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Cells
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Advances in Methods of Molecular Dynamics in Live Cells
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Advances in Methods of Molecular Dynamics in Live Cells

A special issue of Cells (ISSN 2073-4409). This special issue belongs to the section "Cell Methods".

Deadline for manuscript submissions: closed (20 June 2022) | Viewed by 25906

Special Issue Editor

Dr. Bin Wu

E-Mail Website
Guest Editor
Department of Biophysics and Biophysical Chemistry, Johns Hopkins University, Baltimore, MD 21218, USA
Interests: RNA; translation; transcription; single molecule imaging; fluorescence imaging
Special Issues, Collections and Topics in MDPI journals

Special Issue Information

Dear Colleagues,

Live cell research has become an indispensable avenue for cell biology. By examining biomolecules and cellular structures over time to follow their dynamics, scientists can study cellular function under native physiological or pathological conditions. Over the last two decades, advances in microscopy and spectroscopy instrumentation and methodology has increased the spatial and temporal resolution; engineering of novel probes allows diverse biological processes tractable in live cells; revolution in genetic engineering makes it convenient to tag endogenous biomolecules and study them under native concentration and stoichiometry; progress in computational tools synergizes with quantitative live cell experiment and allows scientists to build in silico cell models. We are in an exciting era to further push the boundary of live cell research.

In this Special Issue of Cells, I invite you to contribute original research articles, reviews, or shorter perspective articles on all aspects related to “Advances in Methods of Molecular Dynamics in Live cells”. Expert articles describing innovative instrumentation, probe or sensor design, analysis tools, molecular or cellular models, or novel application of methods to study molecular dynamics in live cells are highly welcome. Relevant topics include but not limited to:

- Microscopy

- Spectroscopy

- Probe design

- Molecular or cellular models

- Analysis tools

- Theoretical modeling

- Fluorescence

- Label free

- Fluorescence recovery after photobleaching

- Foster resonance energy transfer

- Fluorescence correlation spectroscopy

- Fluorescence lifetime

- Fluorescence spectroscopy

Dr. Bin Wu
Guest Editor

Manuscript Submission Information

Manuscripts should be submitted online at www.mdpi.com by registering and logging in to this website. Once you are registered, click here to go to the submission form. Manuscripts can be submitted until the deadline. All submissions that pass pre-check are peer-reviewed. Accepted papers will be published continuously in the journal (as soon as accepted) and will be listed together on the special issue website. Research articles, review articles as well as short communications are invited. For planned papers, a title and short abstract (about 100 words) can be sent to the Editorial Office for announcement on this website.

Submitted manuscripts should not have been published previously, nor be under consideration for publication elsewhere (except conference proceedings papers). All manuscripts are thoroughly refereed through a single-blind peer-review process. A guide for authors and other relevant information for submission of manuscripts is available on the Instructions for Authors page. Cells is an international peer-reviewed open access semimonthly journal published by MDPI.

Please visit the Instructions for Authors page before submitting a manuscript. The Article Processing Charge (APC) for publication in this open access journal is 2700 CHF (Swiss Francs). Submitted papers should be well formatted and use good English. Authors may use MDPI's English editing service prior to publication or during author revisions.

Keywords

  • live cell
  • microscopy
  • Spectroscopy
  • probe design
  • molecular or cellular models
  • analysis tools
  • theoretical modeling
  • fluorescence
  • label free

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Published Papers (7 papers)

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Research

24 pages, 4987 KiB  
Article
A Promising Method for the Determination of Cell Viability: The Membrane Potential Cell Viability Assay
by Eneko Madorran, Andraž Stožer, Zoran Arsov, Uroš Maver and Jan Rožanc
Cells 2022, 11(15), 2314; https://doi.org/10.3390/cells11152314 - 27 Jul 2022
Cited by 7 | Viewed by 4965
Abstract
Determining the viability of cells is fraught with many uncertainties. It is often difficult to determine whether a cell is still alive, approaching the point of no return, or dead. Today, there are many methods for determining cell viability. Most rely on an [...] Read more.
Determining the viability of cells is fraught with many uncertainties. It is often difficult to determine whether a cell is still alive, approaching the point of no return, or dead. Today, there are many methods for determining cell viability. Most rely on an indirect determination of cell death (metabolism, molecular transport, and leakage, to name a few). In contrast, we have developed a promising novel method for a “direct” determination of cell viability. The potential method assesses cell membrane integrity (which is essential for all viable cells) by measuring the electrical potential of the cell membrane. To test the assay, we chose two different cell types, blood macrophages (TLT) and breast cancer epithelial cells (MCF 7). We exposed them to seven different toxic scenarios (arsenic (V), UV light, hydrogen peroxide, nutrient starvation, Tetrabromobisphenol A, fatty acids, and 5-fluorouracil) to induce different cell death pathways. Under controlled test conditions, the assay showed good accuracy when comparing the toxicity assessment with well-established methods. Moreover, the method showed compatibility with live cell imaging. Although we know that further studies are needed to confirm the performance of the assay in other situations, the results obtained are promising for their wider application in the future. Full article
(This article belongs to the Special Issue Advances in Methods of Molecular Dynamics in Live Cells)
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17 pages, 3348 KiB  
Article
Prediction of Sperm Progression in Three Dimensions Using Rapid Optical Imaging and Dynamic Mechanical Modeling
by Mayssam Nassir, Mattan Levi, Gili Dardikman-Yoffe, Simcha K. Mirsky and Natan T. Shaked
Cells 2022, 11(8), 1319; https://doi.org/10.3390/cells11081319 - 13 Apr 2022
Cited by 7 | Viewed by 5391
Abstract
We present a multidisciplinary approach for predicting how sperm cells with various morphologies swim in three-dimensions (3D), from milliseconds to much longer time scales at spatial resolutions of less than half a micron. We created the sperm 3D geometry and built a numerical [...] Read more.
We present a multidisciplinary approach for predicting how sperm cells with various morphologies swim in three-dimensions (3D), from milliseconds to much longer time scales at spatial resolutions of less than half a micron. We created the sperm 3D geometry and built a numerical mechanical model using the experimentally acquired dynamic 3D refractive-index profiles of sperm cells swimming in vitro as imaged by high-resolution optical diffraction tomography. By controlling parameters in the model, such as the size and shape of the sperm head and tail, we can then predict how different sperm cells, normal or abnormal, would swim in 3D, in the short or long term. We quantified various 3D structural factor effects on the sperm long-term motility. We found that some abnormal sperm cells swim faster than normal sperm cells, in contrast to the commonly used sperm selection assumption during in vitro fertilization (IVF), according to which sperm cells should mainly be chosen based on their progressive motion. We thus establish a new tool for sperm analysis and male-infertility diagnosis, as well as sperm selection criteria for fertility treatments. Full article
(This article belongs to the Special Issue Advances in Methods of Molecular Dynamics in Live Cells)
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20 pages, 3261 KiB  
Article
Mechanistic Origin of Different Binding Affinities of SARS-CoV and SARS-CoV-2 Spike RBDs to Human ACE2
by Zhi-Bi Zhang, Yuan-Ling Xia, Jian-Xin Shen, Wen-Wen Du, Yun-Xin Fu and Shu-Qun Liu
Cells 2022, 11(8), 1274; https://doi.org/10.3390/cells11081274 - 9 Apr 2022
Cited by 9 | Viewed by 3138
Abstract
The receptor-binding domain (RBD) of the SARS-CoV-2 spike protein (RBDCoV2) has a higher binding affinity to the human receptor angiotensin-converting enzyme 2 (ACE2) than the SARS-CoV RBD (RBDCoV). Here, we performed molecular dynamics (MD) simulations, binding free energy (BFE) [...] Read more.
The receptor-binding domain (RBD) of the SARS-CoV-2 spike protein (RBDCoV2) has a higher binding affinity to the human receptor angiotensin-converting enzyme 2 (ACE2) than the SARS-CoV RBD (RBDCoV). Here, we performed molecular dynamics (MD) simulations, binding free energy (BFE) calculations, and interface residue contact network (IRCN) analysis to explore the mechanistic origin of different ACE2-binding affinities of the two RBDs. The results demonstrate that, when compared to the RBDCoV2-ACE2 complex, RBDCoV-ACE2 features enhanced dynamicsand inter-protein positional movements and increased conformational entropy and conformational diversity. Although the inter-protein electrostatic attractive interactions are the primary determinant for the high ACE2-binding affinities of both RBDs, the significantly enhanced electrostatic attractive interactions between ACE2 and RBDCoV2 determine the higher ACE2-binding affinity of RBDCoV2 than of RBDCoV. Comprehensive comparative analyses of the residue BFE components and IRCNs between the two complexes reveal that it is the residue changes at the RBD interface that lead to the overall stronger inter-protein electrostatic attractive force in RBDCoV2-ACE2, which not only tightens the interface packing and suppresses the dynamics of RBDCoV2-ACE2, but also enhances the ACE2-binding affinity of RBDCoV2. Since the RBD residue changes involving gain/loss of the positively/negatively charged residues can greatly enhance the binding affinity, special attention should be paid to the SARS-CoV-2 variants carrying such mutations, particularly those near or at the binding interfaces with the potential to form hydrogen bonds and/or salt bridges with ACE2. Full article
(This article belongs to the Special Issue Advances in Methods of Molecular Dynamics in Live Cells)
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20 pages, 8125 KiB  
Article
Investigation of Colonic Regeneration via Precise Damage Application Using Femtosecond Laser-Based Nanosurgery
by Sören Donath, Leon Angerstein, Lara Gentemann, Dominik Müller, Anna E. Seidler, Christian Jesinghaus, André Bleich, Alexander Heisterkamp, Manuela Buettner and Stefan Kalies
Cells 2022, 11(7), 1143; https://doi.org/10.3390/cells11071143 - 28 Mar 2022
Cited by 3 | Viewed by 2919
Abstract
Organoids represent the cellular composition of natural tissue. So called colonoids, organoids derived from colon tissue, are a good model for understanding regeneration. However, next to the cellular composition, the surrounding matrix, the cell–cell interactions, and environmental factors have to be considered. This [...] Read more.
Organoids represent the cellular composition of natural tissue. So called colonoids, organoids derived from colon tissue, are a good model for understanding regeneration. However, next to the cellular composition, the surrounding matrix, the cell–cell interactions, and environmental factors have to be considered. This requires new approaches for the manipulation of a colonoid. Of key interest is the precise application of localized damage and the following cellular reaction. We have established multiphoton imaging in combination with femtosecond laser-based cellular nanosurgery in colonoids to ablate single cells in the colonoids’ crypts, the proliferative zones, and the differentiated zones. We observed that half of the colonoids recovered within six hours after manipulation. An invagination of the damaged cell and closing of the structure was observed. In about a third of the cases of targeted crypt damage, it caused a stop in crypt proliferation. In the majority of colonoids ablated in the crypt, the damage led to an increase in Wnt signalling, indicated via a fluorescent lentiviral biosensor. qRT-PCR analysis showed increased expression of various proliferation and Wnt-associated genes in response to damage. Our new model of probing colonoid regeneration paves the way to better understand organoid dynamics on a single cell level. Full article
(This article belongs to the Special Issue Advances in Methods of Molecular Dynamics in Live Cells)
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18 pages, 6919 KiB  
Article
βIII-Tubulin Structural Domains Regulate Mitochondrial Network Architecture in an Isotype-Specific Manner
by Amelia L. Parker, Wee Siang Teo, Simon Brayford, Ullhas K. Moorthi, Senthil Arumugam, Charles Ferguson, Robert G. Parton, Joshua A. McCarroll and Maria Kavallaris
Cells 2022, 11(5), 776; https://doi.org/10.3390/cells11050776 - 23 Feb 2022
Cited by 3 | Viewed by 3182
Abstract
βIII-tubulin is a neuronal microtubule protein that is aberrantly expressed in epithelial cancers. The microtubule network is implicated in regulating the architecture and dynamics of the mitochondrial network, although the isotype-specific role for β-tubulin proteins that constitute this microtubule network remains unclear. High-resolution [...] Read more.
βIII-tubulin is a neuronal microtubule protein that is aberrantly expressed in epithelial cancers. The microtubule network is implicated in regulating the architecture and dynamics of the mitochondrial network, although the isotype-specific role for β-tubulin proteins that constitute this microtubule network remains unclear. High-resolution electron microscopy revealed that manipulation of βIII-tubulin expression levels impacts the volume and shape of mitochondria. Analysis of the structural domains of the protein identifies that the C-terminal tail of βIII-tubulin, which distinguishes this protein from other β-tubulin isotypes, significantly contributes to the isotype-specific effects of βIII-tubulin on mitochondrial architecture. Mass spectrometry analysis of protein–protein interactions with β-tubulin isotypes identifies that βIII-tubulin specifically interacts with regulators of mitochondrial dynamics that may mediate these functional effects. Advanced quantitative dynamic lattice light sheet imaging of the mitochondrial network reveals that βIII-tubulin promotes a more dynamic and extended reticular mitochondrial network, and regulates mitochondrial volume. A regulatory role for the βIII-tubulin C-terminal tail in mitochondrial network dynamics and architecture has widespread implications for the maintenance of mitochondrial homeostasis in health and disease. Full article
(This article belongs to the Special Issue Advances in Methods of Molecular Dynamics in Live Cells)
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11 pages, 2676 KiB  
Article
Application of Rapid Fluorescence Lifetime Imaging Microscopy (RapidFLIM) to Examine Dynamics of Nanoparticle Uptake in Live Cells
by Aria Ahmed-Cox, Alexander M. Macmillan, Elvis Pandzic, Renee M. Whan and Maria Kavallaris
Cells 2022, 11(4), 642; https://doi.org/10.3390/cells11040642 - 12 Feb 2022
Cited by 3 | Viewed by 3060
Abstract
A key challenge in nanomedicine stems from the continued need for a systematic understanding of the delivery of nanoparticles in live cells. Complexities in delivery are often influenced by the biophysical characteristics of nanoparticles, where even subtle changes to nanoparticle designs can alter [...] Read more.
A key challenge in nanomedicine stems from the continued need for a systematic understanding of the delivery of nanoparticles in live cells. Complexities in delivery are often influenced by the biophysical characteristics of nanoparticles, where even subtle changes to nanoparticle designs can alter cellular uptake, transport and activity. Close examination of these processes, especially with imaging, offers important insights that can aid in future nanoparticle design or translation. Rapid fluorescence lifetime imaging microscopy (RapidFLIM) is a potentially valuable technology for examining intracellular mechanisms of nanoparticle delivery by directly correlating visual data with changes in the biological environment. To date, applications for this technology in nanoparticle research have not been explored. A PicoQuant RapidFLIM system was used together with commercial silica nanoparticles to follow particle uptake in glioblastoma cells. Importantly, RapidFLIM imaging showed significantly improved image acquisition speeds over traditional FLIM, which enabled the tracking of nanoparticle uptake into subcellular compartments. We determined mean lifetime changes and used this to delineate significant changes in nanoparticle lifetimes (>0.39 ns), which showed clustering of these tracks proximal to both extracellular and nuclear membrane boundaries. These findings demonstrate the ability of RapidFLIM to track, localize and quantify changes in single nanoparticle fluorescence lifetimes and highlight RapidFLIM as a valuable tool for multiparameter visualization and analysis of nanoparticle molecular dynamics in live cells. Full article
(This article belongs to the Special Issue Advances in Methods of Molecular Dynamics in Live Cells)
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Graphical abstract

14 pages, 4016 KiB  
Article
Design and Construction of a Chamber Enabling the Observation of Living Cells in the Field of a Constant Magnetic Force
by Daniel Dziob, Jakub Ramian, Jan Ramian, Bartosz Lisowski and Jadwiga Laska
Cells 2021, 10(12), 3339; https://doi.org/10.3390/cells10123339 - 28 Nov 2021
Cited by 2 | Viewed by 2406
Abstract
The aim of the work was to design and construct a microscopic stage that enables the observation of biological cells in a magnetic field with a constant magnetic force. Regarding the requirements for biological observations in the magnetic field, construction was based on [...] Read more.
The aim of the work was to design and construct a microscopic stage that enables the observation of biological cells in a magnetic field with a constant magnetic force. Regarding the requirements for biological observations in the magnetic field, construction was based on the standard automatic stage of an optical microscope ZEISS Axio Observer, and the main challenge was to design a set of magnets which were the source of a field in which the magnetic force was constant in the observation zone. Another challenge was to design a magnet arrangement producing a weak magnetic field to manipulate the cells without harming them. The Halbach array of magnets was constructed using permanent cubic neodymium magnets mounted on a 3D printed polymer ring. Four sets of magnets were used, differing in their dimensions, namely, 20, 15, 12, and 10 mm. The polymer rings were designed to resist magnetic forces and to keep their shape undisturbed when working under biological conditions. To check the usability of the constructs, experiments with magnetic microparticles were executed. Magnetic microparticles were placed under the microscope and their movement was observed to find the acting magnetic force. Full article
(This article belongs to the Special Issue Advances in Methods of Molecular Dynamics in Live Cells)
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