Protein Conformational Changes Research Articles

Differing temperature dependencies of functional homologs zebrafish Abcb4 and human ABCB1

The ATP binding cassette (ABC) transporters human ABCB1 and zebrafish (Danio rerio) Abcb4 are functionally homologous multixenobiotic/multidrug (MXR/MDR) efflux transporters that confer the efflux of a broad range of diverse chemical compounds from the cell. As ATPases, the transporters utilize the energy released by ATP cleavage for protein conformation changes and concomitant active transport of substrate compounds. The temperatures, at which human ABCB1 and zebrafish Abcb4 need to function, can substantially differ: Whereas the ambient temperature of human ABCB1, which is that of the human body, is constant, zebrafish Abcb4 has to be active in a wider temperature range as the body temperature of zebrafish can considerably vary, depending on the ambient water temperature (18°C–40°C). Here, we examined the effect of temperature on the ATPase activities of recombinant human ABCB1 and zebrafish Abcb4 generated with the baculovirus expression system. Incubation temperatures for enzyme reactions were set to 37°C and 27°C, corresponding to the human body temperature and the cultivation temperature of zebrafish in our lab, respectively. For stimulation and inhibition of zebrafish Abcb4 and human ABCB1 ATPase activities verapamil and cyclosporin A were added at different concentrations and 50% effect concentrations (EC50) were determined. The different temperatures had a stronger effect on the human ABCB1 than on the zebrafish Abcb4 ATPase: Differences between EC50 values for verapamil at 37°C and 27°C, respectively, were 1.8-fold for human ABCB1 but only 1.2-fold for zebrafish Abcb4. Activation energies (Ea) of basal and verapamil-stimulated ATPases, calculated based on the Arrhenius equation, were 2-fold (basal) and 1.5-fold (verapamil-stimulated) higher for human ABCB1 than for zebrafish Abcb4. The differences between zebrafish Abcb4 and human ABCB1 ATPases in temperature sensitivity and activation energy could be important for the comparison of the functional properties of the two transporter proteins in the context of pharmaco-/toxicokinetics. Related to this, our finding that at equal reaction conditions the zebrafish Abcb4 ATPase activity tended to be generally higher than that of human ABCB1 may also be important, as this may point to a higher substrate compound transport rate of Abcb4.

A Computational Study of Green Tea Extracts and their Derivatives as Potential Inhibitors for Squalene Monooxygenase.

According to the World Health Organisation, cardiovascular complications have been recognized as the leading course of death between 2000 and 2019. Cardiovascular complications are caused by excess LDL cholesterol in the body or arteries that can build up to form a plaque. There are drugs currently in clinical use called statins that target HMGCoA reductase. However, these drugs result in several side effects. This work investigated using computational approaches to lower cholesterol by investigating green tea extracts as an inhibitors for squalene monooxygenase (the second-rate-controlling step in cholesterol synthesis). Pharmacophore modeling was done to identify possible pharmacophoric sites based on the pIC50 values. The best hypothesis generated by pharmacophore modeling was further validated by atom-based 3D QSAR, where 70% of the data set was treated as the training set. Prior molecular docking ADMET studies were done to investigate the physiochemical properties of these molecules. Glide docking was performed, followed by molecular dynamics to evaluate the protein conformational changes. Pharmacophore results suggest that the best molecules to interact with the biological target should have at least one hydrogen acceptor (A5), two hydrogen donors (D9 and D10), and two benzene rings (R14 and R15) for green tea polyphenols and theasinensin A. ADMET result shows that all molecules in this class have low oral adsorption. Molecular docking results showed that some green tea polyphenols have good binding affinities, with most of these structures having a docking score of less than -10 kcal/mol. Molecular dynamics further illustrated that the best-docked ligands perfectly stay within the active site over a 100 ns simulation. The results obtained from this study suggest that green tea polyphenols have the potential for inhibition of squalene monooxygenase, except for theasinensin A.

Conformation-Dependent Hydrogen-Bonding Interactions in a Switchable Artificial Metalloprotein.

Hydrogen-bonding (H-bonding) interactions in metalloprotein active sites can critically regulate enzyme function. Changes in the protein structure triggered by interplay with substrates, products, and partner proteins are often translated to the metallocofactor by way of specific changes in H-bond networks connected to the active site. However, the complexities of metalloprotein architecture and mechanism often preclude our ability to define the precise molecular interactions giving rise to these intricate regulatory pathways. To address this shortcoming, we have developed conformationally switchable artificial metalloproteins (swArMs) in which allosteric Gln-binding triggers protein conformational changes that impact the microenvironment surrounding an installed metallocofactor. Herein, we report a combined structural, spectroscopic, and computational approach to enhance the conformation-dependent changes in H-bond interactions surrounding the metallocofactor site of a swArM. Structure-informed molecular dynamics simulations were employed to predict point mutations that could enhance active site H-bond interactions preferentially in the Gln-bound holo-conformation of the swArM. Testing our predictions via the unique infrared spectral signals associated with the metallocofactor site, we have identified three key residues capable of imparting conformational control over the metallocofactor microenvironment. The resultant swArMs not only model biologically relevant structural regulation but also provide an enhanced Gln-responsive biological probe to be leveraged in future biosensing applications.

Visualizing Single-Molecule Protein Conformational Transitions and Free Energy Landscape.

Monitoring the conformational dynamics of individual proteins is essential to understand the relationship between structure and function in molecular regulatory mechanisms. However, the fast dynamics of single proteins remain poorly understood. Here, we construct a single-molecule sensing platform by introducing plasmonic imaging of single nanoparticles to sense and report the protein conformational changes at the single-molecule level. Tracking the fluctuations of individual nanoparticles with high resolution, we detect and characterize distinct conformational states of molecular chaperone heat shock protein 90 (Hsp90). We also explore the conformational changes of Hsp90 in situ under different nucleotide conditions. Analysis of the conformational fluctuations between the open and closed states of single Hsp90 provides important information on free energy profiles, effective spring constants, and multiphase behaviors. This method offers a strategy to visualize the conformational changes of single proteins in real-time and provides insights into the underlying molecular mechanisms.

Kinetics and mechanisms of thermal deterioration in silver carp (Hypophthalmichtys molitrix) surimi gel quality under high-temperature sterilization.

The gelation properties of surimi gel under various high temperatures (115, 118, and 121 °C) and sterilization intensities (F0 values of 3-7 min) were systematically investigated. A kinetic model detailed quality changes during heat treatment through mathematical analysis, elucidating mechanisms for gel quality degradation. Increased sterilization intensity significantly reduced the quality characteristics of surimi gel. Compared to the gel without sterilization treatment, when the sterilization intensity was increased to 7 min, the gel strength of the groups treated at 115 °C, 118 °C, and 121 °C decreased by 68.35%, 51.4%, and 51.71%, respectively, and the water-holding capacity decreased by 24.87%, 16.85%, and 22.5%, respectively. The hardness, chewiness, and whiteness of the gel also significantly decreased, and the changes in these indicators all conformed to a first-order kinetic model. Activation energy of 291.52 kJ mol-1 highlighted gel strength as the least heat-resistant. At equivalent sterilization intensities, 115 °C exhibited the poorest gel quality, followed by 121 °C, with 118 °C showing relatively better gel quality. Increased T22 and decreased PT22 suggested heightened water mobility and transition of immobilized water within the gel into free water. Protein degradation, weakened disulfide bonds and hydrophobic interaction, and protein conformation changes collectively led to a rough and incoherent gel network structure with large fissures, as verified by the results of scanning electron microscopy. Correlation analysis indicated potential for precise control over surimi gel quality by modulating physicochemical attributes. The outcomes may be beneficial to improve the production and quality control of ready-to-eat surimi-based products. © 2024 Society of Chemical Industry.

Insights into CLC-0's Slow-Gating from Intracellular Proton Inhibition.

The opening of the Torpedo CLC-0 chloride (Cl-) channel is known to be regulated by two gating mechanisms: fast gating and slow (common) gating. The structural basis underlying the fast-gating mechanism is better understood than that of the slow-gating mechanism, which is still largely a mystery. Our previous study on the intracellular proton (H+i)-induced inhibition of the CLC-0 anionic current led to the conclusion that the inhibition results from the slow-gate closure (also called inactivation). The conclusion was made based on substantial evidence such as a large temperature dependence of the H+i inhibition similar to that of the channel inactivation, a resistance to the H+i inhibition in the inactivation-suppressed C212S mutant, and a similar voltage dependence between the current recovery from the H+i inhibition and the recovery from the channel inactivation. In this work, we further examine the mechanism of the H+i inhibition of wild-type CLC-0 and several mutants. We observe that an anion efflux through the pore of CLC-0 accelerates the recovery from the H+i-induced inhibition, a process corresponding to the slow-gate opening. Furthermore, various inactivation-suppressed mutants exhibit different current recovery kinetics, suggesting the existence of multiple inactivated states (namely, slow-gate closed states). We speculate that protonation of the pore of CLC-0 increases the binding affinity of permeant anions in the pore, thereby generating a pore blockage of ion flow as the first step of inactivation. Subsequent complex protein conformational changes further transition the CLC-0 channel to deeper inactivated states.

Revealing the deterioration mechanism in gelling properties of pork myofibrillar protein gel induced by high-temperature treatments: Perspective on the protein aggregation and conformation

The purpose of the present study was to investigate the mechanism of gel deterioration of myofibrillar proteins (MP) gels induced by high-temperature treatments based on the protein aggregation and conformation. The results showed that the gel strength and water holding capacity of MP obviously increased and then decreased as the temperature increased, reaching the maximum value at 80 °C (P < 0.05). The microstructure analysis revealed that appropriate temperature (80 °C) contributed to the formation of a more homogeneous, denser, and smoother three-dimensional mesh structure when compared other treatment temperatures, whereas excessive temperature (95 °C) resulted in the formation of heterogeneous and large protein aggregates of MP, decreasing the continuity of gel networks. This was verified by the rheological properties of MP gels. The particle size (D4,3 and D3,2) of MP obviously increased with larger clusters at excessive temperature, and the surface hydrophobicity of MP decreased (P < 0.05), which has been linked to the formation of soluble or insoluble protein aggregates. Tertiary structure and secondary structure results revealed that the proteins had a tendency to be more stretched under higher temperature treatments, which resulted in a decrease in covalent interactions and non-covalent interactions, fostering the over-aggregation of MP. Therefore, our present study indicated that the degradation of MP gels treated at high temperatures was explained by protein aggregation and conformational changes in MP.

Insight into the Stabilization Mechanism of Succinylation Modification on Black Bean Protein Gels: Molecular Conformation, Microstructure, and Gel Properties.

The objective of this work was to investigate the effect of succinylation treatment on the physicochemical properties of black bean proteins (BBPI), and the relationship mechanism between BBPI structure and gel properties was further analyzed. The results demonstrated that the covalent formation of higher-molecular-weight complexes with BBPI could be achieved by succinic anhydride (SA). With the addition of SA at 10% (v/v), the acylation of proteins amounted to 92.53 ± 1.10%, at which point there was a minimized particle size of the system (300.90 ± 9.57 nm). Meanwhile, the protein structure was stretched with an irregular curl content of 34.30% and the greatest processable flexibility (0.381 ± 0.004). The dense three-dimensional mesh structure of the hydrogel as revealed by scanning electron microscopy was the fundamental prerequisite for the ability to resist external extrusion. The thermally induced hydrogels of acylated proteins with 10% (v/v) addition of SA showed excellent gel elastic behavior (1.44 ± 0.002 nm) and support capacity. Correlation analysis showed that the hydrogel strength and stability of hydrogels were closely related to the changes in protein conformation. This study provides theoretical guidance for the discovery of flexible proteins and their application in hydrogels.

IMAX FRET (Information Maximized FRET) for Multipoint Single-Molecule Structural Analysis.

Understanding the structure of biomolecules is vital for deciphering their roles in biological systems. Single-molecule techniques have emerged as alternatives to conventional ensemble structure analysis methods for uncovering new biology in molecular dynamics and interaction studies, yet only limited structural information could be obtained experimentally. Here, we address this challenge by introducing iMAX FRET, a one-pot method that allows ab initio 3D profiling of individual molecules using two-color FRET measurements. Through the stochastic exchange of fluorescent weak binders, iMAX FRET simultaneously assesses multiple distances on a biomolecule within a few minutes, which can then be used to reconstruct the coordinates of up to four points in each molecule, allowing structure-based inference. We demonstrate the 3D reconstruction of DNA nanostructures, protein quaternary structures, and conformational changes in proteins. With iMAX FRET, we provide a powerful approach to advance the understanding of biomolecular structure by expanding conventional FRET analysis to three dimensions.

Understanding Microscopic Interactions in Binding Reactions: The pH Titration of EDTA

ABSTRACT Students beginning the study of biochemistry or biophysics at the undergraduate or even early graduate level are often overwhelmed by the complexity of the systems and the nomenclature. By comparison, chemical systems appear simple, as students can more easily relate to introductory chemistry courses, where the molecules are smaller and bind yet smaller ions. This allows students to write the structure of the entire molecule on a piece of paper and see exactly to which functional groups an ion, such as a proton (H+) in the simplest case, binds. Yet, concepts that are fundamental in biochemical macromolecules, namely proteins, can perfectly well be taught at the undergraduate or beginning graduate level, and probably be more easily understood, by using simpler, familiar chemical examples. The concept of interacting binding sites, which is at the root of cooperativity in protein binding reactions and conformational changes, is already present in simple molecules, such as ethylenediaminetetraacetic acid (EDTA). In this article, we show how to teach these topics by using the idea of the partition function, rather than a formal algebraic approach, to treat the binding of protons to EDTA. Profound concepts, such as that of interacting sites, appear naturally in a small molecule, where the origin can be easily ascribed, in this case, mainly to electrostatic interactions. Equipped with this understanding and this approach, students will be able to tackle more complicated biochemical systems, in which the molecules are larger, but the concepts are the same.

Appraising protein conformational changes by resampling time-resolved serial x-ray crystallography data.

With the development of serial crystallography at both x-ray free electron laser and synchrotron radiation sources, time-resolved x-ray crystallography is increasingly being applied to study conformational changes in macromolecules. A successful time-resolved serial crystallography study requires the growth of microcrystals, a mechanism for synchronized and homogeneous excitation of the reaction of interest within microcrystals, and tools for structural interpretation. Here, we utilize time-resolved serial femtosecond crystallography data collected from microcrystals of bacteriorhodopsin to compare results from partial occupancy structural refinement and refinement against extrapolated data. We illustrate the domain wherein the amplitude of refined conformational changes is inversely proportional to the activated state occupancy. We illustrate how resampling strategies allow coordinate uncertainty to be estimated and demonstrate that these two approaches to structural refinement agree within coordinate errors. We illustrate how singular value decomposition of a set of difference Fourier electron density maps calculated from resampled data can minimize phase bias in these maps, and we quantify residual densities for transient water molecules by analyzing difference Fourier and Polder omit maps from resampled data. We suggest that these tools may assist others in judging the confidence with which observed electron density differences may be interpreted as functionally important conformational changes.

Aprotinin (II): Inhalational Administration for the Treatment of COVID-19 and Other Viral Conditions.

Aprotinin is a broad-spectrum inhibitor of human proteases that has been approved for the treatment of bleeding in single coronary artery bypass surgery because of its potent antifibrinolytic actions. Following the outbreak of the COVID-19 pandemic, there was an urgent need to find new antiviral drugs. Aprotinin is a good candidate for therapeutic repositioning as a broad-spectrum antiviral drug and for treating the symptomatic processes that characterise viral respiratory diseases, including COVID-19. This is due to its strong pharmacological ability to inhibit a plethora of host proteases used by respiratory viruses in their infective mechanisms. The proteases allow the cleavage and conformational change of proteins that make up their viral capsid, and thus enable them to anchor themselves by recognition of their target in the epithelial cell. In addition, the activation of these proteases initiates the inflammatory process that triggers the infection. The attraction of the drug is not only its pharmacodynamic characteristics but also the possibility of administration by the inhalation route, avoiding unwanted systemic effects. This, together with the low cost of treatment (≈2 Euro/dose), makes it a good candidate to reach countries with lower economic means. In this article, we will discuss the pharmacodynamic, pharmacokinetic, and toxicological characteristics of aprotinin administered by the inhalation route; analyse the main advances in our knowledge of this medication; and the future directions that should be taken in research in order to reposition this medication in therapeutics.

Differential Scanning Calorimetry: A Powerful and Versatile Tool for Analyzing Proteins and Peptides

Differential Scanning Calorimetry (DSC) is an efficient and versatile analytical technique widely used to study the thermal properties and stability of proteins. This review article provides a comprehensive overview of the principles and applications of DSC in protein research. DSC measures the heat flow associated with temperature-induced conformational changes in proteins, allowing for the direct determination of key thermodynamic parameters such as melting temperature (Tm), enthalpy change (ΔH), and heat capacity change (ΔCp). These parameters provide valuable insights into protein and peptide stability, folding mechanisms, and interactions with ligands. The review discusses the methodological aspects of DSC, including sample preparation, experimental setup, and data analysis techniques. It also highlights the application of DSC in various aspects, such as drug discovery, biopharmaceutical development, and the study of protein-ligand interactions. By elucidating the thermal behavior of proteins, DSC contributes significantly to our understanding of protein and peptide structure, function, and stability, making it an indispensable tool in biochemical and biophysical research.

Molecular dynamics simulations of betaine-based deep eutectic solvents with varying iso-alcohols chain lengths

Betaine-based (BET) deep eutectic solvents (DESs) made with isoalcohols of varying hydrocarbon chain lengths, namely triethylene glycol (TEG), 1, 2-ethanediol (ETD), 1, 3-propanediol (PPD) and 1, 4-butanediol (BTD) were modelled. Their effects on the formation of aqueous biphasic system (ABS) with 2 M dipotassium phosphate salt solution (K2HPO4) as well as the extraction of common protein molecules, bovine serum albumin (BSA), were studied using molecular dynamics simulation with Gromacs. Qualitative and quantitative data were used to analyse the simulation results, which includes visualised systems in equilibrium, root mean square deviation (RMSD), root mean square fluctuation (RMSF), radius of gyration, radial distribution function (RDF) and hydrogen bond analysis. The results and literature research validated the role of inorganic salt solute concentration on the phase forming ability as well as the possibility of protein denaturation. More investigations and experimental works are to be carried out regarding the type of inorganic salt and its concentration for aqueous biphasic systems (ABSs) with alcohol based DESs and salt solution for protein extraction purposes. This is essential to understand the salting-out effect and to isolate the effects of hydrocarbon chain length from other influencing factors. Additionally, inorganic salt concentrations, presence of ether linkage as well as hydrocarbon chain length is shown to play a role in the dynamics between molecules in the system as well as protein conformational changes. Overall, ABS incorporating PPD and BTD with hydrocarbon chain lengths not exceeding C4 demonstrated superior performance in terms of protein conformational stability and interaction, showcasing their efficacy in protein extraction process.

Colorimetric Immunoassays with Boronic Acid-Decorated, Peroxidase-like Metal-Organic Frameworks as the Carriers of Antibodies and Enzymes.

The sensitivity of immunoassays is generally limited by the low signal reporter/recognition element ratio. Nanomaterials serving as the carriers can enhance the loading number of signal reporters, thus improving the detection sensitivity. However, the general immobilization strategies, including direct physical adsorption and covalent coupling, may cause the random orientation and conformational change in proteins, partially or completely suppressing the enzymatic activity and the molecular recognition ability. In this work, we proposed a strategy to load recognition elements of antibodies and enzyme labels using boronic acid-modified metal-organic frameworks (MOFs) as the nanocarriers for signal amplification. The conjugation strategy was proposed based on the boronate ester interactions between the carbohydrate moieties in antibodies and enzymes and the boronic acid moieties on MOFs. Both enzymes and MOFs could catalyze the oxidation of 3,3',5,5'-tetramethylbenzidine (TMB) by H2O2, therefore achieving dual signal amplification. To indicate the feasibility and sensitivity of the strategy, colorimetric immunoassays of prostate specific antigen (PSA) were performed with boronic acid-modified Cu-MOFs as peroxidase mimics to catalyze TMB oxidation and nanocarriers to load antibody and enzyme (horseradish peroxidase, HRP). According to the change in the absorbance intensity of the oxidized TMB (oxTMB), PSA at the concentration range of 1~250 pg/mL could be readily determined. In addition, this work presented a site-specific and oriented conjugation strategy for the modification of nanolabels with recognition elements and signal reporters, which should be valuable for the design of novel biosensors with high sensitivity and selectivity.

Application of soy protein isolate-naringenin complexes as fat replacers in low-fat cream: Based on protein conformational changes, aggregation states and interfacial adsorption behavior

In this study, changes in the structural and functional properties of soybean protein isolate (SPI)-naringenin (NG) complexes under different amounts of naringenin treatments were explored, elucidating the effect of the complexes as fat replacers at the 15 % substitution level on the properties of low-fat cream. Finally, the correlation between the structure and function of the complex and the properties of low-fat cream was further analyzed. The addition of NG promotes the increase of SPI aggregation and particle size, and reduces the interfacial tension of the complex. Meanwhile, at the mass ratio of 48:3, NG and SPI formed a dendritic network structure suitable for stabilizing cream. The fat properties of cream indicate that low-fat creams stabilized by appropriate proportions of SPI-NG complexes displayed small and dense fat crystal network structures. In addition, low-fat cream stabilized by the SPI-NG complexes have improved whipping time, overrun, firmness, storage stability and rheological properties compared to natural SPI. It is worth noting that the overall quality of the cream stabilized by the SPI-NG complex with a mass ratio of 48:3 was almost close to that of full-fat cream. Therefore, this study promotes the potential applications of protein-polyphenol complexes as fat replacers in the food industry.

In silico analysis of fungal prion-like proteins for elucidating their role in plant-fungi interactions.

Prion-like proteins (PrLPs) have emerged as beneficial molecules with implications in adaptive responses. These proteins possess a conserved prion-like domain (PrLD) which is an intrinsically disordered region capable of adopting different conformations upon perceiving external stimuli. Owing to changes in protein conformation, functional characteristics of proteins harboring PrLDs get altered thereby, providing a unique mode of protein-based regulation. Since PrLPs are ubiquitous in nature and involved in diverse functions, through this study, we aim to explore the role of such domains in yet another important physiological process viz. plant-microbe interactions to get insights into the mechanisms dictating cross-kingdom interactions. We have evaluated the presence and functions of PrLPs in 18 different plant-associated fungi of agricultural importance to unravel their role in plant-microbe interactions. Of the 241,997 proteins scanned, 3,820 (~ 1.6%) were identified as putative PrLPs with pathogenic fungi showing significantly higher PrLP density than their beneficial counterparts. Further, through GO enrichment analysis, we could predict several PrLPs from pathogenic fungi to be involved in virulence and formation of stress granules. Notably, PrLPs involved in (retro)transposition were observed exclusively in pathogenic fungi. We even analyzed publicly available data for the expression alterations of fungal PrLPs upon their interaction with their respective hosts which revealed perturbation in the levels of some PrLP-encoding genes during interactions with plants. Overall, our work sheds light into the probable role of prion-like candidates in plant-fungi interaction, particularly in context of pathogenesis, paving way for more focused studies for validating their role.

Combining quantitative proteomics and interactomics for a deeper insight into molecular differences between human cell lines.

Cellular functional pathways have evolved through selection based on fitness benefits conferred through protein intra- and inter-molecular interactions that comprise all protein conformational features and protein-protein interactions, collectively referred to as the interactome. While the interactome is regulated by proteome levels, it is also regulated independently by, post translational modification, co-factor, and ligand levels, as well as local protein environmental factors, such as osmolyte concentration, pH, ionic strength, temperature and others. In modern biomedical research, cultivatable cell lines have become an indispensable tool, with selection of optimal cell lines that exhibit specific functional profiles being critical for success in many cases. While it is clear that cell lines derived from different cell types have differential proteome levels, increased understanding of large-scale functional differences requires additional information beyond abundance level measurements, including how protein conformations and interactions are altered in certain cell types to shape functional landscapes. Here, we employed quantitative in vivo protein cross-linking coupled to mass spectrometry to probe large-scale protein conformational and interaction changes among three commonly employed human cell lines, HEK293, MCF-7, and HeLa cells. Isobaric quantitative Protein Interaction Reporter (iqPIR) technologies were used to obtain quantitative values of cross-linked peptides across three cell lines. These data illustrated highly reproducible (R2 values larger than 0.8 for all biological replicates) quantitative interactome levels across multiple biological replicates. We also measured protein abundance levels in these cells using data independent acquisition quantitative proteomics methods. Combining quantitative interactome and proteomics information allowed visualization of cell type-specific interactome changes mediated by proteome level adaptations as well as independently regulated interactome changes to gain deeper insight into possible drivers of these changes. Among the biggest detected alterations in protein interactions and conformations are changes in cytoskeletal proteins, RNA-binding proteins, chromatin remodeling complexes, mitochondrial proteins, and others. Overall, these data demonstrate the utility and reproducibility of quantitative cross-linking to study systems-level interactome variations. Moreover, these results illustrate how combined quantitative interactomics and proteomics can provide unique insight on cellular functional landscapes.

Information Bottleneck Approach for Markov Model Construction.

Markov state models (MSMs) have proven valuable in studying the dynamics of protein conformational changes via statistical analysis of molecular dynamics simulations. In MSMs, the complex configuration space is coarse-grained into conformational states, with dynamics modeled by a series of Markovian transitions among these states at discrete lag times. Constructing the Markovian model at a specific lag time necessitates defining states that circumvent significant internal energy barriers, enabling internal dynamics relaxation within the lag time. This process effectively coarse-grains time and space, integrating out rapid motions within metastable states. Thus, MSMs possess a multiresolution nature, where the granularity of states can be adjusted according to the time-resolution, offering flexibility in capturing system dynamics. This work introduces a continuous embedding approach for molecular conformations using the state predictive information bottleneck (SPIB), a framework that unifies dimensionality reduction and state space partitioning via a continuous, machine learned basis set. Without explicit optimization of the VAMP-based scores, SPIB demonstrates state-of-the-art performance in identifying slow dynamical processes and constructing predictive multiresolution Markovian models. Through applications to well-validated mini-proteins, SPIB showcases unique advantages compared to competing methods. It autonomously and self-consistently adjusts the number of metastable states based on a specified minimal time resolution, eliminating the need for manual tuning. While maintaining efficacy in dynamical properties, SPIB excels in accurately distinguishing metastable states and capturing numerous well-populated macrostates. This contrasts with existing VAMP-based methods, which often emphasize slow dynamics at the expense of incorporating numerous sparsely populated states. Furthermore, SPIB's ability to learn a low-dimensional continuous embedding of the underlying MSMs enhances the interpretation of dynamic pathways. With these benefits, we propose SPIB as an easy-to-implement methodology for end-to-end MSM construction.

A DNA-based molecular clamp for probing protein interactions and structure under force.

Cellular mechanotransduction, a process central to cell biology, embryogenesis, adult physiology and multiple diseases, is thought to be mediated by force-driven changes in protein conformation that control protein function. However, methods to study proteins under defined mechanical loads on a biochemical scale are lacking. We report the development of a DNA based device in which the transition between single-stranded and double-stranded DNA applies tension to an attached protein. Using a fragment of the talin rod domain as a test case, negative-stain electron microscopy reveals programmable extension while pull down assays show tension-induced binding to two ligands, ARPC5L and vinculin, known to bind to cryptic sites inside the talin structure. These results demonstrate the utility of the DNA clamp for biochemical studies and potential structural analysis.