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SSEThread: Integrative threading of the DNA-PKcs sequence based on data from chemical cross-linking and hydrogen deuterium exchange
Publication date: Available online 27 September 2019Source: Progress in Biophysics and Molecular BiologyAuthor(s): Daniel J. Saltzberg, Morgan Hepburn, Kala Bharath Pilla, David C. Schriemer, Susan P. Lees-Miller, Tom L. Blundell, Andrej SaliAbstractX-ray crystallography and electron microscopy maps resolved to 3–8 Å are generally sufficient for tracing the path of the polypeptide chain in space, while often insufficient for unambiguously registering the sequence on the path (i.e., threading). Frequently, however, additional information is available from other biophysical experiments, physical principles, statistical ...
Source: Progress in Biophysics and Molecular Biology - September 28, 2019 Category: Molecular Biology Source Type: research

Investigation of machine learning techniques on proteomics: A comprehensive survey
Publication date: Available online 27 September 2019Source: Progress in Biophysics and Molecular BiologyAuthor(s): Pravinkumar M. Sonsare, C. GunavathiAbstractProteomics is the extensive investigation of proteins which has empowered the recognizable proof of consistently expanding quantities of protein. Proteins are necessary part of living life form, with numerous capacities. The proteome is the complete arrangement of proteins that are created or altered by a life form or framework of the organism. Proteome fluctuates with time and unambiguous prerequisites, or stresses, that a cell or organism experiences. Proteomics is...
Source: Progress in Biophysics and Molecular Biology - September 28, 2019 Category: Molecular Biology Source Type: research

Polygenic scores: Are they a public health hazard?
Publication date: Available online 6 August 2019Source: Progress in Biophysics and Molecular BiologyAuthor(s): Keith BaverstockAbstractI argue here that polygenic scores are a public health hazard because the underlying methodology, genome wide association, from which they are derived, incorrectly assumes that the information encoded in the genomic DNA sequence is causal in terms of the cellular phenotype. This is not so when the cell is viewed from the perspective of a) fundamental physics, b) the protein chemistry that characterises the cellular cytoplasm and c) the fundamental requirement for evolution to yield unlimite...
Source: Progress in Biophysics and Molecular Biology - September 18, 2019 Category: Molecular Biology Source Type: research

Non-Uniformity of Projection Distributions Attenuates Resolution in Cryo-EM
Publication date: Available online 13 September 2019Source: Progress in Biophysics and Molecular BiologyAuthor(s): Philip R. Baldwin, Dmitry LyumkisAbstractVirtually all single-particle cryo-EM experiments currently suffer from specimen adherence to the air-water interface, leading to a non-uniform distribution in the set of projection views. Whereas it is well accepted that uniform projection distributions can lead to high-resolution reconstructions, non-uniform (anisotropic) distributions can negatively affect map quality, elongate structural features, and in some cases, prohibit interpretation altogether. Although some ...
Source: Progress in Biophysics and Molecular Biology - September 14, 2019 Category: Molecular Biology Source Type: research

Towards Dewetting Monoclonal Antibodies For Therapeutical Purposes
We describe a novel type of high-affinity monoclonal antibody, that: a) targets specific trans-membrane receptor structures of harmful or redundant cells; b) is equipped with lipophilic and/or hydrophobic fragments that prevent physiological water flow inside ion channels. Therefore, we achieve an artificial dewetting transition inside receptor cavities, that causes discontinuity within transmembrane ionic flows, channel blockage, and subsequent damage of morbid cells. As an example, we describe dewetting monoclonal antibodies that target the M2 channel of the Influenza A virus: they might prevent water from entering pores...
Source: Progress in Biophysics and Molecular Biology - September 14, 2019 Category: Molecular Biology Source Type: research

The N-space Episenome unifies cellular information space-time within cognition-based evolution
Publication date: Available online 12 August 2019Source: Progress in Biophysics and Molecular BiologyAuthor(s): William B. Miller, John S. Torday, František BaluškaAbstractSelf-referential cellular homeostasis is maintained by the measured assessment of both internal status and external conditions based within an integrated cellular information field. This cellular field attachment to biologic information space-time coordinates environmental inputs by connecting the cellular senome, as the sum of the sensory experiences of the cell, with its genome and epigenome. In multicellular organisms, individual cellular informatio...
Source: Progress in Biophysics and Molecular Biology - September 13, 2019 Category: Molecular Biology Source Type: research

No light without the dark: Perspectives and hindrances for translation of cardiac optogenetics
Publication date: Available online 9 September 2019Source: Progress in Biophysics and Molecular BiologyAuthor(s): Claudia Richter, Tobias BruegmannAbstractOver the last decade, optogenetic stimulation of the heart and its translational potential for rhythm control attracted more and more interest. Optogenetics allows to stimulate cardiomyocytes expressing the light-gated cation channel Channelrhodopsin 2 (ChR2) with light and thus high spatio-temporal precision. Therefore this new approach can overcome the technical limitations of electrical stimulation. In regard of translational approaches, the prospect of pain-free stim...
Source: Progress in Biophysics and Molecular Biology - September 10, 2019 Category: Molecular Biology Source Type: research

Two-photon excitation of FluoVolt allows improved interrogation of transmural electrophysiological function in the intact mouse heart
ConclusionOur results demonstrate several advantages of two-photon excitation of FluoVolt in functional studies in intact heart preparations, including reduced toxicity and improved fluorescent properties. (Source: Progress in Biophysics and Molecular Biology)
Source: Progress in Biophysics and Molecular Biology - September 4, 2019 Category: Molecular Biology Source Type: research

Recent progress in optical voltage-sensor technology and applications to cardiac research: from single cells to whole hearts
Publication date: Available online 29 August 2019Source: Progress in Biophysics and Molecular BiologyAuthor(s): Corey D. Acker, Ping Yan, Leslie M. LoewAbstractThe first workshop on Novel Optics-based approaches for Cardiac Electrophysiology (NOtiCE) was held in Florence Italy in 2018. Here, we learned how optical approaches have shaped our basic understanding of cardiac electrophysiology and how new technologies and approaches are being developed and validated to advance the field. Several technologies are being developed that may one day allow for new clinical approaches for diagnosing cardiac disorders and possibly inte...
Source: Progress in Biophysics and Molecular Biology - August 30, 2019 Category: Molecular Biology Source Type: research

PBMB Commentary on Editorial by Keith Baverstock
Publication date: Available online 6 August 2019Source: Progress in Biophysics and Molecular BiologyAuthor(s): Denis Noble, Tom Blundell, Peter Kohl (Source: Progress in Biophysics and Molecular Biology)
Source: Progress in Biophysics and Molecular Biology - August 29, 2019 Category: Molecular Biology Source Type: research

DNA damage response mechanisms and structures fundamental to cancer research progress
Publication date: Available online 27 August 2019Source: Progress in Biophysics and Molecular BiologyAuthor(s): Albino Bacolla, John A. Tainer (Source: Progress in Biophysics and Molecular Biology)
Source: Progress in Biophysics and Molecular Biology - August 29, 2019 Category: Molecular Biology Source Type: research

Stability of Multi-Subunit Proteins and Conformational Lock
Publication date: Available online 27 August 2019Source: Progress in Biophysics and Molecular BiologyAuthor(s): L. Alaei, Ali A. Moosavi-MovahediAbstractOne of the important physicochemical features of the proteins specifically multi-subunit types is their stability at high temperatures. The kinetics of the dissociation and denaturation of proteins possessing at least two subunits has certain challenges because the overall mechanism of dissociation can include hidden reversible and/or irreversible steps (conformational lock). There are numerous proteins related to diseases which are in equilibrium with oligomer forms. This...
Source: Progress in Biophysics and Molecular Biology - August 29, 2019 Category: Molecular Biology Source Type: research

Lamarck and Panspermia - On the Efficient Spread of Living Systems Throughout the Cosmos
Publication date: Available online 22 August 2019Source: Progress in Biophysics and Molecular BiologyAuthor(s): Edward J. Steele, Reginald M. Gorczynski, Robyn A. Lindley, Yongsheng Liu, Robert Temple, Gensuke Tokoro, Dayal T. Wickramasinghe, N. Chandra WickramasingheAbstractWe review the main lines of evidence (molecular, cellular and whole organism) published since the 1970s demonstrating Lamarckian Inheritance in animals, plants and microorganisms viz. the transgenerational inheritance of environmentally-induced acquired characteristics. The studies in animals demonstrate the genetic permeability of the soma-germline We...
Source: Progress in Biophysics and Molecular Biology - August 23, 2019 Category: Molecular Biology Source Type: research

Conjugation of NMR and SAXS for Flexible and Multidomain Protein Structure Determination: From Sample Preparation to Model Refinement
Publication date: Available online 21 August 2019Source: Progress in Biophysics and Molecular BiologyAuthor(s): P. Rodríguez-ZamoraAbstractExperimental information from small angle X-ray scattering (SAXS) is conjugated with nuclear magnetic resonance (NMR) spectroscopy data for the improvement of protein structure determination, particularly for flexible, multidomain or intrinsically disordered proteins. Individually, each of these techniques presents capabilities and limitations: NMR excels in local information, providing atomic resolution, but is limited by protein size, whereas SAXS yields a global envelope of the prot...
Source: Progress in Biophysics and Molecular Biology - August 22, 2019 Category: Molecular Biology Source Type: research

Editorial Board
Publication date: September 2019Source: Progress in Biophysics and Molecular Biology, Volume 146Author(s): (Source: Progress in Biophysics and Molecular Biology)
Source: Progress in Biophysics and Molecular Biology - August 18, 2019 Category: Molecular Biology Source Type: research