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Biophysical Journal

Shankar Lalitha Sridhar, Joseph K E Ortega, Franck J Vernerey
Expansive growth is a process by which walled cells of plants, algae, and fungi use turgor pressure to mediate irreversible wall deformation and regulate their shape and volume. The molecular structure of the primary cell wall must therefore perform multiple functions simultaneously, including providing structural support by combining elastic and irreversible deformation and facilitating the deposition of new material during growth. This is accomplished by a network of microfibrils and tethers composed of complex polysaccharides and proteins that can dynamically mediate the network topology via periodic detachment and reattachment events...
November 17, 2018: Biophysical Journal
Biena Mathew, Silvia Muñoz-Descalzo, Elena Corujo-Simon, Christian Schröter, Ernst H K Stelzer, Sabine C Fischer
During mammalian preimplantation, cells of the inner cell mass (ICM) adopt either an embryonic or an extraembryonic fate. This process is tightly regulated in space and time and has been studied previously in mouse embryos and embryonic stem cell models. Current research suggests that cell fates are arranged in a salt-and-pepper pattern of random cell positioning or a spatially alternating pattern. However, the details of the three-dimensional patterns of cell fate specification have not been investigated in the embryo nor in in vitro systems...
November 16, 2018: Biophysical Journal
Anna D Kuprash, Alexey M Shibeko, Ramya Vijay, Sukesh C Nair, Alok Srivastava, Fazoil I Ataullakhanov, Mikhail A Panteleev, Anna N Balandina
Blood coagulation is a delicately regulated space- and time-dependent process that leads to the formation of fibrin clots preventing blood loss upon vascular injury. The sensitivity of the coagulation network was previously investigated without accounting for transport processes. To investigate its sensitivity to coagulation factor deficiencies in a spatial reaction-diffusion system, we combined an in vitro experimental design with a computational systems biology model. Clot formation in platelet-free plasma supplemented with phospholipids was activated with identical amounts of tissue factor (TF) either homogeneously distributed (concentration 5 pM, homogeneous model) or immobilized on the surface (surface density 100 pmole/m2 , spatially heterogeneous model)...
November 14, 2018: Biophysical Journal
Casper Højgaard, Henrik Vinther Sørensen, Jan Skov Pedersen, Jakob Rahr Winther, Daniel Erik Otzen
Does sodium dodecyl sulfate (SDS) denature proteins through electrostatic SDS-protein interactions? We show that a protein completely lacking charged side chains is unfolded by SDS in a manner similar to charged proteins, revealing that formal protein charges are not required for SDS-induced protein unfolding or binding.
November 14, 2018: Biophysical Journal
Zhaoyang Zhang, Oleg A Igoshin, Christopher R Cotter, Lawrence J Shimkets
Myxococcus xanthus is a soil bacterium that serves as a model system for biological self-organization. Cells form distinct, dynamic patterns depending on environmental conditions. An agent-based model was used to understand how M. xanthus cells aggregate into multicellular mounds in response to starvation. In this model, each cell is modeled as an agent represented by a point particle and characterized by its position and moving direction. At low agent density, the model recapitulates the dynamic patterns observed by experiments and a previous biophysical model...
November 10, 2018: Biophysical Journal
Hongwu Yu, Cheng Xue, Mengping Long, Huiqiang Jia, Guosheng Xue, Shengwang Du, Yves Coello, Toyotaka Ishibashi
Regulation of transcription elongation is one of the key mechanisms employed to control gene expression. The single-subunit mitochondrial RNA polymerase (mtRNAP) transcribes mitochondrial genes, such as those related to ATP synthesis. We investigated how mitochondrial transcription elongation factor (TEFM) enhances mtRNAP transcription elongation using a single-molecule optical-tweezers transcription assay, which follows transcription dynamics in real time and allows the separation of pause-free elongation from transcriptional pauses...
November 10, 2018: Biophysical Journal
Xian Wang, Zhuoran Zhang, Hirotaka Tao, Jun Liu, Sevan Hopyan, Yu Sun
It has long been recognized that mechanical forces underlie mammalian embryonic shape changes. Before gastrulation, the blastocyst embryo undergoes significant shape changes, namely, the blastocyst cavity emerges and expands, and the inner cell mass (ICM) forms and changes in shape. The embryo's inner pressure has been hypothesized to be the driving mechanical input that causes the expansion of the blastocyst cavity and the shape changes of the ICM. However, how the inner pressure and the mechanics of the trophoblast and the ICM change during development is unknown because of the lack of a suitable tool for quantitative characterization...
November 10, 2018: Biophysical Journal
Radoslaw Bomba, Witek Kwiatkowski, Antoni Sánchez-Ferrer, Roland Riek, Jason Greenwald
Interactions between biological membranes and disease-associated amyloids are well documented, and their prevalence suggests that an inherent affinity exists between these molecular assemblies. Our interest in the molecular origins of life have led us to investigate the nature of such interactions in the context of their molecular predecessors (i.e., vesicle-forming amphiphiles and small peptides). Under certain conditions, amyloidogenic peptides or fatty acids are each able to form ordered structures on their own; however, we report here on their cooperative assembly into novel, to our knowledge, highly ordered structures...
November 10, 2018: Biophysical Journal
Adam Connolly, Allen Kelly, Fernando O Campos, Rachel Myles, Godfrey Smith, Martin J Bishop
BACKGROUND: Understanding the biophysical processes by which electrical stimuli applied to cardiac tissue may result in local activation is important in both the experimental and clinical electrophysiology laboratory environments, as well as for gaining a more in-depth knowledge of the mechanisms of focal-trigger-induced arrhythmias. Previous computational models have predicted that local myocardial tissue architecture alone may significantly modulate tissue excitability, affecting both the local stimulus current required to excite the tissue and the local effective refractory period (ERP)...
November 9, 2018: Biophysical Journal
Chitrak Gupta, Yue Ren, Blake Mertz
Peptides with the ability to bind and insert into the cell membrane have immense potential in biomedical applications. pH (low) insertion peptide (pHLIP), a water-soluble polypeptide derived from helix C of bacteriorhodopsin, can insert into a membrane at acidic pH to form a stable transmembrane α-helix. The insertion process takes place in three stages: pHLIP is unstructured and soluble in water at neutral pH (state I), unstructured and bound to the surface of a membrane at neutral pH (state II), and inserted into the membrane as an α-helix at low pH (state III)...
November 7, 2018: Biophysical Journal
Shashank Ranjan Srivastava, Punit Zadafiya, Radhakrishnan Mahalakshmi
The human mitochondrial outer membrane protein voltage-dependent anion channel isoform 2 (hVDAC2) is a β-barrel metabolite flux channel that is indispensable for cell survival. It is well established that physical forces imposed on a transmembrane protein by its surrounding lipid environment decide protein structure and stability. Yet, how the mitochondrial membrane and protein-lipid interplay together regulate hVDAC2 stability is unknown. Here, we combine experimental biophysical investigations of protein stability with all-atom molecular dynamics simulations to study the effect of the most abundant mitochondrial phosphocholine (PC) lipids on hVDAC2...
November 7, 2018: Biophysical Journal
Andrew Hsu, Fabien Ferrage, Arthur G Palmer
Spin relaxation in solution-state NMR spectroscopy is a powerful approach to explore the conformational dynamics of biological macromolecules. Probability distribution functions for overall or internal correlation times have been used previously to model spectral density functions central to spin-relaxation theory. Applications to biological macromolecules rely on transverse relaxation rate constants, and when studying nanosecond timescale motions, sampling at ultralow frequencies is often necessary. Consequently, appropriate distribution functions necessitate spectral density functions that are accurate and convergent as frequencies approach zero...
November 6, 2018: Biophysical Journal
Anh Tuan Tran, Aude Sadet, Paolo Calligari, Philippe Lopes, Jamal Ouazzani, Matthieu Sollogoub, Emeric Miclet, Daniel Abergel
Human African trypanosomiasis, or sleeping sickness, is a lethal disease caused by the protozoan parasite Trypanosoma brucei. However, although many efforts have been made to understand the biochemistry of this parasite, drug development has led to treatments that are of limited efficiency and of great toxicity. To develop new drugs, new targets must be identified, and among the several metabolic processes of trypanosomes that have been proposed as drug targets, carbohydrate metabolism (glycolysis and the pentose phosphate pathway (PPP)) appears as a promising one...
November 6, 2018: Biophysical Journal
Sudipta Lahiri, Yan Li, Manju M Hingorani, Ishita Mukerji
In many organisms, MutSγ plays a role in meiotic recombination, facilitating crossover formation between homologous chromosomes. Failure to form crossovers leads to improper segregation of chromosomes and aneuploidy, which in humans result in infertility and birth defects. To improve current understanding of MutSγ function, this study investigates the binding affinities and structures of MutSγ in complex with DNA substrates that model homologous recombination intermediates. For these studies, we overexpressed and isolated from Escherichia coli the yeast MutSγ protein Saccharomyces cerevisiae (Sc) Msh4-Msh5...
November 6, 2018: Biophysical Journal
Gonca Erdemci-Tandogan, Madeline J Clark, Jeffrey D Amack, M Lisa Manning
In embryonic development, cell shape changes are essential for building functional organs, but in many cases, the mechanisms that precisely regulate these changes remain unknown. We propose that fluid-like drag forces generated by the motion of an organ through surrounding tissue could generate changes to its structure that are important for its function. To test this hypothesis, we study the zebrafish left-right organizer, Kupffer's vesicle (KV), using experiments and mathematical modeling. During development, monociliated cells that comprise KV undergo region-specific shape changes along the anterior-posterior axis that are critical for KV function: anterior cells become long and thin, whereas posterior cells become short and squat...
November 6, 2018: Biophysical Journal
Richard Ballweg, Suengwon Lee, Xiaonan Han, Philip K Maini, Helen Byrne, Christian I Hong, Tongli Zhang
During differentiation, intestinal stem cells (ISCs), a prototypical adult stem cell pool, become either secretory transit-amplifying cells, which give rise to all secretory cell types, or absorptive transit-amplifying cells, which give rise to enterocytes. These cells exhibit distinct cell cycle dynamics: ISCs cycle with a period of 24 h and absorptive transit-amplifying cells cycle with a period of ∼12 h, whereas secretory transit-amplifying cells arrest their cycle. The cell cycle dynamics of ISCs and their progeny are a systems-level property that emerges from interactions between the cell cycle control machinery and multiple regulatory pathways...
November 3, 2018: Biophysical Journal
Quinton Banks, Stephen Joseph Paul Pratt, Shama Rajan Iyer, Richard Michael Lovering, Erick Omar Hernández-Ochoa, Martin Frederick Schneider
Skeletal muscle fibers have been used to examine a variety of cellular functions and pathologies. Among other parameters, skeletal muscle action potential (AP) propagation has been measured to assess the integrity and function of skeletal muscle. In this work, we utilize 1-(3-sulfonatopropyl)-4[β[2-(Di-n-octylamino)-6-naphtyl]vinyl]pyridinium betaine, a potentiometric dye, and mag-fluo-4, a low-affinity intracellular Ca2+ indicator, to noninvasively and reliably measure AP conduction velocity in skeletal muscle...
November 3, 2018: Biophysical Journal
Doreen E Culham, David Marom, Rebecca Boutin, Jennifer Garner, Tugba Nur Ozturk, Naheda Sahtout, Laura Tempelhagen, Guillaume Lamoureux, Janet M Wood
ProP is a member of the major facilitator superfamily, a proton-osmolyte symporter, and an osmosensing transporter. ProP proteins share extended cytoplasmic carboxyl terminal domains (CTDs) implicated in osmosensing. The CTDs of the best characterized, group A ProP orthologs, terminate in sequences that form intermolecular, antiparallel α-helical coiled coils (e.g., ProPEc, from Escherichia coli). Group B orthologs lack that feature (e.g., ProPXc, from Xanthomonas campestris). ProPXc was expressed and characterized in E...
November 2, 2018: Biophysical Journal
Felix Leeb, Lutz Maibaum
We study the effect of cholesterol on the structure of dipalmitoylphosphatidylcholine phospholipid bilayers. Using extensive molecular dynamics computer simulations at atomistic resolution, we observe and quantify several structural changes upon increasing cholesterol content that are collectively known as the condensing effect: a thickening of the bilayer, an increase in lipid tail order, and a decrease in lateral area. We also observe a change in leaflet interdigitation and a lack thereof in the distributions of dipalmitoylphosphatidylcholine headgroup orientations...
November 2, 2018: Biophysical Journal
Bhavik Nathwani, William M Shih, Wesley P Wong
Life operates at the intersection of chemistry and mechanics. Over the years, we have made remarkable progress in understanding life from a biochemical perspective and the mechanics of life at the single-molecule scale. Yet the full integration of physical and mechanical models into mainstream biology has been impeded by technical and conceptual barriers, including limitations in our ability to 1) easily measure and apply mechanical forces to biological systems, 2) scale these measurements from single-molecule characterization to more complex biomolecular systems, and 3) model and interpret biophysical data in a coherent way across length scales that span single molecules to cells to multicellular organisms...
November 1, 2018: Biophysical Journal
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