Stepwise Conformational Changes Research Articles

Structural Basis for Polθ-Helicase DNA Binding and Microhomology-Mediated End-Joining.

DNA double-strand breaks (DSBs) present a critical threat to genomic integrity, often precipitating genomic instability and oncogenesis. Repair of DSBs predominantly occurs through homologous recombination (HR) and non-homologous end joining (NHEJ). In HR-deficient cells, DNA polymerase theta (Polθ) becomes critical for DSB repair via microhomology-mediated end joining (MMEJ), also termed theta-mediated end joining (TMEJ). Thus, Polθ is synthetically lethal with BRCA1/2 and other HR factors, underscoring its potential as a therapeutic target in HR-deficient cancers. However, the molecular mechanisms governing Polθ-mediated MMEJ remain poorly understood. Here we present a series of cryo-electron microscopy structures of the Polθ helicase domain (Polθ-hel) in complex with DNA containing 3'-overhang. The structures reveal the sequential conformations adopted by Polθ-hel during the critical phases of DNA binding, microhomology searching, and microhomology annealing. The stepwise conformational changes within the Polθ-hel subdomains and its functional dimeric state are pivotal for aligning the 3'-overhangs, facilitating the microhomology search and subsequent annealing necessary for DSB repair via MMEJ. Our findings illustrate the essential molecular switches within Polθ-hel that orchestrate the MMEJ process in DSB repair, laying the groundwork for the development of targeted therapies against the Polθ-hel.

Gαs slow conformational transition upon GTP binding and a novel Gαs regulator

G proteins are major signaling partners for G protein-coupled receptors (GPCRs). Although stepwise structural changes during GPCR-G protein complex formation and guanosine diphosphate (GDP) release have been reported, no information is available with regard to guanosine triphosphate (GTP) binding. Here, we used a novel Bayesian integrative modeling framework that combines data from hydrogen-deuterium exchange mass spectrometry, tryptophan-induced fluorescence quenching, and metadynamics simulations to derive a kinetic model and atomic-level characterization of stepwise conformational changes incurred by the β2-adrenergic receptor (β2AR)-Gs complex after GDP release and GTP binding. Our data suggest rapid GTP binding and GTP-induced dissociation of Gαs from β2AR and Gβγ, as opposed to a slow closing of the Gαs α-helical domain (AHD). Yeast-two-hybrid screening using Gαs AHD as bait identified melanoma-associated antigen D2 (MAGE D2) as a novel AHD-binding protein, which was also shown to accelerate the GTP-induced closing of the Gαs AHD.

The proteasome - structural aspects and inhibitors: a second life for a validated drug target

The proteasome is the central component of the adaptable ubiquitin proteasome system (UPS) discovered in the 1980's. It sustains protein homeostasis (proteostasis) under a large variety of physiological and pathological conditions. Its dysregulation has been often associated to various human diseases. Its potential regulation by modulators has emerged as promising avenue to develop treatments of various pathologies. The FDA approval in 2003 of the proteasome inhibitor bortezomib to treat multiple myeloma, then mantle lymphoma in 2006, has considerably increased the clinical interest of proteasome inhibition. Second-generation proteasome inhibitors (carfilzomib and ixazomib) have been approved to overcome bortezomib resistance and improved toxicity profile and route of administration. Selective inhibition of immunoproteasome is a promising approach towards the development of immunomodulatory drugs. The design of these drugs relies greatly on the elucidation of high-resolution structures of the targeted proteasomes. The ATPase-dependent 26S proteasome (2.4 MDa) consists of a 20S proteolytic core and one or two 19S regulatory particles. The 20S core contains three types of catalytic sites. In recent years, due to technical advances especially in atomic cryo-electron microscopy, significant progress has been made in the understanding of 26S proteasome structure and its dynamics. Stepwise conformational changes of the 19S particle induced by ATP hydrolysis lead to substrate translocation, 20S pore opening and processive protein degradation by the 20S proteolytic subunits (2β1, 2β2 and 2β5). A large variety of structurally different inhibitors, both natural products or synthetic compounds targeting immuno- and constitutive proteasomes, has been discovered. The latest advances in this drug discovery are presented. Knowledge about structures, inhibition mechanism and detailed biological regulations of proteasomes can guide strategies for the development of next-generation inhibitors to treat human diseases, especially cancers, immune disorders and pathogen infections. Proteasome activators are also potentially applicable to the reduction of proteotoxic stresses in neurodegeneration and aging.

Exploring reaction pathways for the structural rearrangements of the Mn cluster induced by water binding in the S3 state of the oxygen evolving complex of photosystem II

Photosynthetic oxidation of water to dioxygen is catalyzed by the Mn4CaO5 cluster in the protein-cofactor complex photosystem II. The light-driven catalytic cycle consists of four observable intermediates (S0, S1, S2, and S3) and one transient S4 state. Recently, using X-ray free-electron laser crystallography, two experimental groups independently observed incorporation of one additional oxygen into the cluster during the S2 to S3 transition, which is likely to represent a substrate. The present study implicates two competing reaction routes encountered during the structural rearrangement of the catalyst induced by the water binding and immediately preceding the formation of final stable forms in the S3 state. This mutually exclusive competition involves concerted versus stepwise conformational changes between two isomers, called open and closed cubane structures, which have different consequences on the immediate product in the S3 state. The concerted pathway involves a one-step conversion between two isomeric hydroxo forms without changes to the metal oxidation and total spin (Stotal = 3) states. Alternatively, in the stepwise process, the bound waters are oxidized and transformed into an oxyl–oxo form in a higher spin (Stotal = 6) state. Here, density functional calculations are used to characterize all relevant intermediates and transition structures and demonstrate that the stepwise pathway to the substrate activation is substantially favored over the concerted one, as evidenced by comparison of the activation barriers (11.1 and 20.9 kcal mol−1, respectively). Only after formation of the oxyl–oxo precursor can the hydroxo species be generated; this occurs with a slow kinetics and an activation barrier of 17.8 kcal mol−1. The overall thermodynamic driving force is likely to be controlled by the movements of two glutamate ligands, D1-Glu189 and CP43-Glu354, in the active site and ranges from very weak (+0.4 kcal mol−1) to very strong (–23.5 kcal mol−1).

Dynamic mechanisms driving conformational conversions of the β and ε subunits involved in rotational catalysis of F<sub>1</sub>-ATPase

F-type ATPase is a ubiquitous molecular motor. Investigations on thermophilic F1-ATPase and its subunits, β and ε, by NMR were reviewed. Using specific isotope labeling, pKa of the putative catalytic carboxylate in β was estimated. Segmental isotope-labeling enabled us to monitor most residues of β, revealing that the conformational conversion from open to closed form of β on nucleotide binding found in ATPase was an intrinsic property of β and could work as a driving force of the rotational catalysis. A stepwise conformational change was driven by switching of the hydrogen bond networks involving Walker A and B motifs. Segmentally labeled ATPase provided a well resolved NMR spectra, revealing while the open form of β was identical for β monomer and ATPase, its closed form could be different. ATP-binding was also a critical factor in the conformational conversion of ε, an ATP hydrolysis inhibitor. Its structural elucidation was described.

Structural basis for dynamic regulation of the human 26S proteasome

The proteasome is the major engine of protein degradation in all eukaryotic cells. At the heart of this machine is a heterohexameric ring of AAA (ATPases associated with diverse cellular activities) proteins that unfolds ubiquitylated target proteins that are concurrently translocated into a proteolytic chamber and degraded into peptides. Using cryoelectron microscopy, we determined a near-atomic-resolution structure of the 2.5-MDa human proteasome in its ground state, as well as subnanometer-resolution structures of the holoenzyme in three alternative conformational states. The substrate-unfolding AAA-ATPase channel is narrowed by 10 inward-facing pore loops arranged into two helices that run in parallel with each other, one hydrophobic in character and the other highly charged. The gate of the core particle was unexpectedly found closed in the ground state and open in only one of the alternative states. Coordinated, stepwise conformational changes of the regulatory particle couple ATP hydrolysis to substrate translocation and regulate gating of the core particle, leading to processive degradation.

Developing soluble mimetics of the chemokine receptor CCR5 for the study of HIV Env/receptor interactions (CCR6P.216)

Abstract During HIV entry, the surface-exposed gp120 subunit of the envelope glycoprotein (Env) undergoes a series of stepwise conformational changes in response to interactions with the primary receptor CD4, and co-receptors, CCR5 or CXCR4. Obtaining structural information on the various intermediates during viral entry is a key focus of antiviral and vaccine research and could open the doors for more effective treatment and prevention. This project aims to develop recombinant soluble co-receptor mimetics featuring critical determinants of the chemokine receptor, CCR5, using two approaches: fusing the CCR5 moieties to soluble CD4 by flexible polypeptide linkers and using a globular, stable scaffold protein to orient the co-receptor determinants in an optimal conformation to recreate the binding interaction with gp120. We have successfully overexpressed and purified the recombinant proteins from mammalian cells. Characterization of the gp120-binding properties of the variants is underway using a vaccinia-based cell fusion assay where soluble CD4 has been shown to induce membrane fusion between Env-expressing effector cells and target cells bearing CCR5, but no CD4. The CCR5 moieties of the sCD4-fused constructs compete with cell-surface CCR5 for binding to gp120, leading to impaired activation of membrane fusion compared with sCD4. The soluble variants of CCR5 will be used in experiments to elucidate the conformational changes in gp120 that immediately precede membrane fusion.

Programmable self-assembly of carbon nanotubes assisted by reversible denaturation of a protein

Self-assembly of pristine multi-walled carbon nanotubes (CNTs) in aqueous dispersion using a protein, bovine serum albumin (BSA), has been demonstrated. Step-wise conformational changes in BSA as a function of temperature have been deployed to direct the assembly of nanotubes. More specifically, CNTs distributed randomly in native BSA at 35 °C as well as completely denatured BSA solution at 80 °C self-assemble in the intermediate temperature range of 45–65 °C, as evident from scanning and transmission electron microscopy. Fourier transform infrared (FTIR) and fluorescence studies indicate significant changes in the α-helical content of the protein with respect to the amide I and II bands and tryptophan emission intensity, respectively. The stability of CNT dispersion in BSA solution has been attributed to the hydrophobic interaction between nanotubes and the protein molecule by adding sodium cholate to the dispersion. Moreover, a mechanism based on electrostatic repulsion between BSA-bound CNTs has been proposed for the thermally reversible assembly of CNTs in BSA solution based on evidence from zeta potential measurements and FTIR spectroscopy. Thus the present report demonstrates bio-mimetic self-assembly of as-synthesized CNTs using changes in surface charge and conformation of an unfolding protein for biomedical applications and nanobiotechnology.

Dynamic secondary structural changes in Ca2+-saturated calmodulin upon interaction with the antagonist, W-7

Although the 3D structure of the Ca2+-bound CaM (Ca2+/CaM) complex with the antagonist, N-(6-aminohexyl)-5-chloro-1-naphthalenesulphonamide (W-7), has been resolved, the dynamic changes in Ca2+/CaM structure upon interaction with W-7 are still unknown. We investigated time- and temperature-dependent dynamic changes in Ca2+/CaM interaction with W-7 in physiological conditions using one- and two-dimensional Fourier-transformed infrared spectroscopy (2D-IR). We observed changes in the α-helix secondary structure of Ca2+/CaM when complexed with W-7 at a molar ratio of 1:2, but not at higher molar ratios (between 1:2 and 1:5). Kinetic studies revealed that, during the initial 125s at 25°C, Ca2+/CaM underwent formation of secondary coil and turn structures upon binding to W-7. Variations in temperature that induced significant changes in the structure of the Ca2+/CaM complex failed to do so when Ca2+/CaM was complexed with W-7. We concluded that W-7 induced stepwise conformational changes in Ca2+/CaM that resulted in a rigidification of the complex and its inability to interact with target proteins and/or polypeptides.

The transformation of chiral signals into macroscopic properties of materials using chirality-responsive polymers

The ability to transform the chiral signals of molecules into the macroscopic properties of a material will offer significant advantages in the development of chiral functional devices and chirality-related applications. Chirality-responsive polymers provide an excellent platform to realize this objective, which often involves two basic strategies. The first strategy is to utilize various external stimuli to directly mediate the chiral conformations of a polymer, through which the energy input is transformed into a macroscopic change in the properties of a material. The second strategy is to utilize the enantioselective interaction between polymers and guest chiral molecules to trigger a stepwise conformational change in smart polymers, which then results in transformation of the macroscopic properties. This review summarizes recent progress in generating chirality-responsive polymers based on these strategies and discusses advances in their applications as chiral sensors, liquid crystals, optical and electrical devices, nanomachines and so on. We then introduce the emerging field of chiral bio-interface materials, in which chiral signals are transformed into changes in the macroscopic behavior of cells and biomacromolecules based on the stereo-specific interactions between biological systems and artificial materials.

Oxidation-Induced Conformational Change of a Prokaryotic Molecular Chaperone, Hsp33, Monitored by Selective Isotope Labeling

Hsp33, a prokaryotic molecular chaperone, exerts holdase activity in response to oxidative stress. In this study, the stepwise conformational change of Hsp33 upon oxidation was monitored by NMR. In order to overcome its high molecular weight (33 kDa as a monomer and 66 kDa as a dimer), spectra were simplified using a selectively ( 15 N)His-labeled protein. All of the eight histidines were observed in the TROSY spectrum of the reduced Hsp33. Among them, three peaks showed dramatic resonance shifts dependent on the stepwise oxidation, indicating a remarkable conformational change. The results suggest that unfolding of the linker domain is associated with dimerization, but not entire region of the linker domain is unfolded.

Sequential Events in the Irreversible Thermal Denaturation of Human Brain-Type Creatine Kinase by Spectroscopic Methods

The non-cooperative or sequential events which occur during protein thermal denaturation are closely correlated with protein folding, stability, and physiological functions. In this research, the sequential events of human brain-type creatine kinase (hBBCK) thermal denaturation were studied by differential scanning calorimetry (DSC), CD, and intrinsic fluorescence spectroscopy. DSC experiments revealed that the thermal denaturation of hBBCK was calorimetrically irreversible. The existence of several endothermic peaks suggested that the denaturation involved stepwise conformational changes, which were further verified by the discrepancy in the transition curves obtained from various spectroscopic probes. During heating, the disruption of the active site structure occurred prior to the secondary and tertiary structural changes. The thermal unfolding and aggregation of hBBCK was found to occur through sequential events. This is quite different from that of muscle-type CK (MMCK). The results herein suggest that BBCK and MMCK undergo quite dissimilar thermal unfolding pathways, although they are highly conserved in the primary and tertiary structures. A minor difference in structure might endow the isoenzymes dissimilar local stabilities in structure, which further contribute to isoenzyme-specific thermal stabilities.

Allosteric Communication between cAMP Binding Sites in the RI Subunit of Protein Kinase A Revealed by NMR

The activation of protein kinase A involves the synergistic binding of cAMP to two cAMP binding sites on the inhibitory R subunit, causing release of the C subunit, which subsequently can carry out catalysis. We used NMR to structurally characterize in solution the RIalpha-(98-381) subunit, a construct comprising both cyclic nucleotide binding (CNB) domains, in the presence and absence of cAMP, and map the effects of cAMP binding at single residue resolution. Several conformationally disordered regions in free RIalpha become structured upon cAMP binding, including the interdomain alphaC:A and alphaC':A helices that connect CNB domains A and B and are primary recognition sites for the C subunit. NMR titration experiments with cAMP, B site-selective 2-Cl-8-hexylamino-cAMP, and A site-selective N(6)-monobutyryl-cAMP revealed that cyclic nucleotide binding to either the B or A site affected the interdomain helices. The NMR resonances of this interdomain region exhibited chemical shift changes upon ligand binding to a single site, either site B or A, with additional changes occurring upon binding to both sites. Such distinct, stepwise conformational changes in this region reflect the synergistic interplay between the two sites and may underlie the positive cooperativity of cAMP activation of the kinase. Furthermore, nucleotide binding to the A site also affected residues within the B domain. The present NMR study provides the first structural evidence of unidirectional allosteric communication between the sites. Trp(262), which lines the CNB A site but resides in the sequence of domain B, is an important structural determinant for intersite communication.

On the spontaneous encapsulation of proteins in carbon nanotubes

Biomolecules–carbon nanotube (CNT) interactions are of great importance in CNT-based drug delivery systems and biomedical devices. In this study, a spontaneous encapsulation of a globular protein into the CNT was observed through molecular dynamics simulation. The free energy of the system was found to be decreased after the encapsulation, which is the most fundamental reason for this spontaneous process. The system enthalpy decrease was found to make a dominant contribution to the free-energy change, and the system entropy increase also contributes to the spontaneous process. During the insertion, the protein makes a stepwise conformational change to maximize its affinity to the CNT walls as well as the protein–CNT interactions, mainly resulting in the deformation of the β-sheets in the protein. As a whole, the CNT was considered to attract protein molecules nonspecifically although the groups with high hydrophobicity and/or aromatic rings show great affinity.

Induced stepwise conformational change of human serum albumin on carbon nanotube surfaces

Non-covalent adsorption of proteins onto carbon nanotubes is important to understand the environmental and biological activity of carbon nanotubes as well as their potential applications in nanostructure fabrication. In this study, the adsorption dynamics and features of a model protein (the A sub-domain of human serum albumin) onto the surfaces of carbon nanotubes with different diameters were investigated out by molecular dynamics simulation. The adsorption behaviors were observed by both trajectory and quantitative analyses. During the adsorption process, the secondary structures of α-helices in the model protein were slightly affected. However, the random coils connecting these α-helices were strongly affected and this made the tertiary structure of protein change. The conformation and orientation selection of the protein were induced by the properties and the texture of surfaces indicated by the interaction curve. In addition, the stepwise adsorption dynamics of these processes are found. The mechanism of induced stepwise conformational change of protein on carbon nanotube surfaces would be helpful to better understand the protein–surface interaction at the molecular level.

Transcription Initiation in a Single-Subunit RNA Polymerase Proceeds through DNA Scrunching and Rotation of the N-Terminal Subdomains

Elucidating the mechanism of transcription initiation by RNA polymerases (RNAP) is essential for understanding gene transcription and regulation. Although several models, such as DNA scrunching, RNAP translation, and RNAP rotation, have been proposed, the mechanism of initiation by T7 RNAP has remained unclear. Using ensemble and single-molecule Förster resonance energy transfer (FRET) studies, we provide evidence for concerted DNA scrunching and rotation during initiation by T7 RNAP. A constant spatial distance between the upstream and downstream edges of initiation complexes making 4-7 nt RNA supports the DNA scrunching model, but not the RNAP translation or the pure rotation model. DNA scrunching is accompanied by moderate hinging motion (18 degrees +/- 4 degrees ) of the promoter toward the downstream DNA. The observed stepwise conformational changes provide a basis to understand abortive RNA synthesis during early stages of initiation and promoter escape during the later stages that allows transition to processive elongation.

Regulation of the calcium signal by calmodulin.

Stimulus-response coupling mediated by calmodulin involves several steps: a transitory increase in calcium concentration from 0.1 to 10 microM, induced by external stimuli; interaction of calcium with calmodulin, accompanied by stepwise structural transitions; the coordinated interaction with and activation of the many calmodulin-regulated enzymes and proteins. The binding of calcium to calmodulin is a cooperative and selective process that is modulated by magnesium. At physiological ionic strength, and only in the presence of magnesium, a large difference is seen between the affinities of sites III and IV (0.09 X 10(6) M-1) and sites I and II (0.0007 X 10(6) M-1) for calcium. This difference, together with the positive cooperativity previously observed, explains the stepwise conformational changes induced by calcium. The interaction of calmodulin with its target proteins requires the integrity of different portions of the calmodulin molecule. Calmodulin-regulated enzymes can be divided into three classes according to their abilities to bind with and to be activated by calmodulin fragments: enzymes which are activated by the C-terminal fragment, such as the Ca2+-ATPase and phosphorylase kinase; enzymes which require both halves of the molecule, such as cyclic AMP phosphodiesterase and myosin light chain kinase; and enzymes whose interaction with calmodulin fragments is too weak to be detected by activation, such as calcineurin and the multiprotein kinase. Thus different enzymes may be activated by different calmodulin conformers and the stepwise changes exhibited by calmodulin at different calcium levels can be used to regulate different metabolic pathways.

Seeing the Process of Histidine Phosphorylation in Human Bisphosphoglycerate Mutase

Bisphosphoglycerate mutase is an erythrocyte-specific enzyme catalyzing a series of intermolecular phosphoryl group transfer reactions. Its main function is to synthesize 2,3-bisphosphoglycerate, the allosteric effector of hemoglobin. In this paper, we directly observed real-time motion of the enzyme active site and the substrate during phosphoryl transfer. A series of high resolution crystal structures of human bisphosphoglycerate mutase co-crystallized with 2,3-bisphosphoglycerate, representing different time points in the phosphoryl transfer reaction, were solved. These structures not only clarify the argument concerning the substrate binding mode for this enzyme family but also depict the entire process of the key histidine phosphorylation as a "slow movie". It was observed that the enzyme conformation continuously changed during the different states of the reaction. These results provide direct evidence for an "in line" phosphoryl transfer mechanism, and the roles of some key residues in the phosphoryl transfer process are identified.

Specific Hydrogen-Bonding Networks Responsible for Selective O2 Sensing of the Oxygen Sensor Protein HemAT from Bacillus subtilis

HemAT from Bacillus subtilis (HemAT-Bs) is a heme-based O2 sensor protein that acts as a signal transducer responsible for aerotaxis. HemAT-Bs discriminates its physiological effector, O2, from other gas molecules to generate the aerotactic signal, but the detailed mechanism of the selective O2 sensing is not obvious. In this study, we measured electronic absorption, electron paramagnetic resonance (EPR), and resonance Raman spectra of HemAT-Bs to elucidate the mechanism of selective O2 sensing by HemAT-Bs. Resonance Raman spectroscopy revealed the presence of a hydrogen bond between His86 and the heme propionate only in the O2-bound form, in addition to that between Thr95 and the heme-bound O2. The disruption of this hydrogen bond by the mutation of His86 caused the disappearance of a conformer with a direct hydrogen bond between Thr95 and the heme-bound O2 that is present in WT HemAT-Bs. On the basis of these results, we propose a model for selective O2 sensing by HemAT-Bs as follows. The formation of the hydrogen bond between His86 and the heme propionate induces a conformational change of the CE-loop and the E-helix by which Thr95 is located at the proper position to form the hydrogen bond with the heme-bound O2. This stepwise conformational change would be essential to selective O2 sensing and signal transduction by HemAT-Bs.

Differential Activation of a Latent Polyphenol Oxidase Mediated by Sodium Dodecyl Sulfate

A kinetic study of the activity of soluble and membrane-bound latent polyphenol oxidase (PPO) extracted from beet root (Beta vulgaris) was carried out. For the first time, two types of behavior (hyperbolic and sigmoid) are reported in the same enzyme for PPO activation by the surfactant sodium dodecyl sulfate (SDS), depending on substrate nature. A kinetic model based on cooperative systems is developed to describe the activation effect of SDS, enabling the determination of the number of surfactant molecules binding to the enzyme in the activation process. The results indicate that the active site of the enzyme is not affected by SDS and that a stepwise conformational change favors the access of hydrophobic substrates compared to hydrophilic ones. Differential activation of PPO mediated by SDS may be of relevance in the control of PPO activity since the enzyme is able to express activity toward a specific substrate while remaining latent to others.