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ENRICH: A fast method to improve the quality of flexible macromolecular reconstructions Prog. Biophys. Mol. Biol. (IF 2.175) Pub Date : 2021-01-12 M. Kazemi; C.O.S. Sorzano; J.M. Carazo; A. des Georges; V. Abrishami; J. Vargas
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Action potential alterations induced by single F11 neuronal cell loading Prog. Biophys. Mol. Biol. (IF 2.175) Pub Date : 2021-01-12 Miren Tamayo-Elizalde; Haoyu Chen; Majid Malboubi; Hua Ye; Antoine Jerusalem
Several research programmes have demonstrated how Transcranial Ultrasound Stimulation (TUS) can non-invasively and reversibly mechanically perturb neuronal functions. However, the mechanisms through which such reversible and a priori non-damaging behaviour can be observed remain largely unknown. While several TUS protocols have demonstrated motor and behavioural alterations in in vivo models, in vitro
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Regulation of DNA break repair by RNA Prog. Biophys. Mol. Biol. (IF 2.175) Pub Date : 2020-12-30 Luke A. Yates
Genomic stability is critical for cell survival and its effective repair when damaged is a vital process for preserving genetic information. Failure to correctly repair the genome can lead to the accumulation of mutations that ultimately drives carcinogenesis. Life has evolved sophisticated surveillance, repair pathways, and mechanisms to recognize and mend genomic lesions to preserve its integrity
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Infrared neural stimulation at different wavelengths and pulse shapes Prog. Biophys. Mol. Biol. (IF 2.175) Pub Date : 2020-12-24 Yingyue Xu; Mario Magnuson; Aditi Agarwal; Xiaodong Tan; Claus-Peter Richter
Neural stimulation with infrared radiation has been explored for brain tissue, peripheral nerves, and cranial nerves including the auditory nerve. Initial experiments were conducted at wavelengths between λ = 1,850 and λ = 2,140 nm and the radiant energy was delivered with square pulses. Water absorption of the infrared radiation at λ = 1,860 nm is similar to absorption at wavelengths between λ = 1
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The multiple biological roles of the cholinesterases Prog. Biophys. Mol. Biol. (IF 2.175) Pub Date : 2020-12-08 Israel Silman
It is tacitly assumed that the biological role of acetylcholinesterase is termination of synaptic transmission at cholinergic synapses. However, together with its structural homolog, butyrylcholinesterase, it is widely distributed both within and outside the nervous system, and, in many cases, the role of both enzymes remains obscure. The transient appearance of the cholinesterases in embryonic tissues
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Stages, scaffolds and strings in the spatial organisation of non-homologous end joining: Insights from X-ray diffraction and Cryo-EM Prog. Biophys. Mol. Biol. (IF 2.175) Pub Date : 2020-12-04 Shikang Liang; Amanda K. Chaplin; Antonia Kefala Stavridi; Robert Appleby; Ales Hnizda; Tom L. Blundell
Non-homologous end joining (NHEJ) is the preferred pathway for the repair of DNA double-strand breaks in humans. Here we describe three structural aspect aspects of the repair pathway: stages, scaffolds and strings. We discuss their orchestration of DNA repair to guarantee robust and efficient NHEJ. We focus on structural studies over the past two decades not only using X-ray diffraction, but also
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Reversibility of excitation waves in brain and heart and the energy of interfacial water. Can reversibility be explained by it? Prog. Biophys. Mol. Biol. (IF 2.175) Pub Date : 2020-12-03 Vera Maura Fernandes de Lima; Wolfgang Hanke
In this manuscript, we interpret the implications of a discovery we made in 1993 for the understanding of the spread of excitation waves in axon, central gray matter (isolated retina) and heart. We propose that the initial burst of energy dissipation in these waves measured as potentials drops, ionic activities marked changes or optical properties being mostly the effect of dissociated water becoming
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Roles of ATM and ATR in DNA double strand breaks and replication stress Prog. Biophys. Mol. Biol. (IF 2.175) Pub Date : 2020-11-28 Rhys M. Williams; Xiaodong Zhang
The maintenance of genome integrity is critical for the faithful replication of the genome during cell division and for protecting cells from accumulation of DNA damage, which if left unrepaired leads to a loss of genetic information, a breakdown in cell function and ultimately cell death and cancer. ATM and ATR are master kinases that are integral to homologous recombination-mediated repair of double
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The role of non-coding genome in the behavior of infiltrated myeloid-derived suppressor cells in tumor microenvironment; a perspective and state-of-the-art in cancer targeted therapy Prog. Biophys. Mol. Biol. (IF 2.175) Pub Date : 2020-11-28 Arezoo Gowhari Shabgah; Arash Salmaninejad; Lakshmi Thangavelu; Markov Alexander; Alexei Valerievich Yumashev; Pouya Goleij; Mahdiyeh Hedayati-Moghadam; Hamed Mohammadi; Majid Ahmadi; Jamshid Gholizadeh Navashenaq
Cancer is one of the healthcare problems that affect many communities around the world. Many factors contribute to cancer development. Besides, these factors are counted as the main impediment in cancer immunotherapy. Myeloid-derived suppressor cells (MDSCs) are one of these impediments. MDSCs inhibit the immune responses through various mechanisms such as inhibitory cytokine release and nitric oxide
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Optical studies of membrane state during action potential propagation Prog. Biophys. Mol. Biol. (IF 2.175) Pub Date : 2020-11-20 Simon Fabiunke; Christian Fillafer; Anne Paeger; Matthias F. Schneider
One of the most striking phenomena in biology is the action potential (AP), a nonlinear pulse with threshold and amplitude saturation (all-or-none-behavior) that propagates along neurons and other cells. In the classical interpretation the AP is considered to be an electrical phenomenon – a regenerating current flowing in a “biological cable”. In contrast, the thermodynamic interpretation has emphasized
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Structural basis of the (in)activity of the apical DNA damage response kinases ATM, ATR and DNA-PKcs Prog. Biophys. Mol. Biol. (IF 2.175) Pub Date : 2020-11-07 Marijke Jansma; Karl-Peter Hopfner
The DNA damage response (DDR) is orchestrated by three apical signalling kinases: ATM, ATR and DNA-PKcs. Despite their central roles, structural and biochemical understanding has remained limited, mainly due to their large size. Recent advances in cryo-electron microscopy allowed for the structural analysis of these kinases, revealing their overall architecture and providing high resolution structures
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Something's gotta give: How PCNA alters its structure in response to mutations and the implications on cellular processes Prog. Biophys. Mol. Biol. (IF 2.175) Pub Date : 2020-11-05 Lynne Dieckman
Proliferating cell nuclear antigen (PCNA) is an essential protein that regulates the systematic recruitment and activity of proteins in a multitude of biochemical processes. Very few proteins, if any, bear similar responsibilities to those of PCNA, and its list of roles only continues to expand. However, even as one of the most well-studied proteins in research, many questions still remain about the
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Human coronavirus spike protein-host receptor recognition Prog. Biophys. Mol. Biol. (IF 2.175) Pub Date : 2020-10-31 Lalitha Guruprasad
A variety of coronaviruses (CoVs) have infected humans and caused mild to severe respiratory diseases that could result in mortality. The human CoVs (HCoVs) belong to the genera of α- and β-CoVs that originate in rodents and bats and are transmitted to humans via zoonotic contacts. The binding of viral spike proteins to the host cell receptors is essential for mediating fusion of viral and host cell
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Fragment- and structure-based drug discovery for developing therapeutic agents targeting the DNA Damage Response Prog. Biophys. Mol. Biol. (IF 2.175) Pub Date : 2020-10-25 David M. Wilson; Ashley M. Deacon; Matthew A.J. Duncton; Patricia Pellicena; Millie M. Georgiadis; Andrew P. Yeh; Andrew S. Arvai; Davide Moiani; John A. Tainer; Debanu Das
Cancer will directly affect the lives of over one-third of the population. The DNA Damage Response (DDR) is an intricate system involving damage recognition, cell cycle regulation, DNA repair, and ultimately cell fate determination, playing a central role in cancer etiology and therapy. Two primary therapeutic approaches involving DDR targeting include: combinatorial treatments employing anticancer
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The dynamic nature of the Mre11-Rad50 DNA break repair complex Prog. Biophys. Mol. Biol. (IF 2.175) Pub Date : 2020-10-24 Mahtab Beikzadeh; Michael P. Latham
The Mre11-Rad50-Nbs1/Xrs2 protein complex plays a pivotal role in the detection and repair of DNA double strand breaks. Through traditional and emerging structural biology techniques, various functional structural states of this complex have been visualized; however, relatively little is known about the transitions between these states. Indeed, it is these structural transitions that are important
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Living systems approached from physical principles Prog. Biophys. Mol. Biol. (IF 2.175) Pub Date : 2020-10-15 Matthias F. Schneider
This article attempts to review our work in the field since 2008, attempts to put it in a coherent framework and takes a courageous look vis-à-vis the bigger picture. It summarizes our approach, successes and open questions to start from physical principles when approaching living systems. It stresses the importance of conservation laws versus material and/or structural approaches to living systems
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A mammalian system for high-resolution imaging of intact cells by cryo-electron tomography Prog. Biophys. Mol. Biol. (IF 2.175) Pub Date : 2020-10-13 Xia Li; Donghyun Park; Yunjie Chang; Abhijith Radhakrishnan; Hangjun Wu; Pei Wang; Jun Liu
Mammalian cells contain an elaborate network of organelles and molecular machines that orchestrate essential cellular processes. Visualization of this network at a molecular level is vital for understanding these cellular processes. Here we present a model system based on nerve growth factor (NGF)-differentiated PC12 cells (PC12+) and suitable for high resolution imaging of organelles and molecular
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The living state: How cellular excitability is controlled by the thermodynamic state of the membrane Prog. Biophys. Mol. Biol. (IF 2.175) Pub Date : 2020-10-13 Christian Fillafer; Anne Paeger; Matthias F. Schneider
The thermodynamic (TD) properties of biological membranes play a central role for living systems. It has been suggested, for instance, that nonlinear pulses such as action potentials (APs) can only exist if the membrane state is in vicinity of a TD transition. Herein, two membrane properties in living systems – excitability and velocity – are analyzed for a broad spectrum of conditions (temperature
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The ubiquitination machinery of the Fanconi Anemia DNA repair pathway, Prog. Biophys. Mol. Biol. (IF 2.175) Pub Date : 2020-10-12 Winnie Tan; Andrew J. Deans
The Fanconi Anemia (FA) pathway maintains genome stability by preventing DNA damage from occurring when replication is blocked. Central to the FA pathway is the monoubiquitination of FANCI-FANCD2 mediated by a ubiquitin RING-E3 ligase complex called the FA core complex. Genetic mutation in any component of the FA core complex results in defective FANCI-FANCD2 monoubiquitination and phenotypes of DNA
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A survey of pathways for mechano-electric coupling in the atria Prog. Biophys. Mol. Biol. (IF 2.175) Pub Date : 2020-10-11 Marta Varela; Aditi Roy; Jack Lee
Mechano-electric coupling (MEC) in atrial tissue has received sparse investigation to date, despite the well-known association between chronic atrial dilation and atrial fibrillation (AF). Of note, no fewer than six different mechanisms pertaining to stretch-activated channels, cellular capacitance and geometric effects have been identified in the literature as potential players. In this mini review
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Uncovering DNA-PKcs ancient phylogeny, unique sequence motifs and insights for human disease Prog. Biophys. Mol. Biol. (IF 2.175) Pub Date : 2020-10-06 James P. Lees-Miller; Alexander Cobban; Panagiotis Katsonis; Albino Bacolla; Susan E. Tsutakawa; Michal Hammel; Katheryn Meek; Dave W. Anderson; Olivier Lichtarge; John A. Tainer; Susan P. Lees-Miller
DNA-dependent protein kinase catalytic subunit (DNA-PKcs) is a key member of the phosphatidylinositol-3 kinase-like (PIKK) family of protein kinases with critical roles in DNA-double strand break repair, transcription, metastasis, mitosis, RNA processing, and innate and adaptive immunity. The absence of DNA-PKcs from many model organisms has led to the assumption that DNA-PKcs is a vertebrate-specific
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A quantitative approach relating emergent features of complex traits to protein expression Prog. Biophys. Mol. Biol. (IF 2.175) Pub Date : 2020-10-06 Lars H. Wegner; Zhifeng Hao
Linking complex, multigenic traits to protein activity is an important challenge in current biology, including applications in the medical sciences, agriculture, or forestry. Two simple algorithms are presented here to establish that link. The first one describes synergistic interactions of n proteins in shaping a complex trait (‘weak emergence’) as opposed to a simply additive ‘modular’ contribution
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New role of TRPM4 channel in the cardiac excitation-contraction coupling in response to physiological and pathological hypertrophy in mouse Prog. Biophys. Mol. Biol. (IF 2.175) Pub Date : 2020-10-05 Christophe Hedon; Karen Lambert; Nourdine Chakouri; Jérôme Thireau; Franck Aimond; Cécile Cassan; Patrice Bideaux; Sylvain Richard; Adèle Faucherre; Jean-Yves Le Guennec; Marie Demion
The transient receptor potential Melastatin 4 (TRPM4) channel is a calcium-activated non-selective cation channel expressed widely. In the heart, using a knock-out mouse model, the TRPM4 channel has been shown to be involved in multiple processes, including β-adrenergic regulation, cardiac conduction, action potential duration and hypertrophic adaptations. This channel was recently shown to be involved
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The role of stochasticity in biological communication processes Prog. Biophys. Mol. Biol. (IF 2.175) Pub Date : 2020-10-01 Denis Noble
Stochastic processes at molecular, cellular and higher levels in organisms are not simply noise. Organisms also use stochasticity at all levels to generate new DNA sequences, as in the immune system, and new forms of behaviour, as in the nervous system. The harnessing of stochasticity therefore endows organisms with the means to actively influence the direction of their development and evolution.
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MicroRNAs: New contributors to mechano-electric coupling and atrial fibrillation Prog. Biophys. Mol. Biol. (IF 2.175) Pub Date : 2020-10-01 Flavia Ravelli; Michela Masè
Atrial fibrillation (AF) is a multifactorial disease, which often occurs in the presence of underlying cardiac abnormalities and is supported by electrophysiological and structural alterations, generally referred to as atrial remodeling. Abnormal substrates are commonly encountered in various conditions that predispose to AF, such as hypertension, heart failure, obesity, and sleep apnea, in which atrial
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Amorphous nickel titanium alloy film: A new choice for cryo electron microscopy sample preparation. Prog. Biophys. Mol. Biol. (IF 2.175) Pub Date : 2020-08-03 Xiaojun Huang,Lei Zhang,Zuoling Wen,Hui Chen,Shuoguo Li,Gang Ji,Chang-Cheng Yin,Fei Sun
Cryo-electron microscopy (cryoEM) has become one of the most important approach for structural biology. However, barriers are still there for an increased successful rate, a better resolution and improved efficiency from sample preparation, data collection to image processing. CryoEM sample preparation is one of the bottlenecks with many efforts made recently, including the optimization of supporting
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Evidence for DNA resonance signaling via longitudinal hydrogen bonds. Prog. Biophys. Mol. Biol. (IF 2.175) Pub Date : 2020-07-23 Ivan Savelev,Max Myakishev-Rempel
The theory of the morphogenic field suggests that chemical signaling is supplemented by electromagnetic signaling governing the structure and shape of tissues, organs and the body. The theory of DNA resonance suggests that the morphogenic field is created by the genomic DNA which sends and receives electromagnetic signals in a sequence-specific manner. Previously, the authors have proposed the existence
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Cellular senomic measurements in Cognition-Based Evolution. Prog. Biophys. Mol. Biol. (IF 2.175) Pub Date : 2020-07-30 William B Miller,František Baluška,John S Torday
All living entities are cognitive and dependent on ambiguous information. Any assessment of that imprecision is necessarily a measuring function. Individual cells measure information to sustain self-referential homeostatic equipoise (self-identity) in juxtaposition to the external environment. The validity of that information is improved by its collective assessment. The reception of cellular information
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“Thermoeconomics”: Time to move beyond the second law Prog. Biophys. Mol. Biol. (IF 2.175) Pub Date : 2020-09-22 Peter A. Corning
The term “thermoeconomics” denotes a paradigm shift in our understanding of the role of energy in living systems, and in evolution. It is based on the proposition that energy in biological evolution can best be defined and understood, not in terms of the Second Law of Thermodynamics but in terms of such economic criteria as productivity, efficiency, and especially the costs and benefits (or “profitability”)
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Visualizing functional dynamicity in the DNA-dependent protein kinase holoenzyme DNA-PK complex by integrating SAXS with cryo-EM. Prog. Biophys. Mol. Biol. (IF 2.175) Pub Date : 2020-09-20 Michal Hammel,Daniel J Rosenberg,Jan Bierma,Gregory L Hura,Susan P Lees-Miller,John A Tainer
Assembly of KU and DNA-dependent protein kinase catalytic subunit (DNA-PKcs) at DNA double strand breaks (DSBs) forms DNA-PK holoenzyme as a critical initiating step for non-homologous end joining (NHEJ) repair of DSBs produced by radiation and chemotherapies. Advanced cryo-electron microscopy (cryo-EM) imaging together with breakthrough macromolecular X-ray crystal (MX) structures of KU and DNA-PKcs
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Abiotic stress elements in in vitro potato (Solanum tuberosum L.) exposed to air-based and liquid-based ultrasound: A comparative transcriptomic assessment. Prog. Biophys. Mol. Biol. (IF 2.175) Pub Date : 2020-09-08 Judit Dobránszki,Norbert Hidvégi,Andrea Gulyás,Bianka Tóth,Jaime A Teixeira da Silva
Ultrasound (US) can modify the plant growth and development. Previous assessments of the transcriptome of in vitro potato (Solanum tuberosum L.) exposed to US transmitted through air (AB-US) or liquid (PE-US) revealed the up- or down-regulation of several stress-related differentially expressed genes (DEGs) related to abiotic stress. In a bid to better characterize stress-related elements over a four-week
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Fanconi anemia-independent DNA inter-strand crosslink repair in eukaryotes. Prog. Biophys. Mol. Biol. (IF 2.175) Pub Date : 2020-08-30 Cody M Rogers,Robert H Simmons Iii,Gabriella E Fluhler Thornburg,Nicholas J Buehler,Matthew L Bochman
DNA inter-strand crosslinks (ICLs) are dangerous lesions that can be caused by a variety of endogenous and exogenous bifunctional compounds. Because covalently linking both strands of the double helix locally disrupts DNA replication and transcription, failure to remove even a single ICL can be fatal to the cell. Thus, multiple ICL repair pathways have evolved, with the best studied being the canonical
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State-dependent sequential allostery exhibited by chaperonin TRiC/CCT revealed by network analysis of Cryo-EM maps. Prog. Biophys. Mol. Biol. (IF 2.175) Pub Date : 2020-08-28 Yan Zhang,James Krieger,Karolina Mikulska-Ruminska,Burak Kaynak,Carlos Oscar S Sorzano,José-María Carazo,Jianhua Xing,Ivet Bahar
The eukaryotic chaperonin TRiC/CCT plays a major role in assisting the folding of many proteins through an ATP-driven allosteric cycle. Recent structures elucidated by cryo-electron microscopy provide a broad view of the conformations visited at various stages of the chaperonin cycle, including a sequential activation of its subunits in response to nucleotide binding. But we lack a thorough mechanistic
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Sound pulses in lipid membranes and their potential function in biology. Prog. Biophys. Mol. Biol. (IF 2.175) Pub Date : 2020-08-27 Matan Mussel,Matthias F Schneider
Experimental observations in lipid monolayers at the air-water interface have demonstrated that solitary sound pulses can be excited. These pulses propagate electrical, chemical, and thermal variations in addition to the mechanical changes in lateral pressure and lipid density, and can interact with nearby ions, polymers, and water. In addition, it was demonstrated that sound pulses that reversibly
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The surprising heart revisited: an early history of the funny current with modern lessons. Prog. Biophys. Mol. Biol. (IF 2.175) Pub Date : 2020-08-27 Denis Noble
40 years ago a single experiment upset a decade of painstaking research on the mechanisms of rhythm generation in the heart. It did so by turning a theory of pacemaker activity upside down. Instead of attributing rhythm to decaying potassium current carrying outward current, it attributed the pacemaker depolarization to the slow activation of a channel conducting sodium ions into cardiac cells. But
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Autonomic modulation of sinoatrial node: Role of pacemaker current and calcium sensitive adenylyl cyclase isoforms. Prog. Biophys. Mol. Biol. (IF 2.175) Pub Date : 2020-08-24 Richard B Robinson,Wen Dun,Penelope A Boyden
This article reviews work over the past three decades that is related to the contribution of the pacemaker current, If, to basal and autonomically regulated spontaneous rate in the sinoatrial node. It also addresses how the actions of the pacemaker current relate to those of Ca homeostasis with respect to basal and autonomically regulated rhythm. In this regard, it explores the relative contributions
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Cryo-EM reveals infection steps of single-stranded RNA bacteriophages. Prog. Biophys. Mol. Biol. (IF 2.175) Pub Date : 2020-08-22 Karl Victor Gorzelnik,Junjie Zhang
Single-stranded RNA bacteriophages (ssRNA phages) are small spherical RNA viruses that infect bacteria with retractile pili. The single positive-sense genomic RNA of ssRNA phages, which is protected by a capsid shell, is delivered into the host via the retraction of the host pili. Structures involved in ssRNA phage infection cycle are essential for understanding the underlying mechanisms that can be
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Mathematical modelling of the mechano-electric coupling in the human cardiomyocyte electrically connected with fibroblasts. Prog. Biophys. Mol. Biol. (IF 2.175) Pub Date : 2020-08-23 Anastasia Bazhutina,Nathalie A Balakina-Vikulova,Alexander Kursanov,Olga Solovyova,Alexander Panfilov,Leonid B Katsnelson
Cardiac fibroblasts are interspersed within mammalian cardiac tissue. Fibroblasts are mechanically passive; however, they may communicate electrically with cardiomyocytes via gap junctions and thus affect the electrical and mechanical activity of myocytes. Several in-silico studies at both cellular (0D) and ventricular (3D) levels analysed the effects of fibroblasts on the myocardial electrical function
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Quantum information theoretic approach to the mind-brain problem. Prog. Biophys. Mol. Biol. (IF 2.175) Pub Date : 2020-08-18 Danko D Georgiev
The brain is composed of electrically excitable neuronal networks regulated by the activity of voltage-gated ion channels. Further portraying the molecular composition of the brain, however, will not reveal anything remotely reminiscent of a feeling, a sensation or a conscious experience. In classical physics, addressing the mind–brain problem is a formidable task because no physical mechanism is able
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The important consequences of the reversible heat production in nerves and the adiabaticity of the action potential. Prog. Biophys. Mol. Biol. (IF 2.175) Pub Date : 2020-08-14 Thomas Heimburg
It has long been known that there is no measurable heat production associated with the nerve pulse. Rather, one finds that heat production is biphasic, and a heat release during the first phase of the action potential is followed by the reabsorption of a similar amount of heat during the second phase. We review the long history the measurement of heat production in nerves and provide a new analysis
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GHK eq. and HH eq. for a real system is mathematically associable to each other but their physiological interpretation needs a reconsideration. Prog. Biophys. Mol. Biol. (IF 2.175) Pub Date : 2020-08-11 Hirohisa Tamagawa,Titus Mulembo,Vera Maura Fernandes de Lima,Wolfgang Hanke
Despite the long and broad acceptance of the Goldman - Hodgkin - Katz equation (GHK eq.) and the Hodgkin - Huxley equation (HH eq.) as strong tools for the quantitative analysis of the membrane potential behavior, for a long time they have been utilized as separate concepts. That is the GHK eq. and the HH eq. have not been associated with each other mathematically. In this paper, an attempt to associate
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Accounting for cardiac t-tubule increase with age and myocyte volume to improve measurements of its membrane area and ionic current densities. Prog. Biophys. Mol. Biol. (IF 2.175) Pub Date : 2020-08-10 Georges Christé,Robert Bonvallet,Christophe Chouabe
In-silico models of cardiac myocytes allow simulating experiments in numbers on series of myocytes as well as on large populations of myocytes assembled in 3D structures. The simulated myocyte populations should have realistic values and statistical dispersions of biophysical parameters such as myocyte dimensions and volume and areas of the peripheral membrane and transverse-axial tubular system (TATS)
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In vitro cell stretching technology (IsoStretcher) as an approach to unravel Piezo1-mediated cardiac mechanotransduction. Prog. Biophys. Mol. Biol. (IF 2.175) Pub Date : 2020-08-05 Yang Guo,Anna-Lena Merten,Ulrike Schöler,Ze-Yan Yu,Jasmina Cvetkovska,Diane Fatkin,Michael P Feneley,Boris Martinac,Oliver Friedrich
The transformation of electrical signals into mechanical action of the heart underlying blood circulation results in mechanical stimuli during active contraction or passive filling distention, which conversely modulate electrical signals. This feedback mechanism is known as cardiac mechano-electric coupling (MEC). The cardiac MEC involves complex activation of mechanical biosensors initiating short-term
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Structural interpretation of cryo-EM image reconstructions. Prog. Biophys. Mol. Biol. (IF 2.175) Pub Date : 2020-07-29 Maximilian Beckers,Daniel Mann,Carsten Sachse
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Transcriptional signatures regulated by TRPC1/C4-mediated Background Ca2+ entry after pressure-overload induced cardiac remodelling. Prog. Biophys. Mol. Biol. (IF 2.175) Pub Date : 2020-07-29 Juan E Camacho Londoño,Vladimir Kuryshev,Markus Zorn,Kathrin Saar,Qinghai Tian,Norbert Hübner,Peter Nawroth,Alexander Dietrich,Lutz Birnbaumer,Peter Lipp,Christoph Dieterich,Marc Freichel
Aims After summarizing current concepts for the role of TRPC cation channels in cardiac cells and in processes triggered by mechanical stimuli arising e.g. during pressure overload, we analysed the role of TRPC1 and TRPC4 for background Ca2+ entry (BGCE) and for cardiac pressure overload induced transcriptional remodelling. Methods and results Mn2+-quench analysis in cardiomyocytes from several Trpc-deficient
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Comparison of CryoEM and X-ray structures of dimethylformamidase. Prog. Biophys. Mol. Biol. (IF 2.175) Pub Date : 2020-07-28 Kutti R Vinothkumar,Chetan Kumar Arya,Gurunath Ramanathan,Ramaswamy Subramanian
Dimethylformamidase (DMFase) catalyzes the hydrolysis of dimethylformamide, an industrial solvent, introduced into the environment by humans. Recently, we determined the structures of dimethylformamidase by electron cryo microscopy and X-ray crystallography revealing a tetrameric enzyme with a mononuclear iron at the active site. DMFase from Paracoccus sp. isolated from a waste water treatment plant
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In-silico human electro-mechanical ventricular modelling and simulation for drug-induced pro-arrhythmia and inotropic risk assessment. Prog. Biophys. Mol. Biol. (IF 2.175) Pub Date : 2020-07-22 Francesca Margara,Zhinuo J Wang,Francesc Levrero-Florencio,Alfonso Santiago,Mariano Vázquez,Alfonso Bueno-Orovio,Blanca Rodriguez
Human-based computational modelling and simulation are powerful tools to accelerate the mechanistic understanding of cardiac patho-physiology, and to develop and evaluate therapeutic interventions. The aim of this study is to calibrate and evaluate human ventricular electro-mechanical models for investigations on the effect of the electro-mechanical coupling and pharmacological action on human ventricular
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Computational models of cardiac hypertrophy. Prog. Biophys. Mol. Biol. (IF 2.175) Pub Date : 2020-07-21 Kyoko Yoshida,Jeffrey W Holmes
Cardiac hypertrophy, defined as an increase in mass of the heart, is a complex process driven by simultaneous changes in hemodynamics, mechanical stimuli, and hormonal inputs. It occurs not only during pre- and post-natal development but also in adults in response to exercise, pregnancy, and a range of cardiovascular diseases. One of the most exciting recent developments in the field of cardiac biomechanics
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Tools for visualizing and analyzing Fourier space sampling in Cryo-EM. Prog. Biophys. Mol. Biol. (IF 2.175) Pub Date : 2020-07-06 Philip R Baldwin,Dmitry Lyumkis
A complete understanding of how an orientation distribution contributes to a cryo-EM reconstruction remains lacking. It is necessary to begin critically assessing the set of views to gain an understanding of its effect on experimental reconstructions. Toward that end, we recently suggested that the type of orientation distribution may alter resolution measures in a systematic manner. We introduced
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High resolution single particle Cryo-EM refinement using JSPR. Prog. Biophys. Mol. Biol. (IF 2.175) Pub Date : 2020-07-03 Chen Sun,Brenda Gonzalez,Frank S Vago,Wen Jiang
JSPR is a single particle cryo-EM image processing and 3D reconstruction software developed in the Jiang laboratory at Purdue University. It began as a few refinement scripts for symmetric and asymmetric reconstructions of icosahedral viruses, but has grown into a comprehensive suite of tools for building ab initio reconstructions, high resolution refinements of viruses, protein complexes of arbitrary
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Intrinsic disorder in proteins: Relevance to protein assemblies, drug design and host-pathogen interactions. Prog. Biophys. Mol. Biol. (IF 2.175) Pub Date : 2020-07-03 Tom L Blundell,Munishwar N Gupta,Seyed E Hasnain
Intrinsic disorder in proteins resulting in considerable variation in structure can lead to multiple functions including multi-specificity and diverse pathologies. Protein interfaces can involve disordered regions that assemble through a concerted-fold-and-bind mechanism. The binding involves both enthalpic and entropic gains by exploiting ‘hot spots’ on the partner and displacing water molecules placed
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The origin of the heartbeat and theories of muscle contraction. Physiological concepts and conflicts in the 19th century. Prog. Biophys. Mol. Biol. (IF 2.175) Pub Date : 2020-07-03 Johann P Kuhtz-Buschbeck,Jochen Schaefer,Nicolaus Wilder,Wilhelm T Wolze
The origin of the incessant rhythmical heartbeat and the mechanism of muscle contraction have fascinated scientists over centuries. This short review outlines physiological explanations that were discussed in the 19th century starting with Albrecht von Haller (1708–1777), an 18th century physiologist who proposed that the heart has an intrinsic irritability. He argued that under normal conditions the
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Distribution of data in cellular electrophysiology: Is it always normal? Prog. Biophys. Mol. Biol. (IF 2.175) Pub Date : 2020-07-01 Roman Kula,Markéta Bébarová,Peter Matejovič,Jiří Šimurda,Michal Pásek
The distribution of data presented in many electrophysiological studies is presumed to be normal without any convincing evidence. To test this presumption, the cell membrane capacitance and magnitude of inward rectifier potassium currents were recorded by the whole-cell patch clamp technique in rat atrial myocytes. Statistical analysis of the data showed that these variables were not distributed normally
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Towards high-throughput in situ structural biology using electron cryotomography. Prog. Biophys. Mol. Biol. (IF 2.175) Pub Date : 2020-06-21 Jan Böhning,Tanmay A M Bharat
Electron cryotomography is a rapidly evolving method for imaging macromolecules directly within the native environment of cells and tissues. Combined with sub-tomogram averaging, it allows structural and cell biologists to obtain sub-nanometre resolution structures in situ. However, low throughput in cryo-ET sample preparation and data acquisition, as well as difficulties in target localisation and
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Toward more accurate data in cardiac cellular electrophysiology. Prog. Biophys. Mol. Biol. (IF 2.175) Pub Date : 2020-06-23 Markéta Bébarová,Michal Pásek,Ivan Zahradník
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Cellular metabolism and colloids: Realistically linking physiology and biological physical chemistry. Prog. Biophys. Mol. Biol. (IF 2.175) Pub Date : 2020-06-18 Luis A Bagatolli,Agustín Mangiarotti,Roberto P Stock
Important concepts from colloidal physical chemistry such as coacervation, phase transitions, emergent properties and ionic association, are currently emerging in the lexicon of cellular biology, prompted mostly by recent experimental observations of liquid phase coexistence in the cell cytosol. Nevertheless, from an historical point of view, the application of these concepts in cell biology is not
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TRPV2 channel-based therapies in the cardiovascular field. Molecular underpinnings of clinically relevant therapies. Prog. Biophys. Mol. Biol. (IF 2.175) Pub Date : 2020-06-18 Brian O'Connor,Nathan Robbins,Sheryl E Koch,Jack Rubinstein
The transient receptor potential (TRP) ion channel family is composed of twenty-seven channel proteins that are ubiquitously expressed in the human body. The TRPV (vanilloid) subfamily has been a recent target of investigation within the cardiovascular field. TRPV1, which is sensitive to heat as well as vanilloids, is the best characterized TRPV channel and is the namesake for the subfamily that includes
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Mechanosensitive TREK-1 two-pore-domain potassium (K2P) channels in the cardiovascular system. Prog. Biophys. Mol. Biol. (IF 2.175) Pub Date : 2020-06-15 Felix Wiedmann,Susanne Rinné,Birgit Donner,Niels Decher,Hugo A Katus,Constanze Schmidt
TWIK-related K+ channel (TREK-1) two-pore-domain potassium (K2P) channels mediate background potassium currents and regulate cellular excitability in many different types of cells. Their functional activity is controlled by a broad variety of different physiological stimuli, such as temperature, extracellular or intracellular pH, lipids and mechanical stress. By linking cellular excitability to mechanical
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Localized reconstruction in Scipion expedites the analysis of symmetry mismatches in cryo-EM data. Prog. Biophys. Mol. Biol. (IF 2.175) Pub Date : 2020-05-26 Vahid Abrishami,Serban L Ilca,Josue Gomez-Blanco,Ilona Rissanen,José Miguel de la Rosa-Trevín,Vijay S Reddy,José-Maria Carazo,Juha T Huiskonen
Technological advances in transmission electron microscopes and detectors have turned cryogenic electron microscopy (cryo-EM) into an essential tool for structural biology. A commonly used cryo-EM data analysis method, single particle analysis, averages hundreds of thousands of low-dose images of individual macromolecular complexes to determine a density map of the complex. The presence of symmetry
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The role of pacing rate in the modulation of mechano-induced immediate and delayed changes in the force and Ca-transient of cardiac muscle. Prog. Biophys. Mol. Biol. (IF 2.175) Pub Date : 2020-05-23 Oleg Lookin,Xenia Butova,Yuri Protsenko
Myocardial function is tuned by dynamic changes in length and load via mechano-calcium feedback. This regulation may be significantly affected by heart rhythm. We evaluated the mechano-induced modulation of contractility and Ca-transient (CaT) in the rat myocardium subjected to twitch-by-twitch shortening–re-lengthening (↓–↑) trains of different lengths (N = 1 … 720 cycles) at low (1 Hz) and near-physiological
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