Intracellular environment can change protein conformational dynamics in cells through weak interactions

Article Biochemistry & Molecular Biology

A Difference between In Vitro and In-Cell Protein Dimer Formation

I-Te Chu et al.

Summary: The chemical interactions in cells play a crucial role in the stability of proteins and protein complexes. Research found that these interactions can unfold the molten globule form of proteins and alter the species present in cells.

BIOCHEMISTRY (2022)

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Review Chemistry, Multidisciplinary

Radio Signals from Live Cells: The Coming of Age of In-Cell Solution NMR

Enrico Luchinat et al.

Summary: A detailed understanding of the complex processes that contribute to the functionality of cells and organisms is crucial for disease comprehension and drug development. Among the available structural techniques, solution NMR is the only method capable of investigating macromolecular structures and dynamic behaviors directly within living cells. Over the past 20 years, in-cell NMR has emerged as a powerful tool, allowing researchers to study cell samples, isotopic labeling, and bioreactor devices, thus enhancing the lifetime of cells for real-time monitoring of intracellular metabolites and proteins.

CHEMICAL REVIEWS (2022)

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Review Chemistry, Multidisciplinary

In-Cell Structural Biology by NMR: The Benefits of the Atomic Scale

Francois-Xavier Theillet

Summary: In-cell structural biology by NMR spectroscopy aims to extract structural information of proteins or nucleic acids in their native cellular environments. This review provides comprehensive but accessible information on the methods, fundamental knowledge, and applications of in-cell structural biology by NMR, along with an overview of other related techniques. In the era of large-scale screenings and deep learning, NMR spectroscopy plays a vital role in providing accurate and qualitative experimental evidence to understand the cellular interior.

CHEMICAL REVIEWS (2022)

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Article Chemistry, Multidisciplinary

In-Cell Quantification of Drugs by Magic-Angle Spinning Dynamic Nuclear Polarization NMR

Andrea Bertarello et al.

Summary: Determination of intracellular drug concentrations is crucial for understanding drug function and efficacy, but currently there is no experimental technique that satisfies the requirements of nondestructive measurement, no modification of drugs or targets, and detection of low concentrations. In this study, the use of magic-angle spinning dynamic nuclear polarization technique is proposed to fulfill these requirements, and successful estimation of intracellular drug amounts is demonstrated for the first time.

JOURNAL OF THE AMERICAN CHEMICAL SOCIETY (2022)

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Review Chemistry, Multidisciplinary

Radio Signals from Live Cells: The Coming of Age of In-Cell Solution NMR

Enrico Luchinat et al.

Summary: Understanding the complex processes that keep cells and organisms alive is essential for comprehending diseases and developing new drugs. Solution NMR is a key technique to investigate the structure and dynamic behavior of biological macromolecules within living cells at high resolution.

CHEMICAL REVIEWS (2022)

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Review Chemistry, Multidisciplinary

In-Cell Structural Biology by NMR: The Benefits of the Atomic Scale

Francois-Xavier Theillet

Summary: In-cell structural biology by NMR aims to extract structural information about proteins or nucleic acids in their natural cell environment. NMR spectroscopy plays a crucial role in providing accurate and quantitative experimental evidence for understanding the interior life of cells.

CHEMICAL REVIEWS (2022)

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Article Chemistry, Multidisciplinary

In-Cell NMR Spectroscopy of Functional Riboswitch Aptamers in Eukaryotic Cells

P. Broft et al.

Summary: This study reports the in-cell NMR-spectroscopic observation of the binding of the bacterial riboswitch ligand with the aptamer domain in eukaryotic cells, demonstrating the maintenance of binding mode in eukaryotic cellular environment. Additionally, the study shows that the in-cell NMR setup can be used for characterization of large, non-modified RNA molecules in cells.

ANGEWANDTE CHEMIE-INTERNATIONAL EDITION (2021)

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Article Chemistry, Multidisciplinary

Broadband Dynamics of Ubiquitin by Anionic and Cationic Nanoparticle Assisted NMR Spin Relaxation

Stacey Wardenfelt et al.

Summary: This study utilizes a new method to investigate the dynamics of protein interactions with nanoparticles. The results indicate that the interaction between proteins and silica nanoparticles of different sizes is not significant, and the backbone dynamics are confined to sub-nanosecond timescales.

ANGEWANDTE CHEMIE-INTERNATIONAL EDITION (2021)

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Article Biochemistry & Molecular Biology

Dynamical spectroscopy and microscopy of proteins in cells

Martin Gruebele et al.

Summary: Research combining in-cell NMR spectroscopy and time-resolved fluorescence microscopies has accelerated the study of fast cell dynamics, revealing protein surfaces as critical components in controlling protein mobility, function, and communication in cells through post-translational modifications.

CURRENT OPINION IN STRUCTURAL BIOLOGY (2021)

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Article Chemistry, Multidisciplinary

Impact of In-Cell and In-Vitro Crowding on the Conformations and Dynamics of an Intrinsically Disordered Protein

Iwo Konig et al.

Summary: The concentrations of macromolecules within cells can affect the conformations and dynamics of proteins. By reducing cell volume through hyperosmotic stress, it was found that intrinsically disordered proteins exhibit compaction and slower dynamics in more crowded cells. This concentration and length-scale dependence of crowding can be explained by polymer theory and depletion interactions.

ANGEWANDTE CHEMIE-INTERNATIONAL EDITION (2021)

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Article Biochemistry & Molecular Biology

Polyanions Cause Protein Destabilization Similar to That in Live Cells

Therese Sorensen et al.

Summary: The structural stability of proteins changes significantly upon transfer to the crowded interior of live cells. The intracellular environment behaves like a polyanionic system, which influences protein stability through preferential interactions with globally unfolded proteins. This generic influence of polyanions on protein stability needs to be considered in the evaluation of in vivo data in addition to sequence-specific contributions.

BIOCHEMISTRY (2021)

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Article Chemistry, Multidisciplinary

Quantifying Protein Electrostatic Interactions in Cells by Nuclear Magnetic Resonance Spectroscopy

Xiangfei Song et al.

Summary: This study investigated how the cellular environment affects electrostatic interactions between protein charges using in-cell nuclear magnetic resonance spectroscopy. The results showed that the transfer free energy in cells can modulate protein electrostatic interactions, with a larger effect on the interactions in the unfolded state compared to the folded state. This work highlights the importance of direct in-cell studies for understanding protein interactions and function.

JOURNAL OF THE AMERICAN CHEMICAL SOCIETY (2021)

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Article Chemistry, Multidisciplinary

Sequestration of Proteins in Stress Granules Relies on the In-Cell but Not the In Vitro Folding Stability

Nirnay Samanta et al.

Summary: The folding stability of SOD1 determines its association with SGs, regardless of aggregation. Specific protein-protein interactions within the cytoplasm compared to SGs play a role in determining the partitioning of folding states during heat stress.

JOURNAL OF THE AMERICAN CHEMICAL SOCIETY (2021)

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Article Chemistry, Multidisciplinary

Identification and Quantification of Glycans in Whole Cells: Architecture of Microalgal Polysaccharides Described by Solid-State Nuclear Magnetic Resonance

Alexandre Poulhazan et al.

Summary: The article presents a widely applicable protocol for identifying and quantifying the carbohydrate content of microalgae using magic-angle-spinning solid-state NMR spectroscopy, with validation from mass-spectrometry analysis; it is found that starch is the most abundant polysaccharide in a cellulose-deficient microalga, adopting an organized and rigid structure in the cell; the research suggests that most carbohydrates in the cell wall of the microalga are largely mobile.

JOURNAL OF THE AMERICAN CHEMICAL SOCIETY (2021)

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Article Multidisciplinary Sciences

The intracellular environment affects protein-protein interactions

Shannon L. Speer et al.

Summary: Protein-protein interactions are more influenced by chemical interactions than hard-core repulsions in cells; increasing negative charge on the homodimer surface enhances stability in cells; oocytes are less crowded than E. coli cells, leading to greater stability of protein complexes.

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2021)

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Article Biochemistry & Molecular Biology

Osmolytes Can Destabilize Proteins in Cells by Modulating Electrostatics and Quinary Interactions

Xiangfei Song et al.

Summary: This study found that glycerol stabilizes protein folding, while betaine and taurine destabilize protein folding by affecting folding rates and instability. Betaine and taurine enhance quinary interactions between the protein and cellular environment, weakening electrostatic attraction in protein salt bridges, leading to protein destabilization in E. coli cells. These factors counteract the preferential exclusion mechanism used by osmolytes to stabilize proteins.

ACS CHEMICAL BIOLOGY (2021)

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Article Chemistry, Physical

NMR Spin Relaxation Theory of Biomolecules Undergoing Highly Asymmetric Exchange with Large Interaction Partners

Gregory Jameson et al.

Summary: This study discusses the enhanced nuclear magnetic resonance relaxation effects resulting from transient interactions of proteins and other molecules with larger structures, such as nanoparticles. A unified theoretical framework based on the stochastic Liouville equation is proposed to analyze these effects and provide insights into the dynamics of protein-nanoparticle interactions. Theoretical and practical implications of the framework are demonstrated, showing how transverse relaxation can report on internal dynamics impacted by the kinetics of binding across various timescales.

JOURNAL OF CHEMICAL THEORY AND COMPUTATION (2021)

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Article Chemistry, Physical

Cellular Sticking Can Strongly Reduce Complex Binding by Speeding Dissociation

Caitlin M. Davis et al.

Summary: The cellular environment significantly influences protein-RNA binding affinities and dynamics, with in vivo binding affinities often significantly lower compared to in vitro. Experimental results and a quantitative model indicate that cellular components can affect the binding of U1A and SL2 in live cells, suggesting that higher binding affinities measured or designed in vitro are necessary for proper binding in vivo.

JOURNAL OF PHYSICAL CHEMISTRY B (2021)

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Article Chemistry, Multidisciplinary

Observation of Sub-Microsecond Protein Methyl-Side Chain Dynamics by Nanoparticle-Assisted NMR Spin Relaxation

Xinyao Xiang et al.

Summary: Amino-acid side-chain properties play a crucial role in determining protein function. The introduced method of nano-particle-assisted NMR spin relaxation (NASR) provides insight into the dynamics of side chains on a wider range of time scales. This method offers new perspectives on the interplay between protein structure, dynamics, and molecular interactions influencing protein function.

JOURNAL OF THE AMERICAN CHEMICAL SOCIETY (2021)

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Article Chemistry, Multidisciplinary

Drug Screening in Human Cells by NMR Spectroscopy Allows the Early Assessment of Drug Potency

Enrico Luchinat et al.

ANGEWANDTE CHEMIE-INTERNATIONAL EDITION (2020)

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Article Chemistry, Multidisciplinary

Quantitative Cooperative Binding Model for Intrinsically Disordered Proteins Interacting with Nanomaterials

Da-Wei Li et al.

JOURNAL OF THE AMERICAN CHEMICAL SOCIETY (2020)

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Article Chemistry, Analytical

Real-Time Quantitative In-Cell NMR: Ligand Binding and Protein Oxidation Monitored in Human Cells Using Multivariate Curve Resolution

Enrico Luchinat et al.

ANALYTICAL CHEMISTRY (2020)

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In-cell destabilization of a homodimeric protein complex detected by DEER spectroscopy

Yin Yang et al.

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2020)

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Generating Five Independent Molecular Alignments for Simultaneous Protein Structure and Dynamics Determination Using Nuclear Magnetic Resonance Spectroscopy

Yefei Wang et al.

ANALYTICAL CHEMISTRY (2020)

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Connecting Longitudinal and Transverse Relaxation Rates in Live-Cell NMR

Sarah Leeb et al.

JOURNAL OF PHYSICAL CHEMISTRY B (2020)

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Stability Effect of Quinary Interactions Reversed by Single Point Mutations

David Gnutt et al.

JOURNAL OF THE AMERICAN CHEMICAL SOCIETY (2019)

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Quantifying protein dynamics and stability in a living organism

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NATURE COMMUNICATIONS (2019)

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High-Resolution Protein 3D Structure Determination in Living Eukaryotic Cells

Takashi Tanaka et al.

ANGEWANDTE CHEMIE-INTERNATIONAL EDITION (2019)

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Site-Specific Tagging of Proteins with Paramagnetic Ions for Determination of Protein Structures in Solution and in Cells

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ACCOUNTS OF CHEMICAL RESEARCH (2019)

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Characterization of Residue Specific Protein Folding and Unfolding Dynamics in Cells

Xiangfei Song et al.

JOURNAL OF THE AMERICAN CHEMICAL SOCIETY (2019)

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Functional protein dynamics on uncharted time scales detected by nanoparticle-assisted NMR spin relaxation

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Potent Inhibitors of Mycobacterium tuberculosis Growth Identified by Using in-Cell NMR-based Screening

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Balanced Regulation of Redox Status of Intracellular Thioredoxin Revealed by in-Cell NMR

Ayano Mochizuki et al.

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Quantitative Binding Behavior of Intrinsically Disordered Proteins to Nanoparticle Surfaces at Individual Residue Level

Mouzhe Xie et al.

CHEMISTRY-A EUROPEAN JOURNAL (2018)

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Microviscosity in E-coli Cells from Time-Resolved Linear Dichroism Measurements

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In-Cell Titration of Small Solutes Controls Protein Stability and Aggregation

Shahar Sukenik et al.

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Physicochemical code for quinary protein interactions in Escherichia coli

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Atomic resolution conformational dynamics of intrinsically disordered proteins from NMR spin relaxation

Nicola Salvi et al.

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A cell is more than the sum of its (dilute) parts: A brief history of quinary structure

Rachel D. Cohen et al.

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Short Arginine Motifs Drive Protein Stickiness in the Escherichia coli Cytoplasm

Ciara Kyne et al.

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Entropy Drives the Formation of Salt Bridges in the Protein GB3

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Specific Detection of Cellular Glutamine Hydrolysis in Live Cells Using HNCO Triple Resonance NMR

Sujin Lee et al.

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3D structure determination of a protein in living cells using paramagnetic NMR spectroscopy

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The Role of Protein Loops and Linkers in Conformational Dynamics and Allostery

Elena Papaleo et al.

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In-Cell Protein Structures from 2D NMR Experiments

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Electrostatic Contributions to Protein Quinary Structure

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Structural disorder of monomeric α-synuclein persists in mammalian cells

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NATURE (2016)

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Intracellular repair of oxidation-damaged alpha-synuclein fails to target C-terminal modification sites

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Enzyme Dynamics from NMR Spectroscopy

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Probing Protein Quinary Interactions by In-Cell Nuclear Magnetic Resonance Spectroscopy

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Thermodynamics of protein destabilization in live cells

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Quinary structure modulates protein stability in cells

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Residue level quantification of protein stability in living cells

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Quinary protein structure and the consequences of crowding in living cells: Leaving the test-tube behind

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19F NMR Spectroscopy as a Probe of Cytoplasmic Viscosity and Weak Protein Interactions in Living Cells

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Molecular Crowding Drives Active Pin1 into Nonspecific Complexes with Endogenous Proteins Prior to Substrate Recognition

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Pruning the ALS-Associated Protein SOD1 for in-Cell NMR

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Structure of Proteins in Eukaryotic Compartments

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Protein-binding dynamics imaged in a living cell

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Macromolecular Crowding Fails To Fold a Globular Protein in Cells

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Evaluation of backbone proton positions and dynamics in a small protein by liquid crystal NMR spectroscopy

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Characterization of the overall and local dynamics of a protein with intermediate rotational anisotropy: Differentiating between conformational exchange and anisotropic diffusion in the B3 domain of protein G

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Intracellular environment can change protein conformational dynamics in cells through weak interactions

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