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Progress in Biophysics and Molecular Biology

Fridolin Gross, Miles MacLeod
There are currently no widely shared criteria by which to assess the validity of computational models in systems biology. Here we discuss the feasibility and desirability of implementing validation standards for modeling. Having such a standard would facilitate journal review, interdisciplinary collaboration, model exchange, and be especially relevant for applications close to medical practice. However, even though the production of predictively valid models is considered a central goal, in practice modeling in systems biology employs a variety of model structures and model-building practices...
January 12, 2017: Progress in Biophysics and Molecular Biology
M Michael Gromiha, K Yugandhar
Protein-protein interactions perform several functions inside the cell. Understanding the recognition mechanism and binding affinity of protein-protein complexes is a challenging problem in experimental and computational biology. In this review, we focus on two aspects (i) understanding the recognition mechanism and (ii) predicting the binding affinity. The first part deals with computational techniques for identifying the binding site residues and the contribution of important interactions for understanding the recognition mechanism of protein-protein complexes in comparison with experimental observations...
January 7, 2017: Progress in Biophysics and Molecular Biology
Christian Domilongo Bope, Dudu Tong, Xiuting Li, Lanyuan Lu
Elastic network models (ENMs) based on simple harmonic potential energy function have been proven over the last decade to be reliable computational models for understanding the intrinsic dynamics of biomacromolecules. In the original ENMs, the spring constants for different contact pairs are assumed to be identical, while there are a number of recent developments to determine non-uniform spring constants from atomistic force fields or experimental information. In particular, the fluctuation matching approaches in coarse-grained modeling can be applied to build more realistic heterogeneous ENMs, using information from an atomistic force field or experimental B-factors...
December 30, 2016: Progress in Biophysics and Molecular Biology
Alexey V Melkikh, Andrei Khrennikov
The background of this study is that models of the evolution of living systems are based mainly on the evolution of replicators and cannot explain many of the properties of biological systems such as the existence of the sexes, molecular exaptation and others. The purpose of this study is to build a complete model of the evolution of organisms based on a combination of quantum-like models and models based on partial directivity of evolution. We also used optimal control theory for evolution modeling. We found that partial directivity of evolution is necessary for the explanation of the properties of an evolving system such as the stability of evolutionary strategies, aging and death, the presence of the sexes...
December 15, 2016: Progress in Biophysics and Molecular Biology
Anil Kumar, Ranjit Ranbhor, Kirti Patel, Vibin Ramakrishnan, Susheel Durani
Protein design has an eventful history spanning over three decades, with handful of success stories reported, and numerous failures not reported. Design practices have benefited tremendously from improvements in computer hardware and advances in scientific algorithms. Though protein folding problem still remains unsolved, the possibility of having multiple sequence solutions for a single fold makes protein design a more tractable problem than protein folding. One of the most significant advancement in this area is the implementation of automated design algorithms on pre-defined templates or completely new folds, optimized through deterministic and heuristic search algorithms...
December 12, 2016: Progress in Biophysics and Molecular Biology
Bernard Korzeniewski
The mechanisms responsible for matching of the highly varying ATP demand by ATP supply in muscle are of primary importance for pure science, sport science and medicine. According to the traditional opinion ATP supply is activated by elevated ADP and Pi resulting from ATP hydrolysis during intensive work. Theoretical studies using the computer model of oxidative phosphorylation (OXPHOS) and the entire cell bioenergetic system developed by the author and co-workers lead to the each-step-activation (ESA) mechanism of the regulation of the system in skeletal muscle, heart and other tissues during work transitions...
December 8, 2016: Progress in Biophysics and Molecular Biology
Ahmad W Almawi, Lindsay A Matthews, Alba Guarné
Forkhead-associated (FHA) domains are small phosphopeptide recognition modules found in eubacterial and eukaryotic, but not archeal, genomes. Although they were originally found in forkhead-type transcription factors, they have now been identified in many other signaling proteins. FHA domains share a remarkably conserved fold despite very low sequence conservation. They only have five conserved amino acids that are important for binding to phosphorylated epitopes. Recent work from several laboratories has demonstrated that FHA domains can mediate many interactions that do not depend on their ability to recognize a phosphorylated threonine...
December 8, 2016: Progress in Biophysics and Molecular Biology
Muwen Kong, Bennett Van Houten
Since Robert Brown's first observations of random walks by pollen particles suspended in solution, the concept of diffusion has been subject to countless theoretical and experimental studies in diverse fields from finance and social sciences, to physics and biology. Diffusive transport of macromolecules in cells is intimately linked to essential cellular functions including nutrient uptake, signal transduction, gene expression, as well as DNA replication and repair. Advancement in experimental techniques has allowed precise measurements of these diffusion processes...
December 7, 2016: 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
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
Ira Cohen, Denis Noble
No abstract text is available yet for this article.
December 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...
December 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...
December 2016: Progress in Biophysics and Molecular Biology
Ira S Cohen, Richard T Mathias
No abstract text is available yet for this article.
December 2016: Progress in Biophysics and Molecular Biology
Bas J Boukens, Richard Walton, Veronique M Meijborg, Ruben Coronel
Heterogeneous distribution of electrophysiological behavior across the heart is essential for normal cardiac function. If this heterogeneity becomes excessive it may contribute to arrhythmogenesis and sudden cardiac death. Controversy exists regarding the localization of activation and repolarization gradients in the diseased heart and how these heterogeneities contribute to arrhythmogenesis. In this review we focus on the genesis and existence of transmural heterogeneity in activation and repolarization. We will describe a possible embryonic origin of these heterogeneities and address the question how heterogeneities contribute to the genesis of the electrocardiogram and how they may cause reentrant arrhythmias...
December 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
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