Biophysics Community Research Articles

Endogenous Cu(II) Labeling for Distance Measurements on Proteins by EPR.

In-cell measurements of the relationship between structure and dynamics to protein function is at the forefront of biophysics. Recently, developments in EPR methodology have demonstrated the sensitivity and power of this method to measure structural constraints in-cell. However, the need to spin label proteins ex-situ or use noncanonical amino acids to achieve endogenous labeling remains a bottleneck. In this work we expand the methodology to endogenously spin label proteins with Cu(II) spin labels and describe how to assess in-cell spin labeling. We quantify the amount of Cu(II)-NTA in cells, assess spin labeling, and account for orientational effects during distance measurements. We compare the efficacy of using heat-shock and hypotonic swelling to deliver spin label, showing that hypotonic swelling is a facile and reproducible method to efficiently deliver Cu(II)-NTA into E. coli. Notably, over six repeats we accomplish a bulk average of 57 μM spin labeled sites, surpassing existing endogenous labeling methods. The results of this work open the door for endogenous spin labeling that is easily accessible to the broader biophysical community.

Ubiquitin's Conformational Heterogeneity as Discerned by Nuclear Magnetic Resonance Spectroscopy.

Visualizing a protein's molecular motions has been a long standing topic of research in the biophysics community. Largely this has been done by exploiting nuclear magnetic resonance spectroscopy (NMR), and arguably no protein's molecular motions have been better characterized by NMR than that of ubiquitin (Ub), a 76 amino acid polypeptide essential in ubiquitination-a key regulatory system within cells. Herein, we discuss ubiquitin's conformational plasticity as visualized, at atomic resolution, by more than 35 years of NMR work. In our discussions we point out the differences between data acquired in vitro, ex vivo, as well as in vivo and stress the need to investigate Ub's conformational plasticity in more biologically representative backgrounds.

Cover Image

Peptide Science publishes peer‐reviewed papers covering all aspects of peptide synthesis, materials, structure and bioactivity. The journal includes both experimental and theoretical studies and serves the interdisciplinary biochemical, biomaterials, biophysical and biomedical research communities. image

Chromatin remodelers: a concise introduction for biophysicists.

Chromatin remodelers are molecular motors that act on nucleosomes: they move them along DNA or (dis-)assemble them. Despite the fact that they perform essential regulatory functions in cells-their deregulation can contribute to the development of cancers and lead to cell death-chromatin remodelers have only received meager attention in the biophysics community so far. In this short text, we attempt to present the key features of this interesting class of enzymes obtained with different experimental and theoretical methods, thereby providing a concise introduction for biophysicists to further stimulate interest in their properties.

Cover Image

Peptide Science publishes peer‐reviewed papers covering all aspects of peptide synthesis, materials, structure and bioactivity. The journal includes both experimental and theoretical studies and serves the interdisciplinary biochemical, biomaterials, biophysical and biomedical research communities. image

Cover Image

Peptide Science publishes peer‐reviewed papers covering all aspects of peptide synthesis, materials, structure and bioactivity. The journal includes both experimental and theoretical studies and serves the interdisciplinary biochemical, biomaterials, biophysical and biomedical research communities. image

Cover Image

Peptide Science publishes peer‐reviewed papers covering all aspects of peptide synthesis, materials, structure and bioactivity. The journal includes both experimental and theoretical studies and serves the interdisciplinary biochemical, biomaterials, biophysical and biomedical research communities. image

Cover Image

Peptide Science publishes peer‐reviewed papers covering all aspects of peptide synthesis, materials, structure and bioactivity. The journal includes both experimental and theoretical studies and serves the interdisciplinary biochemical, biomaterials, biophysical and biomedical research communities. image

Cover Image

BiopolymersVolume 114, Issue 6 e23504 COVER IMAGEFree Access Cover Image First published: 20 June 2023 https://doi.org/10.1002/bip.23504AboutPDF ToolsRequest permissionExport citationAdd to favoritesTrack citation ShareShare Give accessShare full text accessShare full-text accessPlease review our Terms and Conditions of Use and check box below to share full-text version of article.I have read and accept the Wiley Online Library Terms and Conditions of UseShareable LinkUse the link below to share a full-text version of this article with your friends and colleagues. Learn more.Copy URL Graphical Abstract Biopolymers celebrates its 60th anniversary! The journal was established in 1963 by Professor Murray Goodman as a founding editor and serves the interdisciplinary biochemical, biophysical, biomaterials and biomedical research communities. Volume114, Issue6June 2023e23504 RelatedInformation

Cover Image

BiopolymersVolume 114, Issue 5 e23502 COVER IMAGEFree Access Cover Image First published: 24 May 2023 https://doi.org/10.1002/bip.23502AboutPDF ToolsRequest permissionExport citationAdd to favoritesTrack citation ShareShare Give accessShare full text accessShare full-text accessPlease review our Terms and Conditions of Use and check box below to share full-text version of article.I have read and accept the Wiley Online Library Terms and Conditions of UseShareable LinkUse the link below to share a full-text version of this article with your friends and colleagues. Learn more.Copy URL Graphical Abstract Biopolymers celebrates its 60th anniversary! The journal was established in 1963 by Professor Murray Goodman as a founding editor and serves the interdisciplinary biochemical, biophysical, biomaterials and biomedical research communities. Volume114, Issue5May 2023e23502 RelatedInformation

Simulation of Gilbert theory for self-association in sedimentation velocity experiments: a guide to evaluate best fitting models.

There is a long tradition in the Biophysics community of using simulations as a means to understand macromolecular behavior in various physicochemical methods. This allows a rigorous means to interpret observations in terms of fundamental principles, including chemical equilibrium, reaction kinetics, transport processes and thermodynamics. Here we simulate data for the Gilbert Theory for self-association, a fundamental analytical ultracentrifuge (AUC) technique to understand the shape of sedimentation velocity reaction boundaries that involve reversible monomer-Nmer interactions. Simulating monomer-dimer through monomer-hexamer systems as a function of concentration about the equilibrium constant allows a visual means to differentiate reaction stoichiometry by determining end points and inflection positions. Including intermediates (eg A1-A2-A3-A4-A5-A6) in the simulations reveals the smoothing of the reaction boundary and the removal of sharp inflections between monomers and polymers. The addition of cooperativity restores sharp boundaries or peaks to the observation and allows more discrimination in the selection of possible fitting models. Thermodynamic nonideality adds additional features when applied across wide ranges of concentration that might be appropriate for high-concentration therapeutic monoclonal antibody (mAb) solutions. This presentation serves as a tutorial for using modern AUC analysis software like SEDANAL for selecting potential fitting models.

Unraveling the key-lock interaction mechanisms of the human neuropeptide Y type 4 receptor (hY4R) via solid-state NMR spectroscopy.

Human neuropeptide Y receptors (hYxR) are rhodopsin-like, peptide-binding G-protein coupled receptors (GPCRs). They are expressed within the gut-brain axis network, which allows several possible activation mechanisms, and thus downstream signaling pathways. hYxR therefore regulate a broad spectrum of biological functions (e.g., metabolic balance, vasoconstriction/dilation, circadian rhythm), and also play a central role in the development of several wide-spread pathologies such as several types of cancer, obesity/anorexia, anxiety and depression. Their functions and dysfunctions are tightly dependent on the specific extra- and intracellular coupling partners, as well as on the type of lipid membrane in which they are embedded. Understanding this complex interplay of receptor conformations/bound ligands/lipid environment has received much attention in the biochemical and biophysical communities, especially over the last 20 years, often motivated by the urgent need to develop selective therapeutics, based on receptor-specific lock-key mechanisms. Here, we present our novel approach to the study of conformational dynamics of the human Y receptor subtype 4 (hY4R - the lock), which has received very little attention compared to the rest of the hYxR family. Using cell-free protein expression strategies and solid-state NMR spectroscopy, we characterize structural changes of the receptor at the molecular level, when activated by different endogenous peptide ligands (the keys), namely pancreatic polypeptide (PP) and neuropeptide Y (NPY). This approach has the enormous potential to bringing us one step closer to understanding the specific key-lock interactions, which give rise to particular biological functions, and thus to the development of subtype-specific therapeutics.

Electrochemical Energy Harvesting Using Microbial Active Matter.

With the continuous growth in world population and economy, the global energy demand is increasing rapidly. Given that non-renewable energy sources will eventually deplete, there is increasing need for clean, alternative renewable energy sources, which will be inexpensive and involve minimum risk of environmental pollution. In this paper, harnessing the activity of cupric reductase NDH-2 enzyme present in Escherichia coli bacterial cells, we demonstrate a simple and efficient energy harvesting strategy within an electrochemical chamber without the requirement of any external fuels or force fields. The transduction of energy has been demonstrated with various strains of E. coli, indicating that this strategy could, in principle, be applicable for other microbial catalytic systems. We offer a simple mechanism of the energy transduction process considering the bacterial enzyme-mediated redox reaction occurring over the working electrode of the electrochemical cell. Also, the amount of energy generated has been found to be depending on the motility of bacteria within the experimental chamber, suggesting possible opportunities for developing microbial motility-controlled small scale power generators. Finally, we show that the Faradaic electrochemical energy harvested is large enough to power a commercial light emitting diode connected to an amplifier circuit. We expect the present study to generate sufficient interest within soft condensed matter and biophysics communities, and offer useful platforms for controlled energy generation at the small scales.

TriMem: A parallelized hybrid Monte Carlo software for efficient simulations of lipid membranes.

Lipid membranes are integral building blocks of living cells and perform a multitude of biological functions. Currently, molecular simulations of cellular-scale membrane remodeling processes at atomic resolution are extremely difficult, due to their size, complexity, and the large times-scales on which these processes occur. Instead, elastic membrane models are used to simulate membrane shapes and transitions between them and to infer their properties and functions. Unfortunately, an efficiently parallelized open-source simulation code to do so has been lacking. Here, we present TriMem, a parallel hybrid Monte Carlo simulation engine for triangulated lipid membranes. The kernels are efficiently coded in C++ and wrapped with Python for ease-of-use. The parallel implementation of the energy and gradient calculations and of Monte Carlo flip moves of edges in the triangulated membrane enable us to simulate large and highly curved membrane structures. For validation, we reproduce phase diagrams of vesicles with varying surface-to-volume ratios and area difference. We also compute the density of states to verify correct Boltzmann sampling. The software can be used to tackle a range of large-scale membrane remodeling processes as a step toward cell-scale simulations. Additionally, extensive documentation make the software accessible to the broad biophysics and computational cell biology communities.

Protein dynamics developments for the large scale and cryoEM: case study of ProDy 2.0.

Cryo-electron microscopy (cryoEM) has become a well established technique with the potential to produce structures of large and dynamic supramolecular complexes that are not amenable to traditional approaches for studying structure and dynamics. The size and low resolution of such molecular systems often make structural modelling and molecular dynamics simulations challenging and computationally expensive. This, together with the growing wealth ofstructural data arising from cryoEM and other structural biology methods, hasdriven a trend in the computational biophysics community towards the development of new pipelines for analysing global dynamics using coarse-grained models and methods. At the centre of this trend has been a return to elastic network models, normal mode analysis (NMA) and ensemble analyses such as principal component analysis, and the growth of hybrid simulation methodologies that make use of them. Here, this field is reviewed with a focus on ProDy, the Python application programming interface for protein dynamics, which has been developed over the last decade. Two key developments in this area are highlighted: (i) ensemble NMA towards extracting and comparing the signature dynamics of homologous structures, aided by the recent SignDy pipeline, and (ii) pseudoatom fitting for more efficient global dynamics analyses of large and low-resolution supramolecular assemblies from cryoEM, revisited in the CryoDy pipeline. It is believed that such a renewal and extension of old models and methods in new pipelines will be critical for driving the field forward into the next cryoEM revolution.

Perspectives on How 1.5 Years of the COVID-19 Pandemic Have Impacted Biophysicists at Primarily Undergraduate Institutions

Perspectives on How 1.5 Years of the COVID-19 Pandemic Have Impacted Biophysicists at Primarily Undergraduate Institutions

The PCDDB (Protein Circular Dichroism Data Bank): A Bioinformatics Resource for Protein Characterisations and Methods Development

The Protein Circular Dichroism Data Bank (PCDDB) [https://pcddb.cryst.bbk.ac.uk] is an established resource for the biological, biophysical, chemical, bioinformatics, and molecular biology communities. It is a freely-accessible repository of validated protein circular dichroism (CD) spectra and associated sample and metadata, with entries having links to other bioinformatics resources including, amongst others, structure (PDB), AlphaFold, and sequence (UniProt) databases, as well as to published papers which produced the data and cite the database entries. It includes primary (unprocessed) and final (processed) spectral data, which are available in both text and pictorial formats, as well as detailed sample and validation information produced for each of the entries. Recently the metadata content associated with each of the entries, as well as the number and structural breadth of the protein components included, have been expanded. The PCDDB includes data on both wild-type and mutant proteins, and because CD studies primarily examine proteins in solution, it also contains examples of the effects of different environments on their structures, plus thermal unfolding/folding series. Methods for both sequence and spectral comparisons are included.The data included in the PCDDB complement results from crystal, cryo-electron microscopy, NMR spectroscopy, bioinformatics characterisations and classifications, and other structural information available for the proteins via links to other databases. The entries in the PCDDB have been used for the development of new analytical methodologies, for interpreting spectral and other biophysical data, and for providing insight into structures and functions of individual soluble and membrane proteins and protein complexes.

Ina

Forest Management Unit (FMU)’s one of the site-level agencies that has information on forest biophysical condition and community socio-culture, so it has a significant role on Social Forestry (SF)’s success. The willingness and role of the FMU in the implementation of the SF program as an organization at the site level needs to be studied, especially from the perspective of the stakeholders involved in the SF. This study examines the role of FMUs to implement Social Forestry (SF) programs through the perspective of the parties involved in SF. This role is measured through the attitudes, orientation and actions shift of FMUs towards SF. The research hypothesis is that FMU’s roles through attitudes, orientations and actions influence the outcomes of social forestry. The study uses a quantitative approach involving 60 respondents with purpossive sampling, data processing and analysis using a scoring method to see the attitudes, orientations and actions shift and success of SF, and Pearson correlation analysis to confirmed the influence of FMU’s roles through attitudes, orientations and actions on SF’s success. The results of the study revealed that the attitudes of Production FMU Kerinci and Protection FMU Sijunjung support SF, while the FMUs' actions are based on site specific priorities. Under these conditions the shifting of FMUs attitudes and actions can explain the success of the SF in social and economy field.

Colloid-like solution behavior of computationally designed coiled coil bundlemers

The use of isotropic potential models of simple colloids for describing complex protein–protein interactions is a topic of ongoing debate in the biophysical community. This contention stems from the unavailability of synthetic protein-like model particles that are amenable to systematic experimental characterization. In this article, we test the utility of colloidal theory to capture the solution structure, interactions and dynamics of novel globular protein-mimicking, computationally designed peptide assemblies called bundlemers that are programmable model systems at the intersection of colloids and proteins. Small-angle neutron scattering (SANS) measurements of semi-dilute bundlemer solutions in low and high ionic strength solution indicate that bundlemers interact locally via repulsive interactions that can be described by a screened repulsive potential. We also present neutron spin echo (NSE) spectroscopy results that show high-Q freely-diffusive dynamics of bundlemers. Importantly, formation of clusters due to short-range attractive, inter-bundlemer interactions is observed in SANS even at dilute bundlemer concentrations, which is indicative of the complexity of the bundlemer charged surface. The similarities and differences between bundlemers and simple colloidal as well as complex protein–protein interactions is discussed in detail.

Suitability and development strategy for Turtle Ecotourism in Kapoposang Islands Marine Tourism Park, South Sulawesi, Indonesia

Turtles are a tourist attraction that can be developed using an ecotourism approach. This approach is expected to provide economic benefits without neglecting the conservation aspects of protected marine life, including turtles in the Kapoposang Islands Marine Tourism Park (TWP), Pangkep Regency, South Sulawesi, Indonesia. This study aimed to assess the suitability of turtle ecotourism and determine a strategy for developing turtle ecotourism in Kapoposang Island. This research was conducted in February and March 2020. The data collected during this study were divided into 3 groups of data with the aspects studied including; biophysics (beach slope, coastal vegetation, beach width, light intensity, distance from settlement and tides), biological (secondary data), and social community. The analysis performed were a tourism suitability index analysis, SWOT analysis, and descriptive analysis. The results indicate that the suitability of four stations in the Kapoposang Island for turtle nesting tourism ranges from “appropriate” to “unsuitable” categories. The suitability analysis results for station I (57.58%), station II (57.58%), and station IV (63.64%) were in the appropriate category while Station III (46.97%) was in the unsuitable category. The incubation process of newly hatched eggs and hatchlings carried out by the “Bahari Lestari” community group was no longer operating. The recommended development strategy directions based on the SWOT analysis are: (1) capacity building training and assistance to organize community groups in an integrated manner, (2) repairs, maintenance, and additional supporting facilities for tourism with a scenario to guide organized turtle tourism activities, (3) conduct study tours to areas that are considered successful in optimizing the potential of ecotourism.