Proton Saturation Research Articles

Simulation of Structural Transformations in Modified Near-Surface Layers of Crystals

Superlattice formation in thin layers of oxidizing crystals and the effect of near-surface proton saturation on structure ordering,formation and periodical distribution of quantum wells have been discussed. The paper shows, it is necessary to develop non-Euclidean approach to the crystal’s internal geometry and consider, in consecutive order, the question of the four-dimentional Riemannian space into three-dimentional Eucliden space interpretation (REinterpretation).

Unraveling Sugar Binding Modes to DC-SIGN by Employing Fluorinated Carbohydrates.

A fluorine nuclear magnetic resonance (19F-NMR)-based method is employed to assess the binding preferences and interaction details of a library of synthetic fluorinated monosaccharides towards dendritic cell-specific intercellular adhesion molecule 3-grabbing non-integrin (DC-SIGN), a lectin of biomedical interest, which is involved in different viral infections, including HIV and Ebola, and is able to recognize a variety of self- and non-self-glycans. The strategy employed allows not only screening of a mixture of compounds, but also obtaining valuable information on the specific sugar–protein interactions. The analysis of the data demonstrates that monosaccharides Fuc, Man, Glc, and Gal are able to bind DC-SIGN, although with decreasing affinity. Moreover, a new binding mode between Man moieties and DC-SIGN, which might have biological implications, is also detected for the first time. The combination of the 19F with standard proton saturation transfer difference (1H-STD-NMR) data, assisted by molecular dynamics (MD) simulations, permits us to successfully define this new binding epitope, where Man coordinates a Ca2+ ion of the lectin carbohydrate recognition domain (CRD) through the axial OH-2 and equatorial OH-3 groups, thus mimicking the Fuc/DC-SIGN binding architecture.

Saturation scale fluctuations and multiparticle rapidity correlations

We study the effect of intrinsic fluctuations of the proton saturation momentum scale on event-by-event rapidity distributions. Saturation scale fluctuations generate an asymmetry in the single particle rapidity distribution in each event resulting in genuine n-particle correlations having a component linear in the rapidities of the produced particles, $y_1\cdots y_n$. We introduce a color domain model that naturally explains the centrality dependence of the two-particle rapidity correlations recently measured by ATLAS while constraining the probability distribution of saturation scale fluctuations in the proton. Predictions for n = 4, 6 and 8 particle correlations find that the four and eight-particle cumulant change sign at an intermediate multiplicity, a signature which could be tested experimentally.

Probing proton fluctuations with asymmetric rapidity correlations

Intrinsic fluctuations of the proton saturation momentum generate asymmetric rapidity distributions on an event-by-event basis. We argue that the asymmetric component, $\ensuremath{\langle}{a}_{1}^{2}\ensuremath{\rangle}$, of the orthogonal polynomial decomposition of the two-particle rapidity correlation function is a sensitive probe to this distribution of fluctuations. We present a simple model connecting the experimentally measured $\ensuremath{\langle}{a}_{1}^{2}\ensuremath{\rangle}$ to the variance, $\ensuremath{\sigma}$, of the distribution of the logarithm of the proton saturation scale. We find that $\ensuremath{\sigma}\ensuremath{\approx}0.5--1$ describes the asymmetric component of the rapidity correlations recently measured by the ATLAS Collaboration.

Saturation and Geometrical Scaling in Small Systems

Saturation and geometrical scaling (GS) of gluon distributions are a consequence of the non-linear evolution equations of QCD. We argue that in pp GS holds for the inelastic cross-section rather than for the multiplicity distributions. We also discuss possible fluctuations of the proton saturation scale in pA collisions at the LHC.

Intrinsic fluctuations of the proton saturation momentum scale in high multiplicity p+p collisions

High multiplicity events in p+p collisions are studied using the theory of the Color Glass Condensate. We show that intrinsic fluctuations of the proton saturation momentum scale are needed in addition to the sub-nucleonic color charge fluctuations to explain the very high multiplicity tail of distributions in p+p collisions. The origin of such intrinsic fluctuations is presumably non-perturbative in nature. Classical Yang Mills simulations using the IP-Glasma model are performed to make quantitative estimations. We find that fluctuations as large as O(1) of the average values of the saturation momentum scale can lead to rare high multiplicity events seen in p+p data at RHIC and LHC energies. Using the available data on multiplicity distributions we try to constrain the distribution of the proton saturation momentum scale and make predictions for the multiplicity distribution in 13 TeV p+p collisions.

Correction of B1-inhomogeneities for relaxation-compensated CEST imaging at 7 T.

Chemical exchange saturation transfer (CEST) imaging of endogenous agents in vivo is influenced by direct water proton saturation (spillover) and semi-solid macromolecular magnetization transfer (MT). Lorentzian fit isolation and application of the inverse metric yields the pure CEST contrast AREX, which is less affected by these processes, but still depends on the measurement technique, in particular on the irradiation amplitude B1 of the saturation pulses. This study focuses on two well-known CEST effects in the slow exchange regime originating from amide and aliphatic protons resonating at 3.5 ppm or -3.5 ppm from water protons, respectively. A B1-correction of CEST contrasts is crucial for the evaluation of data obtained in clinical studies at high field strengths with strong B1-inhomogeneities. Herein two approaches for B1-inhomogeneity correction, based on either CEST contrasts or Z-spectra, are investigated. Both rely on multiple acquisitions with different B1-values. One volunteer was examined with eight different B1-values to optimize the saturation field strength and the correction algorithm. Histogram evaluation allowed quantification of the quality of the B1-correction. Finally, the correction was applied to CEST images of a patient with oligodendroglioma WHO grade 2, and showed improvement of the image quality compared with the non-corrected CEST images, especially in the tumor region.

InverseZ-spectrum analysis for spillover-, MT-, andT1-corrected steady-state pulsed CEST-MRI - application to pH-weighted MRI of acute stroke

Endogenous chemical exchange saturation transfer (CEST) effects are always diluted by competing effects, such as direct water proton saturation (spillover) and semi-solid macromolecular magnetization transfer (MT). This leads to unwanted T2 and MT signal contributions that lessen the CEST signal specificity to the underlying biochemical exchange processes. A spillover correction is of special interest for clinical static field strengths and protons resonating near the water peak. This is the case for all endogenous CEST agents, such as amide proton transfer, -OH-CEST of glycosaminoglycans, glucose or myo-inositol, and amine exchange of creatine or glutamate. All CEST effects also appear to be scaled by the T1 relaxation time of water, as they are mediated by the water pool. This forms the motivation for simple metrics that correct the CEST signal. Based on eigenspace theory, we propose a novel magnetization transfer ratio (MTRRex ), employing the inverse Z-spectrum, which eliminates spillover and semi-solid MT effects. This metric can be simply related to Rex , the exchange-dependent relaxation rate in the rotating frame, and ka , the inherent exchange rate. Furthermore, it can be scaled by the duty cycle, allowing for simple translation to clinical protocols. For verification, the amine proton exchange of creatine in solutions with different agar concentrations was studied experimentally at a clinical field strength of 3 T, where spillover effects are large. We demonstrate that spillover can be properly corrected and that quantitative evaluation of pH and creatine concentration is possible. This proves that MTRRex is a quantitative and biophysically specific CEST-MRI metric. Applied to acute stroke induced in rat brain, the corrected CEST signal shows significantly higher contrast between the stroke area and normal tissue, as well as less B1 dependence, than conventional approaches.

A Novel Non-canonical Forkhead-associated (FHA) Domain-binding Interface Mediates the Interaction between Rad53 and Dbf4 Proteins

Forkhead-associated (FHA) and BRCA1 C-terminal (BRCT) domains are overrepresented in DNA damage and replication stress response proteins. They function primarily as phosphoepitope recognition modules but can also mediate non-canonical interactions. The latter are rare, and only a few have been studied at a molecular level. We have identified a crucial non-canonical interaction between the N-terminal FHA1 domain of the checkpoint effector kinase Rad53 and the BRCT domain of the regulatory subunit of the Dbf4-dependent kinase that is critical to suppress late origin firing and to stabilize stalled forks during replication stress. The Rad53-Dbf4 interaction is phosphorylation-independent and involves a novel non-canonical interface on the FHA1 domain. Mutations within this surface result in hypersensitivity to genotoxic stress. Importantly, this surface is not conserved in the FHA2 domain of Rad53, suggesting that the FHA domains of Rad53 gain specificity by engaging additional interaction interfaces beyond their phosphoepitope-binding site. In general, our results point to FHA domains functioning as complex logic gates rather than mere phosphoepitope-targeting modules.

NMR Analysis of a Novel Enzymatically Active Unlinked Dengue NS2B-NS3 Protease Complex

The dengue virus (DENV) is a mosquito-borne pathogen responsible for an estimated 100 million human infections annually. The viral genome encodes a two-component trypsin-like protease that contains the cofactor region from the nonstructural protein NS2B and the protease domain from NS3 (NS3pro). The NS2B-NS3pro complex plays a crucial role in viral maturation and has been identified as a potential drug target. Using a DENV protease construct containing NS2B covalently linked to NS3pro via a Gly4-Ser-Gly4 linker ("linked protease"), previous x-ray crystal structures show that the C-terminal fragment of NS2B is remote from NS3pro and exists in an open state in the absence of an inhibitor; however, in the presence of an inhibitor, NS2B complexes with NS3pro to form a closed state. This linked enzyme produced NMR spectra with severe signal overlap and line broadening. To obtain a protease construct with a resolved NMR spectrum, we expressed and purified an unlinked protease complex containing a 50-residue segment of the NS2B cofactor region and NS3pro without the glycine linker using a coexpression system. This unlinked protease complex was catalytically active at neutral pH in the absence of glycerol and produced dispersed cross-peaks in a (1)H-(15)N heteronuclear single quantum correlation spectrum that enabled us to conduct backbone assignments using conventional techniques. In addition, titration with an active-site peptide aldehyde inhibitor and paramagnetic relaxation enhancement studies demonstrated that the unlinked DENV protease exists predominantly in a closed conformation in solution. This protease complex can serve as a useful tool for drug discovery against DENV.

Structural Dynamics of Bacterial Translation Initiation Factor IF2

Bacterial translation initiation factor IF2 promotes ribosomal subunit association, recruitment, and binding of fMet-tRNA to the ribosomal P-site and initiation dipeptide formation. Here, we present the solution structures of GDP-bound and apo-IF2-G2 of Bacillus stearothermophilus and provide evidence that this isolated domain binds the 50 S ribosomal subunit and hydrolyzes GTP. Differences between the free and GDP-bound structures of IF2-G2 suggest that domain reorganization within the G2-G3-C1 regions underlies the different structural requirements of IF2 during the initiation process. However, these structural signals are unlikely forwarded from IF2-G2 to the C-terminal fMet-tRNA binding domain (IF2-C2) because the connected IF2-C1 and IF2-C2 modules show completely independent mobility, indicating that the bacterial interdomain connector lacks the rigidity that was found in the archaeal IF2 homolog aIF5B.

Entropy-driven cAMP-dependent Allosteric Control of Inhibitory Interactions in Exchange Proteins Directly Activated by cAMP

Exchange proteins directly activated by cAMP (EPACs) are guanine nucleotide-exchange factors for the small GTPases Rap1 and Rap2 and represent a key receptor for the ubiquitous cAMP second messenger in eukaryotes. The cAMP-dependent activation of apoEPAC is typically rationalized in terms of a preexisting equilibrium between inactive and active states. Structural and mutagenesis analyses have shown that one of the critical determinants of the EPAC activation equilibrium is a cluster of salt bridges formed between the catalytic core and helices alpha1 and alpha2 at the N terminus of the cAMP binding domain and commonly referred to as ionic latch (IL). The IL stabilizes the inactive states in a closed topology in which access to the catalytic domain is sterically occluded by the regulatory moiety. However, it is currently not fully understood how the IL is allosterically controlled by cAMP. Chemical shift mapping studies consistently indicate that cAMP does not significantly perturb the structure of the IL spanning sites within the regulatory region, pointing to cAMP-dependent dynamic modulations as a key allosteric carrier of the cAMP-signal to the IL sites. Here, we have therefore investigated the dynamic profiles of the EPAC1 cAMP binding domain in its apo, cAMP-bound, and Rp-cAMPS phosphorothioate antagonist-bound forms using several 15N relaxation experiments. Based on the comparative analysis of dynamics in these three states, we have proposed a model of EPAC activation that incorporates the dynamic features allosterically modulated by cAMP and shows that cAMP binding weakens the IL by increasing its entropic penalty due to dynamic enhancements.

The Existence of Multiple Conformers of Interleukin-21 Directs Engineering of a Superpotent Analogue

The high resolution three-dimensional structure of human interleukin (hIL)-21 has been resolved by heteronuclear NMR spectroscopy. Overall, the hIL-21 structure is dominated by a well defined central four-helical bundle, arranged in an up-up-down-down topology, as observed for other cytokines. A segment of the hIL-21 molecule that includes the third helical segment, helix C, is observed to exist in two distinct and interchangeable states. In one conformer, the helix C segment is presented in a regular, alpha-helical conformation, whereas in the other conformer, this segment is largely disordered. A structure-based sequence alignment of hIL-21 with receptor complexes of the related cytokines, interleukin-2 and -4, implied that this particular segment is involved in receptor binding. An hIL-21 analog was designed to stabilize the region around helix C through the introduction of a segment grafted from hIL-4. This novel hIL-21 analog was demonstrated to exhibit a 10-fold increase in potency in a cellular assay.

A Model for Agonism and Antagonism in an Ancient and Ubiquitous cAMP-binding Domain

The cAMP-binding domain (CBD) is an ancient and conserved regulatory motif that allosterically modulates the function of a group of diverse proteins, thereby translating the cAMP signal into a controlled biological response. The main receptor for cAMP in mammals is the ubiquitous regulatory (R) subunit of protein kinase A. Despite the recognized significant potential for pharmacological applications of CBDs, currently only one group of competitive inhibitor antagonists is known: the (R(p))-cAMPS family of phosphorothioate cAMP analogs, in which the equatorial exocyclic oxygen of cAMP is replaced by sulfur. It is also known that the diastereoisomer (S(p))-cAMPS with opposite phosphorous chirality is a cAMP agonist, but the molecular mechanism of action of these analogs is currently not fully understood. Previous crystallographic and unfolding investigations point to the enhanced CBD dynamics as a key determinant of antagonism. Here, we investigate the (R(p))- and (S(p))-cAMPS-bound states of R(CBD-A) using a comparative NMR approach that reveals a clear chemical shift and dynamic NMR signature, differentiating the (S(p))-cAMPS agonist from the (R(p))-cAMPS antagonist. Based on these data, we have proposed a model for the (R(p)/S(p))-cAMPS antagonism and agonism in terms of steric and electronic effects on two main allosteric relay sites, Ile(163) and Asp(170), respectively, affecting the stability of a ternary inhibitory complex formed by the effector ligand, the regulatory and the catalytic subunits of protein kinase A. The proposed model not only rationalizes the existing data on the phosphorothioate analogs, but it will also facilitate the design of novel cAMP antagonists and agonists.

Structure and Dynamics of ASC2, a Pyrin Domain-only Protein That Regulates Inflammatory Signaling

Structure and Dynamics of ASC2, a Pyrin Domain-only Protein That Regulates Inflammatory Signaling

Solution Structure of Human Peptidyl Prolyl Isomerase-like Protein 1 and Insights into Its Interaction with SKIP

The human PPIL1 (peptidyl prolyl isomerase-like protein 1) is a specific component of human 35 S U5 small nuclear ribonucleoprotein particle and 45 S activated spliceosome. It is recruited by SKIP, another essential component of 45 S activated spliceosome, into spliceosome just before the catalytic step 1. It stably associates with SKIP, which also exists in 35 S and activated spliceosome as a nuclear matrix protein. We report here the solution structure of PPIL1 determined by NMR spectroscopy. The structure of PPIL1 resembles other members of the cyclophilin family and exhibits PPIase activity. To investigate its interaction with SKIP in vitro, we identified the SKIP contact region by GST pulldown experiments and surface plasmon resonance. We provide direct evidence of PPIL1 stably associated with SKIP. The dissociation constant is 1.25 x 10(-7) M for the N-terminal peptide of SKIP-(59-129) with PPIL1. We also used chemical shift perturbation experiments to show the possible SKIP binding interface on PPIL1. These results illustrated that a novel cyclophilin-protein contact mode exists in the PPIL1-SKIP complex during activation of the spliceosome. The biological implication of this binding with spliceosome rearrangement during activation is discussed.

The Structure of Prp40 FF1 Domain and Its Interaction with the crn-TPR1 Motif of Clf1 Gives a New Insight into the Binding Mode of FF Domains

The yeast splicing factor Prp40 (pre-mRNA processing protein 40) consists of a pair of WW domains followed by several FF domains. The region comprising the FF domains has been shown to associate with the 5' end of U1 small nuclear RNA and to interact directly with two proteins, the Clf1 (Crooked neck-like factor 1) and the phosphorylated repeats of the C-terminal domain of RNA polymerase II (CTD-RNAPII). In this work we reported the solution structure of the first FF domain of Prp40 and the identification of a novel ligand-binding site in FF domains. By using chemical shift assays, we found a binding site for the N-terminal crooked neck tetratricopeptide repeat of Clf1 that is distinct and structurally separate from the previously identified CTD-RNAPII binding pocket of the FBP11 (formin-binding protein 11) FF1 domain. No interaction, however, was observed between the Prp40 FF1 domain and three different peptides derived from the CTD-RNAPII protein. Indeed, the equivalent CTD-RNAPII-binding site in the Prp40 FF1 domain is predominantly negatively charged and thus unfavorable for an interaction with phosphorylated peptide sequences. Sequence alignments and phylogenetic tree reconstructions using the FF domains of three functionally related proteins, Prp40, FBP11, and CA150, revealed that Prp40 and FBP11 are not orthologous proteins and supported the different ligand specificities shown by their respective FF1 domains. Our results also revealed that not all FF domains in Prp40 are functionally equivalent. We proposed that at least two different interaction surfaces exist in FF domains that have evolved to recognize distinct binding motifs.

Spectral spin diffusion and magnetic dipolar energy in the NMR of 13CH 3 compounds

Spin diffusion between 13CH 3 groups in solids is studied both theoretically and experimentally. It is shown to be dominated by mutual spin flip–flops of protons belonging to neighbouring methyl groups. Also nonmethyl protons may contribute significantly if present in the sample. The spin–rotational ground state of 13CH 3 consists of 16 sublevels. When their populations are used to describe spin diffusion, eight population combinations are shown to be important, two of them corresponding to the 13C–proton and proton–proton intra-methyl magnetic dipolar energies, D c and D p, respectively. Spin-diffusion transitions modulate these combinations so that a further reduction to two sets of four combinations is possible, with no coupling between the sets. Coupled differential equations are derived to describe the time dependence of the combinations in each set. They are solved numerically and compared with experimental results on a single crystal of aspirin with 13C-labelled methyl groups at the carbon resonance. The 13C NMR induction signal was observed as a function of time after the preparation either at the carbon resonance (a two-pulse sequence) or at the proton resonance (proton saturation). Usually carbon spectra were computed first and then three of the mentioned population combinations were obtained from the individual spectral components. Some results on the time dependence of D c were also obtained directly from the amplitude of the out-of-phase induction signal. Theoretical predictions are found to describe semiquantitatively the overall time dependence of these three combinations and especially their variation with different initial conditions, which are discussed in detail. Also the partial transfer of the magnetic dipolar energy between D c and D p is nicely explained. Reasons for discrepancies are discussed.

Improvement of duty-cycle heating compensation in NMR spin relaxation experiments

To reliably measure NMR relaxation properties of macromolecules is a prerequisite for precise experiments that identify subtle variations in relaxation rates, as required for the determination of rotational diffusion anisotropy, CSA tensor determination, advanced motional modeling or entropy difference estimations. An underlying problem with current NMR relaxation measurement protocols is maintaining constant sample temperature throughout the execution of the relaxation series especially when rapid data acquisition is required. Here, it is proposed to use a combination of a heating compensation and a proton saturation sequence at the beginning of the NMR relaxation pulse scheme. This simple extension allows reproducible, robust and rapid acquisition of NMR spin relaxation data sets. The method is verified with 15N spin relaxation measurements for human ubiquitin.

Potentiometric titrations of Bacillus subtilis cells to low pH and a comparison of modeling approaches

To provide constraints on the speciation of bacterial surface functional groups, we have conducted potentiometric titrations using the gram-positive aerobic species Bacillus subtilis, covering the pH range 2.1 to 9.8. Titration experiments were conducted using an auto-titrator assembly, with the bacteria suspended in fixed ionic strength (0.01 to 0.3 M) NaClO 4 solutions. We observed significant adsorption of protons over the entire pH range of this study, including to the lowest pH values examined, indicating that proton saturation of the cell wall did not occur under any of the conditions of the experiments. Ionic strength, over the range studied here, did not have a significant effect on the observed buffering behavior relative to experimental uncertainty. Electrophoretic mobility measurements indicate that the cell wall is negatively charged, even under the lowest pH conditions studied. These experimental results necessitate a definition of the zero proton condition such that the total proton concentration at the pH of suspension is offset to account for the negative bacterial surface charge that tends towards neutrality at pH <2. The buffering intensity of the bacterial suspensions reveals a wide spread of apparent pKa values. This spread was modeled using three significantly different approaches: a Non-Electrostatic Model, a Constant Capacitance Model, and a Langmuir-Freundlich Model. The approaches differ in the manner in which they treat the surface electric field effects, and in whether they treat the proton-active sites as discrete functional groups or as continuous distributions of related sites. Each type of model tested, however, provides an excellent fit to the experimental data, indicating that titration data alone are insufficient for characterizing the molecular-scale reactions that occur on the bacterial surface. Spectroscopic data on the molecular-scale properties of the bacterial surface are required to differentiate between the underlying mechanisms of proton adsorption inherent in these models. The applicability and underlying conceptual foundation of each model is discussed in the context of our current knowledge of the structure of bacterial cell walls.