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Progress in Biophysics and Molecular Biology

Harry C Jubb, Arun P Pandurangan, Meghan A Turner, Bernardo Ochoa-Montaño, Tom L Blundell, David B Ascher
Many essential biological processes including cell regulation and signalling are mediated through the assembly of protein complexes. Changes to protein-protein interaction (PPI) interfaces can affect the formation of multiprotein complexes, and consequently lead to disruptions in interconnected networks of PPIs within and between cells, further leading to phenotypic changes as functional interactions are created or disrupted. Mutations altering PPIs have been linked to the development of genetic diseases including cancer and rare Mendelian diseases, and to the development of drug resistance...
November 29, 2016: Progress in Biophysics and Molecular Biology
Jesús Carro, José F Rodríguez-Matas, Violeta Monasterio, Esther Pueyo
Models of ion channel dynamics are usually built by fitting isolated cell experimental values of individual parameters while neglecting the interaction between them. Another shortcoming regards the estimation of ionic current conductances, which is often based on quantification of Action Potential (AP)-derived markers. Although this procedure reduces the uncertainty in the calculation of conductances, many studies evaluate electrophysiological AP-derived markers from single cell simulations, whereas experimental measurements are obtained from tissue preparations...
November 27, 2016: Progress in Biophysics and Molecular Biology
Nahren Manuel Mascarenhas, Shachi Gosavi
In domain-swapping, two or more identical protein monomers exchange structural elements and fold into dimers or multimers whose units are structurally similar to the original monomer. Domain-swapping is of biotechnological interest because inhibiting domain-swapping can reduce disease-causing fibrillar protein aggregation. To achieve such inhibition, it is important to understand both the energetics that stabilize the domain-swapped structure and the protein dynamics that enable the swapping. Structure-based models (SBMs) encode the folded structure of the protein in their potential energy functions...
November 17, 2016: Progress in Biophysics and Molecular Biology
Eric D Carruth, Andrew D McCulloch, Jeffrey H Omens
Although a truly complete understanding of whole heart activation, contraction, and deformation is well beyond our current reach, a significant amount of effort has been devoted to discovering and understanding the mechanisms by which myocardial structure determines cardiac function to better treat patients with cardiac disease. Several experimental studies have shown that transmural fiber strain is relatively uniform in both diastole and systole, in contrast to predictions from traditional mechanical theory...
November 11, 2016: Progress in Biophysics and Molecular Biology
Piero R Bianco
The E. coli single stranded DNA binding protein (SSB) is essential to all aspects of DNA metabolism. Here, it has two seemingly disparate but equally important roles: it binds rapidly and cooperatively to single stranded DNA (ssDNA) and it binds to partner proteins that constitute the SSB interactome. These two roles are not disparate but are instead, intimately linked. A model is presented wherein the intrinsically disordered linker (IDL) is directly responsible for mediating protein-protein interactions...
November 9, 2016: Progress in Biophysics and Molecular Biology
Huipeng Yao, Chenglei Li, Haixia Zhao, Jianlan Zhao, Hui Chen, Tongliang Bu, Wang Anhu, Qi Wu
Black tartary buckwheat is recognized as 'black pearl' because of containg more rutin and other flavonoids as compared to yellow tartary buckwheat (traditional tartary buckwheat). Here, we show a genome-wide comparison of their transcriptomes by using an RNA-seq approach to elucidate the different molecular metabolism on the flowers from Black tartary buckwheat (HEIFENG No1) and yellow tartary buckwheat (XIQIAO No2). Over 48.4 million paired-end reads were assembled into 57,800 unigenes, of which about 57.9% (33, 472 unigenes) were annotated by BLAST searches in the NCBI non-redundant protein database...
November 8, 2016: Progress in Biophysics and Molecular Biology
Josh Hiller, Celeste Vallejo, Leo Betthauser, James Keesling
We investigate and classify several patterns in cancer incidence and relative risk data which persist across different countries and multiple published studies. We then explore biological hypotheses as well as many mathematical models in the literature that attempt to explain these patterns. A general modeling framework is presented which is general enough to model most of observed behaviors. It is our belief that this model has sufficient flexibility to be adapted to new information as it is discovered. As one application of this framework, we give a model for the effect of aging on the process of carcinogenesis...
November 8, 2016: Progress in Biophysics and Molecular Biology
Roland G Huber, Jan K Marzinek, Daniel A Holdbrook, Peter J Bond
Viral pathogens are a significant source of human morbidity and mortality, and have a major impact on societies and economies around the world. One of the challenges inherent in targeting these pathogens with drugs is the tight integration of the viral life cycle with the host's cellular machinery. However, the reliance of the virus on the host cell replication machinery is also an opportunity for therapeutic targeting, as successful entry- and exit-inhibitors have demonstrated. An understanding of the extracellular and intracellular structure and dynamics of the virion - as well as of the entry and exit pathways in host and vector cells - is therefore crucial to the advancement of novel antivirals...
October 17, 2016: Progress in Biophysics and Molecular Biology
Eann A Patterson, Maurice P Whelan
Computational models in biology and biomedical science are often constructed to aid people's understanding of phenomena or to inform decisions with socioeconomic consequences. Model credibility is the willingness of people to trust a model's predictions and is often difficult to establish for computational biology models. A 3 × 3 matrix has been proposed to allow such models to be categorised with respect to their testability and epistemic foundation in order to guide the selection of an appropriate process of validation to supply evidence to establish credibility...
October 1, 2016: Progress in Biophysics and Molecular Biology
David McKinnon, Barbara Rosati
Evolution has acted to shape the action potential in different regions of the heart in order to produce a maximally stable and efficient pump. This has been achieved by creating regional differences in ion channel expression levels within the heart as well as differences between equivalent cardiac tissues in different species. These region- and species-dependent differences in channel expression are established by regulatory evolution, evolution of the regulatory mechanisms that control channel expression levels...
October 1, 2016: Progress in Biophysics and Molecular Biology
Igor N Berezovsky, Enrico Guarnera, Zejun Zheng
Study of the hierarchy of domain structure with alternative sets of domains and analysis of discontinuous domains, consisting of remote segments of the polypeptide chain, raised a question about the minimal structural unit of the protein domain. The hypothesis on the decisive role of the polypeptide backbone in determining the elementary units of globular proteins have led to the discovery of closed loops. It is reviewed here how closed loops form the loop-n-lock structure of proteins, providing the foundation for stability and designability of protein folds/domain and underlying their co-translational folding...
September 30, 2016: Progress in Biophysics and Molecular Biology
Lizhe Zhu, Hanlun Jiang, Fu Kit Sheong, Xuefeng Cui, Yanli Wang, Xin Gao, Xuhui Huang
At the core of RNA interference, the Argonaute proteins (Ago) load and utilize small guide nucleic acids to silence mRNAs or cleave foreign nucleic acids in a sequence specific manner. In recent years, based on extensive structural studies of Ago and its interaction with the nucleic acids, considerable progress has been made to reveal the dynamic aspects of various Ago-mediated processes. Here we review these novel insights into the guide-strand loading, duplex unwinding, and effects of seed mismatch, with a focus on two representative Agos, the human Ago 2 (hAgo2) and the bacterial Thermus thermophilus Ago (TtAgo)...
September 30, 2016: Progress in Biophysics and Molecular Biology
C O S Sorzano, J Vargas, J Otón, V Abrishami, J M de la Rosa-Trevín, J Gómez-Blanco, J L Vilas, R Marabini, J M Carazo
Fourier Shell Correlation, Spectral Signal-to-Noise Ratio, Fourier Neighbour Correlation, and Differential Phase Residual are different measures that have been proposed over time to determine the spatial resolution achieved by a certain 3D reconstruction. Estimates of B-factors to describe the reduction in signal-to-noise ratio with increasing resolution is also a useful parameter. All these concepts are interrelated and different thresholds have been given for each one of them. However, the problem of resolution assessment in 3DEM is still far from settled and preferences are normally adopted in order to choose the "correct" threshold...
September 22, 2016: Progress in Biophysics and Molecular Biology
Togo Shimozawa, Erisa Hirokawa, Fuyu Kobirumaki-Shimozawa, Kotaro Oyama, Seine A Shintani, Takako Terui, Yasuharu Kushida, Seiichi Tsukamoto, Teruyuki Fujii, Shin'ichi Ishiwata, Norio Fukuda
The cardiac pump function is a result of a rise in intracellular Ca(2+) and the ensuing sarcomeric contractions [i.e., excitation-contraction (EC) coupling] in myocytes in various locations of the heart. In order to elucidate the heart's mechanical properties under various settings, cardiac imaging is widely performed in today's clinical as well as experimental cardiology by using echocardiogram, magnetic resonance imaging and computed tomography. However, because these common techniques detect local myocardial movements at a spatial resolution of ∼100 μm, our knowledge on the sub-cellular mechanisms of the physiology and pathophysiology of the heart in vivo is limited...
September 21, 2016: Progress in Biophysics and Molecular Biology
Ira S Cohen, Richard T Mathias
No abstract text is available yet for this article.
September 16, 2016: Progress in Biophysics and Molecular Biology
Philip Turner, Laurent Nottale
Based on laboratory based growth of plant-like structures from inorganic materials, we present new theory for the emergence of plant structure at a range of scales dictated by levels of ionization, which can be traced directly back to proteins transcribed from genetic code and their interaction with external sources of charge in real plants. Beyond a critical percolation threshold, individual charge induced quantum potentials merge to form a complex, interconnected geometric web, creating macroscopic quantum potentials, which lead to the emergence of macroscopic quantum processes...
September 14, 2016: Progress in Biophysics and Molecular Biology
Julie M J Laffy, Tihomir Dodev, Jamie A Macpherson, Catherine Townsend, Hui Chun Lu, Deborah Dunn-Walters, Franca Fraternali
Human B cells produce antibodies, which bind to their cognate antigen based on distinct molecular properties of the antibody CDR loop. We have analysed a set of 10 antibodies showing a clear difference in their binding properties to a panel of antigens, resulting in two subsets of antibodies with a distinct binding phenotype. We call the observed binding multiplicity 'promiscuous' and selected physico-chemical CDRH3 characteristics and conformational preferences may characterise these promiscuous antibodies...
September 14, 2016: Progress in Biophysics and Molecular Biology
Zhimin Li, Charles Shang
A model of growth control system suggests that the organizers in embryogenesis continue to exist and partially retain their function after embryogenesis. The organizers are the macroscopic singular points of the morphogen gradient and bioelectric fields. They have higher metabolic rate, higher density of gap junctions and stem cells than the surrounding tissue. The growth control model predicts that the organizers are likely to exist at the extreme points of surface or interface curvature of the body. Changes in bioelectric field at organizers precede the morphological and anatomical changes in morphogenesis and pathogenesis...
September 12, 2016: Progress in Biophysics and Molecular Biology
Denis Noble
No abstract text is available yet for this article.
November 2016: Progress in Biophysics and Molecular Biology
Xinchang Zhang, Qiangsong Wang, Zongming Wan, Jianyu Li, Lu Liu, Xizheng Zhang
Casein kinase 2-interacting protein 1 (CKIP-1) is a negative regulator for bone formation. CKIP-1 knockout (KO) mice are very important for research on countermeasures to bone loss induced by space microgravity. Under simulated microgravity, the bone metabolism of CKIP-1 KO mice was different than that of wild-type (WT) mice. Many experiments all showed that the KO mice had significantly enhanced ossification in the tail suspension conditions, and the differences were closely related to the time the mice were exposed to the microgravity environment...
November 2016: Progress in Biophysics and Molecular Biology
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