the hysteresis with switching between the two attractors, resulting in highly skewed period distributions. Moreover, intrinsic noise stipulates trains of large-amplitude modulations around the stable steady state outside the hysteresis region, which makes the period distributions bimodal.
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Affiliation(s)
- Ilya Potapov
- Department of Mathematics, Tampere University of Technology, PO Box 553, Tampere 33101, Finland
| | - Boris Zhurov
- Department of Theoretical Physics, Lebedev Physical Institution, Leninskii 53, Moscow, Russia
| | - Evgeny Volkov
- Department of Theoretical Physics, Lebedev Physical Institution, Leninskii 53, Moscow, Russia
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Shin J, Cherstvy AG, Metzler R. Kinetics of polymer looping with macromolecular crowding: effects of volume fraction and crowder size. SOFT MATTER 2015; 11:472-88. [PMID: 25413029 DOI: 10.1039/c4sm02007c] [Citation(s) in RCA: 70] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/23/2023]
Abstract
The looping of polymers such as DNA is a fundamental process in the molecular biology of living cells, whose interior is characterised by a high degree of molecular crowding. We here investigate in detail the looping dynamics of flexible polymer chains in the presence of different degrees of crowding. From the analysis of the looping-unlooping rates and the looping probabilities of the chain ends we show that the presence of small crowders typically slows down the chain dynamics but larger crowders may in fact facilitate the looping. We rationalise these non-trivial and often counterintuitive effects of the crowder size on the looping kinetics in terms of an effective solution viscosity and standard excluded volume. It is shown that for small crowders the effect of an increased viscosity dominates, while for big crowders we argue that confinement effects (caging) prevail. The tradeoff between both trends can thus result in the impediment or facilitation of polymer looping, depending on the crowder size. We also examine how the crowding volume fraction, chain length, and the attraction strength of the contact groups of the polymer chain affect the looping kinetics and hairpin formation dynamics. Our results are relevant for DNA looping in the absence and presence of protein mediation, DNA hairpin formation, RNA folding, and the folding of polypeptide chains under biologically relevant high-crowding conditions.
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Affiliation(s)
- Jaeoh Shin
- Institute for Physics & Astronomy, University of Potsdam, D-14476 Potsdam-Golm, Germany.
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Kalwarczyk T, Sozanski K, Jakiela S, Wisniewska A, Kalwarczyk E, Kryszczuk K, Hou S, Holyst R. Length-scale dependent transport properties of colloidal and protein solutions for prediction of crystal nucleation rates. NANOSCALE 2014; 6:10340-10346. [PMID: 25074030 DOI: 10.1039/c4nr00647j] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/03/2023]
Abstract
We propose a scaling equation describing transport properties (diffusion and viscosity) in the solutions of colloidal particles. We apply the equation to 23 different systems including colloids and proteins differing in size (range of diameters: 4 nm to 1 μm), and volume fractions (10(-3)-0.56). In solutions under study colloids/proteins interact via steric, hydrodynamic, van der Waals and/or electrostatic interactions. We implement contribution of those interactions into the scaling law. Finally we use our scaling law together with the literature values of the barrier for nucleation to predict crystal nucleation rates of hard-sphere like colloids. The resulting crystal nucleation rates agree with existing experimental data.
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Affiliation(s)
- Tomasz Kalwarczyk
- Institute of Physical Chemistry of the Polish Academy of Sciences, Kasprzaka 44/52, 01-224 Warsaw, Poland.
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Paijmans J, ten Wolde PR. Lower bound on the precision of transcriptional regulation and why facilitated diffusion can reduce noise in gene expression. PHYSICAL REVIEW. E, STATISTICAL, NONLINEAR, AND SOFT MATTER PHYSICS 2014; 90:032708. [PMID: 25314474 DOI: 10.1103/physreve.90.032708] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/03/2014] [Indexed: 06/04/2023]
Abstract
The diffusive arrival of transcription factors at the promoter sites on DNA sets a lower bound on how accurately a cell can regulate its protein levels. Using results from the literature on diffusion-influenced reactions, we derive an analytical expression for the lower bound on the precision of transcriptional regulation. In our theory, transcription factors can perform multiple rounds of one-dimensional (1D) diffusion along the DNA and 3D diffusion in the cytoplasm before binding to the promoter. Comparing our expression for the lower bound on the precision against results from Green's function reaction dynamics simulations shows that the theory is highly accurate under biologically relevant conditions. Our results demonstrate that, to an excellent approximation, the promoter switches between the transcription-factor bound and unbound state in a Markovian fashion. This remains true even in the presence of sliding, i.e., with 1D diffusion along the DNA. This has two important implications: (1) Minimizing the noise in the promoter state is equivalent to minimizing the search time of transcription factors for their promoters; (2) the complicated dynamics of 3D diffusion in the cytoplasm and 1D diffusion along the DNA can be captured in a well-stirred model by renormalizing the promoter association and dissociation rates, making it possible to efficiently simulate the promoter dynamics using Gillespie simulations. Based on the recent experimental observation that sliding can speed up the promoter search by a factor of 4, our theory predicts that sliding can enhance the precision of transcriptional regulation by a factor of 2.
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Affiliation(s)
- Joris Paijmans
- FOM Institute AMOLF, Science Park 104, 1098 XG Amsterdam, The Netherlands
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