Intrinsically disordered proteins (IDPs) underlie essential cellular functions and drive neurodegenerative diseases through mutation-induced structural changes, yet their conformational heterogeneity often evades crystallography and cryo-EM. Electron spin resonance (ESR) pulsed dipolar spectroscopy (PDS), which determines distance distributions between a pair of spin-labeled residues in a protein, can provide complementary and meaningful information related to conformational heterogeneity in IDPs. Double quantum coherence (DQC) is an important ESR PDS technique, capable of measuring a wide range of distances (∼10 to at least 80 Å), and is a single-frequency technique with a small background that can be easily removed. This makes DQC an ideal candidate to probe IDPs. We present a complete theoretical framework for DQC data analysis, incorporating pseudosecular dipolar coupling and finite pulse effects, enabling rapid and accurate reconstruction of complex distance distributions in doubly nitroxide-labeled IDPs. We validate the method on rigid biradicals with known interspin distances. The application to a tau protein fragment (jR2R3) reveals distinct end-to-end distance distributions for the wild-type vs the disease-associated P301L mutant. The results expose differences in their conformational distributions, which likely govern their divergent aggregation propensities. This advance also establishes DQC ESR as a powerful, accessible tool for probing disorders in biomolecular systems.

The HIV-1 Vpu membrane protein is crucial to the virus lifecycle. Our recent studies revealed soluble Vpu oligomers, prompting further investigation into their interactions with cellular proteins. Notably, Vpu may form a complex with calmodulin (CaM) due to its putative CaM-binding motif; however, experimental proof of this association is unavailable. Here, we present definitive experimental evidence that the soluble Vpu complex interacts in vitro with calcium-bound CaM (Ca2+-CaM), its active form. Using double electron-electron resonance (DEER) spectroscopy and protein spin labeling, we detected the formation of a soluble Vpu-Ca2+-CaM complex. Both the full-length (FL) and truncated C-terminal regions of Vpu bind Ca2+-CaM. DEER experiments on a spin-labeled CaM cysteine mutant S39C/A103C revealed that, upon association with Vpu, Ca2+-CaM undergoes a transition from an open to a more closed conformation, consistent with previous reports of Ca2+-CaM interactions with other proteins. Furthermore, we observed that the binding of Vpu to Ca2+-CaM leads to dissociation of soluble Vpu oligomers, as evidenced by a reduction in DEER modulation depth for FL Vpu spin-labeled at residue L42C. FRET analysis with a fluorescently labeled C-terminal cysteine mutant of Vpu confirmed this result. Like FL Vpu, the Vpu C-terminal region forms soluble homooligomers that dissociate upon binding to Ca2+-CaM. Collectively, our results suggest that soluble Vpu and Ca2+-CaM form an equimolar complex. DEER analysis of the Vpu C-terminal region spin-labeled at residues Q36C/I61C demonstrated that Vpu undergoes significant conformational changes to facilitate Ca2+-CaM binding. These findings could be relevant to Vpu-CaM interactions under physiological conditions.

Biological membranes define cellular and organelle boundaries, and perform vital functions, providing transport, recognition, signaling, and interaction with other cells. These membranes are majorly composed of lipid bilayers and membrane proteins. Membrane proteins perform most membrane functions. Based on their localization, they are classified as integral and peripheral proteins. In this overview, we provide basic information about membrane proteins structure, conformational dynamics, and functions, and outline the methodologies used to produce highly-pure functional membrane proteins for in vitro biophysical characterizations based on selected examples. To this end, expression of membrane proteins in a host, their extraction, purification and reconstitution in model lipid bilayers are described. Further, biophysical approaches play key role in elucidation of the structure and function of membrane proteins. Our focus here is on the technique of continuous wave electron paramagnetic/spin resonance (CW ESR) spectroscopy applied to spin-labeled membrane proteins. We describe the basic principles of membrane proteins labeling with nitroxide spin labels (paramagnetic tags) and how the CW ESR can be successfully used in elucidating the conformational dynamics of such proteins. We describe the basic principles of the CW ESR technique. The capability of this technique to characterize physiologically relevant conformational dynamics of proteins is demonstrated using two examples of CW ESR studies on spin-labeled human Tau and influenza A M2 proteins. The method is highly suitable to study physiological structure-function relationships of a broad range of proteins, and to explain the malfunctional states of proteins linked to diseases. This review is directed to the broader biophysical community with interest in molecular biophysics of biological membranes.

The HIV-1-encoded membrane protein Vpu plays key roles in virus lifecycle. Our lab recently revealed a soluble form of Vpu, and we strived to determine its possible physiological function. Here, we provide solid experimental proof that soluble Vpu interacts with Ca2+-bound calmodulin (Ca2+-CaM). A putative CaM-binding motif in Vpu was predicted, but there was no experimental evidence of the Vpu-CaM association. We applied double electron electron-resonance (DEER) and protein spin labeling to detect the soluble Vpu-CaM complex. We found that soluble full-length and truncated C-terminal region of Vpu directly interact with Ca2+-CaM. DEER results from the spin-labeled double cysteine mutant S39C/A103C of CaM showed that upon association with Vpu Ca2+-CaM adopts a more closed conformation compared to those in the absence of Vpu. This restructuring is in agreement with previously observed Ca2+-CaM association with cellular and other HIV-1 proteins. Our results indicate that soluble Vpu and CaM form an equimolar complex. DEER results from doubly spin-labeled at residues Q36C/I61C in Vpu C-terminal region suggest that Vpu's helices 2 and 3 move away from each other to facilitated CaM binding. These observations tell that under physiological conditions the soluble Vpu-CaM complex may provide Vpu with a trafficking pathway to membrane destination.

We compared the conformations of the transmembrane domain (TMD) of influenza A M2 (IAM2) protein reconstituted at pH 7.4 in DOPC/DOPS bilayers to those in isolated E. coli membranes, having preserved its native proteins and lipids. IAM2 is a single-pass transmembrane protein known to assemble into homo-tetrameric proton channel. To represent this channel, we made a construct containing the IAM2's TMD region flanked by the juxtamembrane residues. The single cysteine substitute, L43C, of leucine located in the bilayer polar region was paramagnetically tagged with a methanethiosulfonate nitroxide label for the ESR (electron spin resonance) study. We compared the conformations of the spin-labeled IAM2 residing in DOPC/DOPS and native E. coli membranes using continuous-wave (CW) ESR and double electron-electron resonance (DEER) spectroscopy. The total protein-to-lipid molar ratio spanned the range from 1:230 to 1:10,400⩦ The CW ESR spectra corresponded to a nearly rigid limit spin label dynamics in both environments. In all cases, the DEER data were reconstructed into the distance distributions showing well-resolved peaks at 1.68 nm and 2.37 nm. The peak distance ratio was 1.41±0.2 and the amplitude ratio was 2:1. This is what one expects from four nitroxide spin-labels located at the corners of a square, indicative of an axially symmetric tetramer. Distance modeling of DEER data with molecular modeling software applied to the NMR molecular structures (PDB: 2L0J) confirmed the symmetry and closed state of the C-terminal exit pore of the IAM2 tetramer in agreement with the NMR model. Thus, we can conclude that IAM2 TMD has similar conformations in model and native E. coli membranes of comparable thickness and fluidity, notwithstanding the complexity of the E. coli membranes caused by their lipid diversity and the abundance of integral and peripheral membrane proteins.

In vitro studies on transmembrane proteins (TMPs) in lipid bilayers often use synthetic lipid mixtures with known properties. However, the complexity of native membranes caused by lipid diversity aided by the abundance of native membrane proteins, brings to the fore the relevance of protein conformation and dynamics observed in model bilayers to those occurring in native membranes. We compared the assembly and conformation of the transmembrane domain (TMD) of influenza A M2 (IAM2) reconstituted in DOPC/DOPS bilayers to that in isolated E.

We compared the conformations of the transmembrane domain (TMD) of influenza A M2 (IM2) protein reconstituted in 1,2-dioleoyl-sn-glycero-3-phosphocholine/1,2-dioleoyl-sn-glycero-3-phospho-L-serine (DOPC/DOPS) bilayers to those in isolated Escherichia coli (E. coli) membranes, having preserved its native proteins and lipids. IM2 is a single-pass transmembrane protein known to assemble into a homo-tetrameric proton channel. To represent this channel, we made a construct containing the IM2’s TMD region flanked by the juxtamembrane residues. The single cysteine substitution, L43C, of leucine located in the bilayer polar region was paramagnetically tagged with a methanethiosulfonate nitroxide label for the electron spin resonance (ESR) study. For this particular residue, we probed the conformations of the spin-labeled IM2 reconstituted in DOPC/DOPS and isolated E. coli membranes using continuous-wave ESR and double electron-electron resonance (DEER) spectroscopy. The total protein-to-lipid molar ratio spanned the range from 1:230 to 1:10,400. The continuous-wave ESR spectra corresponded to very slow spin-label motion in both environments. In all cases, the DEER data were reconstructed into distance distributions with well-resolved peaks at 1.68 and 2.37 nm in distance and amplitude ratios of 1.41 ± 0.2 and 2:1, respectively. This suggests four nitroxide spin labels located at the corners of a square, indicative of an axially symmetric tetramer. The distance modeling of DEER data with molecular modeling software applied to the NMR molecular structures (PDB: 2L0J) confirmed the symmetry and closed state of the C-terminal exit pore of the IM2 TMD tetramer in agreement with the model. Thus, we can conclude that, under conditions of pH 7.4 used in this study, IM2 TMD has similar conformations in model lipid bilayers and membranes made of native E. coli lipids and proteins of comparable thickness and fluidity, notwithstanding the complexity of the E. coli membranes caused by their lipid diversity and the abundance of integral and peripheral membrane proteins.

ABSTRACT RexA and RexB function as an exclusion system that prevents bacteriophage T4 rII mutants from growing on E. coli λ phage lysogens. Recent data established that RexA is a non-specific DNA binding protein that can act independently of RexB to bias the λ bistable switch toward the lytic state, preventing conversion back to lysogeny. The molecular interactions underlying these activities are unknown, owing in part to a dearth of structural information. Here we present the 2.05-Å crystal structure of the λ RexA dimer, which reveals a two-domain architecture with unexpected structural homology to the recombination-associated protein RdgC. Modelling suggests that our structure adopts a closed conformation and would require significant domain rearrangements to facilitate DNA binding. Mutagenesis coupled with electromobility shift assays, limited proteolysis, and double electron-electron spin resonance spectroscopy support a DNA-dependent conformational change. I n vivo phenotypes of RexA mutants suggest that DNA binding is not a strict requirement for phage exclusion but may directly contribute to modulation of the bistable switch. We further demonstrate that RexA homologs from other temperate phages also dimerize and bind DNA in vitro . Collectively, these findings advance our mechanistic understanding of Rex functions and provide new evolutionary insights into different aspects of phage biology.

We report our findings on the assembly of the HIV-1 protein Vpu into soluble oligomers. Vpu is a key HIV-1 protein. It has been considered exclusively a single-pass membrane protein. Previous observations show that this protein forms stable oligomers in aqueous solution, but details about these oligomers still remain obscure. This is an interesting and rather unique observation, as the number of proteins transitioning between soluble and membrane embedded states is limited. In this study we made use of protein engineering, size exclusion chromatography, cryoEM and electron paramagnetic resonance (EPR) spectroscopy to better elucidate the nature of the soluble oligomers. We found that Vpu oligomerizes via its N-terminal transmembrane domain (TM). CryoEM suggests that the oligomeric state most likely is a hexamer/heptamer equilibrium. Both cryoEM and EPR suggest that, within the oligomer, the distal C-terminal region of Vpu is highly flexible. Our observations are consistent with both the concept of specific interactions among TM helices or the core of the oligomers being stabilized by hydrophobic forces. While this study does not resolve all of the questions about Vpu oligomers or their functional role in HIV-1 it provides new fundamental information about the size and nature of the oligomeric interactions.

The HIV-1-encoded protein Vpu forms an oligomeric ion channel/pore in membranes and interacts with host proteins to support the virus lifecycle. However, Vpu molecular mechanisms are currently not well understood. Here, we report on the Vpu oligomeric organization under membrane and aqueous conditions and provide insights into how the Vpu environment affects the oligomer formation. For these studies, we designed a maltose-binding protein (MBP)-Vpu chimera protein and produced it in E. coli in soluble form. We analyzed this protein using analytical size-exclusion chromatography (SEC), negative staining electron microscopy (nsEM), and electron paramagnetic resonance (EPR) spectroscopy. Surprisingly, we found that MBP-Vpu formed stable oligomers in solution, seemingly driven by Vpu transmembrane domain self-association. A coarse modeling of nsEM data as well as SEC and EPR data suggests that these oligomers most likely are pentamers, similar to what was reported regarding membrane-bound Vpu. We also noticed reduced MBP-Vpu oligomer stability upon reconstitution of the protein in β-DDM detergent and mixtures of lyso-PC/PG or DHPC/DHPG. In these cases, we observed greater oligomer heterogeneity, with MBP-Vpu oligomeric order generally lower than in solution; however, larger oligomers were also present. Notably, we found that in lyso-PC/PG, above a certain protein concentration, MBP-Vpu assembles into extended structures, which had not been reported for Vpu. Therefore, we captured various Vpu oligomeric forms, which can shed light on Vpu quaternary organization. Our findings could be useful in understanding Vpu organization and function in cellular membranes and could provide information regarding the biophysical properties of single-pass transmembrane proteins.

Lipid droplets (LDs) are dynamic organelles that contain an oil core mainly composed of triglycerides (TAG) that is surrounded by a phospholipid monolayer and LD-associated proteins called perilipins (PLINs). During LD biogenesis, perilipin 3 (PLIN3) is recruited to nascent LDs as they emerge from the endoplasmic reticulum. Here, we analyze how lipid composition affects PLIN3 recruitment to membrane bilayers and LDs, and the structural changes that occur upon membrane binding. We find that the TAG precursors phosphatidic acid and diacylglycerol (DAG) recruit PLIN3 to membrane bilayers and define an expanded Perilipin-ADRP-Tip47 (PAT) domain that preferentially binds DAG-enriched membranes. Membrane binding induces a disorder to order transition of alpha helices within the PAT domain and 11-mer repeats, with intramolecular distance measurements consistent with the expanded PAT domain adopting a folded but dynamic structure upon membrane binding. In cells, PLIN3 is recruited to DAG-enriched ER membranes, and this requires both the PAT domain and 11-mer repeats. This provides molecular details of PLIN3 recruitment to nascent LDs and identifies a function of the PAT domain of PLIN3 in DAG binding.

The sensitivity of magnetic resonance force microscopy (MRFM) is limited by surface noise. Coating a thin-film polymer sample with metal has been shown to decrease, by orders of magnitude, sample-related force noise and frequency noise in MRFM experiments. Using both MRFM and inductively detected measurements of electron-spin resonance, we show that thermally evaporating a 12 nm gold layer on a 40 nm nitroxide-doped polystyrene film inactivates the nitroxide spin labels to a depth of 20 nm, making single-spin measurements difficult or impossible. We introduce a "laminated sample" protocol in which the gold layer is first evaporated on a sacrificial polymer. The sample is deposited on the room-temperature gold layer, removed using solvent lift-off, and placed manually on a coplanar waveguide. Electron spin resonance (ESR) of such a laminated sample was detected via MRFM at cryogenic temperatures using a high-compliance cantilever with an integrated 100-nm-scale cobalt tip. A 20-fold increase of spin signal was observed relative to a thin-film sample prepared instead with an evaporated metal coating. The observed signal is still somewhat smaller than expected, and we discuss possible remaining sources of signal loss.

We report on our studies of human virus-encoded viroporins. These proteins reside and function in viral and cellular membranes. In these environments viroporins act as homo-oligomeric ion-conducting channels or non-specific pores, changing the levels of ions, mostly cations, in the viral interior or cellular compartments. Through these channel or pore activities viroporins contribute to virus adaptation, survival and proliferation. Thus, these proteins are targets for drug development. We apply pulse and continuous-wave EPR spectroscopies as powerful tools to investigate the function and structural aspects of viroporins in lipid bilayers at the conditions representing the native membranes. In our studies we characterized the mechanism by which the M2 protein from influenza a virus assembles into a tetrameric proton channel. We established that the functional channel assembles via a cascade mechanism where dimers come first, followed by the formation of tetramer as a dimer-of-dimers. We also found that amantadine drug stabilized the closed (inhibited) form of M2 tetramer. Our further studies of a different p13II protein from human T-cell leukemia virus type 1 revealed that its purified soluble form oligomerizes upon interaction with lipid membrane mimetics. This behavior is relevant to the p13II function in the inner mitochondrial membrane (IMM) where it leads to increased IMM permeability to ions and depolarization. We also discuss our ongoing applications of EPR spectroscopy to viroporins from coronaviruses and hepatitis C virus, aiming at the effects of variations in the amino acid sequence on viroporin structure and function. Acknowledgements: We thank Haley Norman, Nichita Kulkarni, and Christina Fanouraki for their contributions at different stages of these studies.

RGD is a prolific example of a tripeptide used in biomaterials for cell adhesion, but the potency of free or surface-bound RGD tripeptide is orders-of-magnitude less than the RGD domain within natural proteins. We designed a set of peptides with varying lengths, composed of fragments of fibronectin protein whose central three residues are RGD, in order to vary their conformational behavior without changing the binding site's chemical environment. With these peptides, we measure the conformational dynamics and transient structure of the active site. Our studies reveal how flanking residues affect conformational behavior and integrin binding. We find that disorder of the binding site is important to the potency of RGD peptides and that transient hydrogen bonding near the RGD site affects both the energy landscape roughness of the peptides and peptide binding. This phenomenon is independent of longer-range folding interactions and helps explain why short binding sequences, including RGD itself, do not fully replicate the integrin-targeting properties of extracellular matrix proteins. Our studies reinforce that peptide binding is a holistic event and fragments larger than those directly involved in binding should be considered in the design of peptide epitopes for functional biomaterials.

In bacteria, LysE membrane exporters remove the excess of metabolically produced L-lysine and L-arginine from the cytosol. LysE deficiency leads to elevated cellular levels of L-lysine, causing the suppression of bacterial growth. Therefore, LysEs of bacterial pathogens are a potential pharmacological target for inhibition, which requires comprehensive knowledge of these proteins' structures and structure-function relationships. However, thus far, the studies on the LysE exporters have been rather limited.

Human T-cell leukemia virus type 1 is an oncovirus that causes aggressive adult T-cell leukemia but is also responsible for severe neurodegenerative and endocrine disorders. Combatting HTLV-1 infections requires a detailed understanding of the viral mechanisms in the host. Therefore, in vitro studies of important virus-encoded proteins would be critical. Our focus herein is on the HTLV-1-encoded regulatory protein p13II, which interacts with the inner mitochondrial membrane, increasing its permeability to cations (predominantly potassium, K+). Thereby, this protein affects mitochondrial homeostasis. We report on our progress in developing specific protocols for heterologous expression of p13II in E. coli, and methods for its purification and characterization. We succeeded in producing large quantities of highly-pure full-length p13II, deemed to be its fully functional form. Importantly, our particular approach based on the fusion of ubiquitin to the p13II C-terminus was instrumental in increasing the persistently low expression of soluble p13II in its native form. We subsequently developed approaches for protein spin labeling and a conformation study using double electron-electron resonance (DEER) spectroscopy and a fluorescence-based cation uptake assay for p13II in liposomes. Our DEER results point to large protein conformation changes occurring upon transition from the soluble to the membrane-bound state. The functional assay on p13II-assisted transport of thallium (Tl+) through the membrane, wherein Tl+ substituted for K+, suggests transmembrane potential involvement in p13II function. Our study lays the foundation for expansion of in vitro functional and structural investigations on p13II and would aid in the development of structure-based protein inhibitors and markers.

Mycobacterium tuberculosis (Mtb) causes the very severe disease tuberculosis. To fight Mtb infection, detailed understanding of the pathogen molecular mechanisms in the host is needed. To this end, comprehensive knowledge about Mtb membrane transport system, which is currently not well researched, is a high priority. Our focus is on the Mtb‐encoded L‐lysine exporter (LysE), which removes the excess of metabolically produced basic amino acids from the bacterial cytosol. LysE is a target for inhibition, since its deficiency leads to toxic levels of L‐lysine and suppression of bacterial growth. The most studied H37Rv strain of Mtb encodes two LysEs, but one of then, the Rv1986 protein, is considered to be the primary exporter. Also, Rv1986 expression is increased during the early stages of Mtb infection under conditions of hypoxia, thus, the protein could be a vaccine target. Therefore, we selected to study this protein. To do so, we developed custom protocols for its cloning, expression, purification, and initial characterization. To overcome the low expression levels in E. coli, we fused LysE at its C‐terminus to a combination of FLAG and 8xHistidine tags. Through these tags, we employed a dual‐affinity purification. We purified the protein in lipodiscs made of native E. coli membranes and in detergent. We obtained highly pure protein as confirmed by SDS‐PAGE and Western blotting. Both techniques visualized multiple bands at LysE suggesting protein oligomerization. We further created and purified a single cysteine mutant N175C for spin labeling. Pulse EPR study on it also points to multimeric protein organization. These studies as well as electron microscopy on LysE‐nanogold particle complexes are ongoing. To the best of our knowledge, this is the first highly‐pure LysE produced, which will facilitate further thorough investigations of the functional mechanisms of this protein.Support or Funding InformationNIAID R03 AI137735

pH is an important factor that affects the protein structure, stability, and activity. Here, we probe the nature of the low-pH structural form of the homodimeric CcdB (controller of cell death B) protein. Characterization of CcdB protein at pH 4 and 300 K using circular dichroism spectroscopy, 8-anilino-1-naphthalene-sulphonate binding, and Trp solvation studies suggests that it forms a partially unfolded state with a dry core at equilibrium under these conditions. CcdB remains dimeric at pH 4 as shown by multiple techniques, such as size-exclusion chromatography coupled to multiangle light scattering, analytical ultracentrifugation, and electron paramagnetic resonance. Comparative analysis using two-dimensional 15N-1H heteronuclear single-quantum coherence NMR spectra of CcdB at pH 4 and 7 suggests that the pH 4 and native state have similar but nonidentical structures. Hydrogen-exchange-mass-spectrometry studies demonstrate that the pH 4 state has substantial but anisotropic changes in local stability with core regions close to the dimer interface showing lower protection but some other regions showing higher protection relative to pH 7.