Bacterial sodium channels are important models for understanding ion permeation and selectivity. However, their homotetrameric structure limits their use as models for understanding the more complex eukaryotic...
Authors: Huaping Sun, Zeyu Zheng, Olena A. Fedorenko and Stephen K. Roberts
Cellular environments are highly crowded with biological macromolecules resulting in frequent non-specific interactions. While the effect of such crowding on protein structure and dynamics has been studied ext...
Authors: Asli Yildirim, Nathalie Brenner, Robert Sutherland and Michael Feig
Intracellular phase separation and aggregation of proteins with extended poly-glutamine (polyQ) stretches are hallmarks of various age-associated neurodegenerative diseases. Progress in our understanding of su...
Authors: Christian V. Hansen, Hans J. Schroll and Daniel Wüstner
Propensity of phenylalanine (Phe) for nonpolar environments drives its intercalation into phospholipid membranes, which has been implicated in metabolic and neurological disorders. The knowledge of Phe interca...
Authors: Paulina Adamczewski and Valeria Tsoukanova
With the passing of Jörg Langowski 6 May 2017 in a sailplane accident, the scientific community was deprived of a strident and effective voice for DNA and chromatin molecular and computational biophysics, for ...
Authors: Giuseppe Chirico, Alexander Gansen, Sanford H. Leuba, Ada L. Olins, Donald E. Olins, Jeremy C. Smith and Katalin Tóth
Applications of electric-field-induced permeabilization of cells range from cancer therapy to wastewater treatment. A unified understanding of the underlying mechanisms of membrane electropermeabilization, how...
Authors: Esin B. Sözer, C. Florencia Pocetti and P. Thomas Vernier
Astrocytes were conceived for decades only as supporting cells of the brain. However, the observation of Ca2+ waves in astrocyte synctitia, their neurotransmitter receptor expression and gliotransmitter secret...
Authors: Pavel Montes de Oca Balderas and Horacio Montes de Oca Balderas
The pathways of thermal instability of amino acids have been unknown. New mass spectrometric data allow unequivocal quantitative identification of the decomposition products.
Authors: Ingrid M. Weiss, Christina Muth, Robert Drumm and Helmut O. K. Kirchner
Cell based carriers are increasingly recognized as a good system for cargo delivery to cells. One of the reasons is their biocompatibility and low toxicity compared to artificial systems. Giant plasma membrane...
Authors: Špela Zemljič Jokhadar, Urška Klančnik, Maja Grundner, Tjaša Švelc Kebe, Saša Vrhovec Hartman, Mirjana Liović and Jure Derganc
S100A5 is a calcium binding protein found in a small subset of amniote tissues. Little is known about the biological roles of S100A5, but it may be involved in inflammation and olfactory signaling. Previous wo...
Proteins with low sequence identity but almost identical tertiary structure and function have been valuable to uncover the relationship between sequence, tertiary structure, folding mechanism and functions. Tw...
Authors: Baosheng Ge, Xiaoyong Jiang, Yao Chen, Tingting Sun, Qiuxia Yang and Fang Huang
Cellular biomechanics can be manipulated by strong electric fields, manifested by the field-induced membrane deformation and migration (galvanotaxis), which significantly impacts normal cellular physiology. Ar...
RAS protein interactions have predominantly been studied in the context of the RAF and PI3kinase oncogenic pathways. Structural modeling and X-ray crystallography have demonstrated that RAS isoforms bind to ca...
Authors: H. Billur Engin, Daniel Carlin, Dexter Pratt and Hannah Carter
The Cry toxins, or δ-endotoxins, are a diverse group of proteins produced by Bacillus thuringiensis. While DNA secondary structures are biologically relevant, it is unknown if such structures are formed in region...
Authors: Efrain H. Pinzon, Daniel A. Sierra, Miguel O. Suarez, Sergio Orduz and Alvaro M. Florez
Nanoparticles can be used as markers to track the position of biomolecules, such as single proteins, inside living cells. The activity of a protein can sometimes be inferred from changes in the mobility of the...
Authors: Sara Carozza, Jamie Culkin and John van Noort
The Biomembrane Force Probe is an approachable experimental technique commonly used for single-molecule force spectroscopy and experiments on biological interfaces. The technique operates in the range of force...
Authors: Daniel Šmít, Coralie Fouquet, Mohamed Doulazmi, Frédéric Pincet, Alain Trembleau and Martin Zapotocky
Single-molecule microscopic experiments can measure the mechanical response of proteins to pulling forces applied externally along different directions (inducing different residue pairs in the proteins by unia...
Human lactoferrin is an iron-binding protein of the innate immune system consisting of two connected lobes, each with a binding site located in a cleft. The clefts in each lobe undergo a hinge movement from op...
Authors: Clemens Sill, Ralf Biehl, Bernd Hoffmann, Aurel Radulescu, Marie-Sousai Appavou, Bela Farago, Rudolf Merkel and Dieter Richter
The first step in many cellular signaling processes occurs at various types of receptors in the plasma membrane. Membrane cholesterol can alter these signaling pathways of living cells. However, the process in...
Authors: Chien Y. Lin, Jung Y. Huang and Leu-Wei Lo
The viscoelastic properties of cells have been investigated by a variety of techniques. However, the experimental data reported in literature for viscoelastic moduli differ by up to three orders of magnitude. ...
Authors: Yareni A. Ayala, Bruno Pontes, Diney S. Ether, Luis B. Pires, Glauber R. Araujo, Susana Frases, Luciana F. Romão, Marcos Farina, Vivaldo Moura-Neto, Nathan B. Viana and H. Moysés Nussenzveig
Knowing the binding site of protein–protein complexes helps understand their function and shows possible regulation sites. The ultimate goal of protein–protein docking is the prediction of the three-dimensiona...
Authors: Philipp Kynast, Philippe Derreumaux and Birgit Strodel
Transcription in Escherichia coli generates positive supercoiling in the DNA, which is relieved by the enzymatic activity of gyrase. Recently published experimental evidence suggests that transcription initiation...
The pathological hallmark of Parkinson’s disease is the deposition of cytoplasmic neuronal inclusions termed Lewy bodies. The major component of Lewy bodies is amyloid fibrils of α-synuclein. To investigate wh...
Authors: Jia Bai, Zeting Zhang, Maili Liu and Conggang Li
The possibility of validating biological macromolecules with locally disordered domains like RNA against solution properties is helpful to understand their function. In this work, we present a computational sc...
Authors: Aarón Ayllón Benítez, José Ginés Hernández Cifre, Francisco Guillermo Díaz Baños and José García de la Torre
We study the relevance of diffusion for the dynamics of signaling pathways. Mathematical modeling of cellular diffusion leads to a coupled system of differential equations with Robin boundary conditions which ...
Single-molecule techniques have proven to be an excellent approach for quantitatively studying DNA-protein interactions at the single-molecule level. In magnetic tweezers, a force is applied to a biopolymer th...
Authors: Jorine M. Eeftens, Jaco van der Torre, Daniel R. Burnham and Cees Dekker
The biophysical characteristics of cells determine their shape in isolation and when packed within tissues. Cells can form regular or irregular epithelial structures, round up and form clusters, or deform and ...
Authors: Ramiro Magno, Verônica A Grieneisen and Athanasius FM Marée
Spin labels, which are chemically stable radicals attached at specific sites of a bio-molecule, enable investigations on structure and dynamics of proteins and nucleic acids using techniques such as site-direc...
Authors: Phuong H Nguyen, Anna M Popova, Kálmán Hideg and Peter Z Qin
Time-correlated Förster resonance energy transfer (FRET) probes molecular distances with greater accuracy than intensity-based calculation of FRET efficiency and provides a powerful tool to study biomolecular ...
Authors: Christoph Roethlein, Markus S Miettinen and Zoya Ignatova
The cell contains highly dynamic structures exploiting physical principles of self-organisation at the mesoscale (100 nm to 10 μm). Examples include non-membrane bound cytoplasmic bodies, cytoskeleton-based mo...
Authors: Richard P Sear, Ignacio Pagonabarraga and Andrew Flaus
Cells exhibit distortion when exposed to a strong electric field, suggesting that the field imposes control over cellular biomechanics. Closed pure lipid bilayer membranes (vesicles) have been widely used for ...
The recent developments of far-field optical microscopy (single molecule imaging techniques) have overcome the diffraction barrier of light and improve image resolution by a factor of ten compared with convent...
Authors: Renmin Han, Liansan Wang, Fan Xu, Yongdeng Zhang, Mingshu Zhang, Zhiyong Liu, Fei Ren and Fa Zhang
The ion transport stoichiometry (q) of electrogenic transporters is an important determinant of their function. q can be determined by the reversal potential (Erev) if the transporter under study is the only elec...
The polyvalent acidic lipid phosphatidylinositol, 4,5-bisphosphate (PIP2) is important for many cellular functions. It has been suggested that different pools of PIP2 exist in the cytoplasmic leaflet of the plasm...
Authors: Kyu Il Lee, Wonpil Im and Richard W Pastor
A ribosome can translate through both the single-stranded region and duplex region of messenger RNA (mRNA). Recent single molecule fluorescence energy transfer (smFRET) data showed that when the ribosome trans...
Particle-based reaction-diffusion algorithms facilitate the modeling of the diffusional motion of individual molecules and the reactions between them in cellular environments. A physically realistic model, dep...
Authors: Johannes Schöneberg, Alexander Ullrich and Frank Noé
Asymmetric cell division, whereby a parent cell generates two sibling cells with unequal content and thereby distinct fates, is central to cell differentiation, organism development and ageing. Unequal partiti...
Authors: Ali Kinkhabwala, Anton Khmelinskii and Michael Knop
Cells continuously undergo DNA damage from exogenous agents like irradiation or genotoxic chemicals or from endogenous radicals produced by normal cellular metabolic activities. DNA strand breaks are one of th...
Authors: Michael Junk, Judy Salzwedel, Thilo Sindlinger, Alexander Brkle and Maria Moreno-Villanueva
The complement protein C5a acts by primarily binding and activating the G-protein coupled C5a receptor C5aR (CD88), and is implicated in many inflammatory diseases. The cyclic hexapeptide PMX53 (sequence Ace-P...
Authors: Phanourios Tamamis, Chris A Kieslich, Gregory V Nikiforovich, Trent M Woodruff, Dimitrios Morikis and Georgios Archontis
A key challenge in interdisciplinary research is choosing the best approach from a large number of techniques derived from different disciplines and their interfaces.
Authors: Sanford H Leuba, Sean M Carney, Elizabeth M Dahlburg, Rebecca J Eells, Harshad Ghodke, Naveena Yanamala, Grant Schauer and Judith Klein-Seetharaman
Based on the dynamics of antigen recognition from T cell receptor complex and T cell activation, different function of T cells may present different morphology feature, at least at molecular level. Regulatory ...
Authors: Xu Wang, Zhenyi Jin, Xinyu Wang, Shaohua Chen, Lijian Yang, Kanger Zhu, Xiuli Wu and Yangqiu Li
Brownian dynamics (BD) simulations can be used to study very large molecular systems, such as models of the intracellular environment, using atomic-detail structures. Such simulations require strategies to con...
Authors: Paolo Mereghetti, Michael Martinez and Rebecca C Wade
The diffusion-limited reaction rate of a uniform spherical reactant is generalized to anisotropic reactivity. Previous work has shown that the protein model of a uniform sphere is unsatisfactory in many cases....
Viroids are the smallest pathogens of plants. To date the structural and conformational details of the cleavage of Avocado sunblotch viroid (ASBVd) and the catalytic role of Mg2+ ions in efficient self-cleavage a...
Authors: Gaston Hui-Bon-Hoa, Hussein Kaddour, Jacques Vergne, Sergei G Kruglik and Marie-Christine Maurel
The cell and tissue structural properties assessed with a conventional bright-field light microscope play a key role in cancer diagnosis, but they sometimes have limited accuracy in detecting early-stage cance...
Authors: Yang Liu, Shikhar Uttam, Sergey Alexandrov and Rajan K Bista
Lysine Specific Demethylase (LSD1 or KDM1A) in complex with its co-repressor protein CoREST catalyzes the demethylation of the H3 histone N-terminal tail and is currently one of the most promising epigenetic t...
