bluuebunny/crossref_metadata_2025 huggingface dataset:
Influence of crystallization on formation of biomolecular homochirality on Earth
Authors: Konstantinov Konstantin , Konstantinova Alisa
Published: November 2015

A mathematical model of coupled autocatalytic reactions along with crystallization of diastereomers was considered. It was shown that the differences in the physical properties of diastereomers could be a 100% enantioselective factor, which makes it possible to obtain a significant chiral polarization even at low enantioselectivity of autocatalysis. It was shown that molecules, which are more complex, should have higher chiral polarization than simpler ones. The calculation of the dynamics of the model under consideration shows that the presence of binomial coefficients in the reaction of pair formation from two different enantiomers leads to the occurrence of an additional 100% enantioselective factor even in case when diastereomers have identical properties. Estimates show that theoretical difference between right and left-handed molecules (which is due to weak interaction), is sufficient to explain directed symmetry breaking and construction of biological molecules from L-amino acids and D-sugars at the origin of life on Earth. It is shown that such a model constitutes an amplifier with a feedback. It is proposed that a two-layer system with a feedback could be attributed to the formation of longer homochiral chains, which are necessary for the formation of life on Earth.
Pig GTP-specific succinyl-CoA synthetase in complex with succinate
Authors: Huang Ji , Fraser Marie
Published: November 2015

Succinyl-CoA synthetase (SCS) exists in the mitochondria of mammals as two different isoforms; one is ATP-specific and the other is GTP-specific. SCS is a heterodimer, and the two isoforms have a common α-subunit, but different β-subunits [1]. The β-subunit determines nucleotide specificity. Mutations in the α-subunit or the ATP-specific β-subunit can cause encephalomyopathy due to mitochondrial DNA depletion, along with lactic acidosis and methylmalonic aciduria (reviewed in [2]). The reaction catalyzed by SCS, succinyl-CoA+ NDP + Pi⇌succinate +CoA + NTP, is reversible, and the direction depends on the relative concentrations of substrates and products. Only after all substrate-binding sites are discovered can the catalytic mechanism of SCS be fully understood. Structures of SCS with ADP, GDP, GTP, Pi and CoA have been determined, but the succinate-binding site, or the binding site for the succinyl-portion of succinyl-CoA, is still unknown. Succinate is predicted to bind to the conserved sequence Gly-Gly-Ile-Val (327β-330β) located in a loop of the β-subunit of GTP-specific SCS. Crystals of other complexes with pig GTP-specific SCS have diffracted well, so we are crystallizing this enzyme in complex with succinate. Initially, plasmid containing the genes encoding pig GTP-specific SCS was transformed into E coli. After overproducing the desired protein with a 6-His tag on the C-terminus of the α-subunit, three different purification columns were used to obtain the GTP-SCS protein at high purity. Succinate was then co-crystallized with GTP-SCS under conditions containing polyethylene glycol 3350, magnesium formate and HEPES, pH 7.0.
Structural analyses of the two cysteine desulfurases from Aquifex aeolicus
Authors: Hirabayashi Kei , Iwanaga Tomoko , Yamakawa Makoto , Tanaka Naoyuki , Fukuyama Keiichi , Takahashi Yasuhiro , Wada Kei
Published: November 2015

The cysteine desulfurase IscS is a highly conserved master enzyme initiating sulfur transfer to a wide range of acceptor proteins. IscS degrades L-cysteine into L-alanine and a sulfur atom in a pyridoxal 5'-phosphate (PLP) dependent manner. In this reaction, it is essential for a conserved Lys residue of IscS to form Schiff base (the covalent bonding interaction) with PLP. Recent accumulations of genomic information have revealed that some IscS homologues in archaea and thermophilic bacteria lack this invariant Lys. Here we report the crystal structures of two paralogous cysteine desulfurases, the canonical Aa IscS1 and the invariant Lys lacking Aa IscS2, from Aquifex aeolicus. Aa IscS1/Aa IscS2 were overproduced in E. coli, and purified by heat-treatment and several column chromatography, and crystallized. The structure of Aa IscS1 was determined at 2.00 Å (Rcryst= 19.4% and Rfree = 22.0%), and Aa IscS2 at 2.55 Å (Rcryst= 21.8% and Rfree = 27.0%). Overall structures as well as orientations of the residues in the active site were quite similar to each other. In Aa IscS1 the PLP adduct was anchored in the catalytic pocket of Aa IscS1 by the formation of the aldimine Schiff base with the invariant Lys. Whereas in Aa IscS2 the PLP was not seen in the active pocket, since the catalytic Lys was substituted by Leu. Alternatively, an electron density derived from unknown-small molecule was located in the catalytic site of Aa IscS2. The shape of this electron density was completely different from that of PLP. The Bijvoet difference map calculated from data collected at λ=1.7 Å overlapped with the electron density observed in the active site; the unknown-small molecule probably contains such metals as iron atoms. Furthermore, the ICP-MS analysis demonstrated that as-isolated Aa IscS2 harbored the iron atom in the solution state. More recently we obtained the experimental evidences that non-canonical Aa IscS2 was able to form the binary complex with Aa IscU, which is responsible for a scaffold for the assembly of a nascent Fe-S cluster. Base on the structural/biochemcal results, possible physiological functions of two cysteine desulfrurases will be discussed.
Studies of the Type IV Pilus of Neisseria meningitidis
Authors: Harding Rachel , Exley Rachel , Tang Christoph , Lea Susan
Published: November 2015

Neisseria meningitidis is largely a commensal species, resident specifically in the human nasopharynx but can also cause endemic and epidemic disease. Type IV pili of N. meningitidis have long been implicated as important colonisation and virulence factors that initiate attachment to host cells. The major pilin subunit, of which thousands of copies make the pilus shaft, is thought to be important in contributing to the adhesive properties of the type IV pilus and has potential as a vaccine candidate against N. meningitidis. To further understand the major pilins role and potential therapeutic properties, a protocol to make soluble PilE, the major pilin of N.meningitidis, from a variety of strains was established; and the structure of PilE from strain MC58 was solved by X-ray crystallography. The structure of PilE was solved to 1.4Å resolution revealing a classic pilin fold indicating the pilus may have a similar super-structure to that of the closely related Neisseria gonorrhoeae. Immunisations were carried out in mice with the pilins from different strains of N. meningitidis. Preliminary results indicate the sera generated have no bactericidal activity but can discriminate between the two classes of major pilins. Future work aims to further investigate the properties of this sera and attempt structure solution of major pilins from different strains of N. meningitidis.
Comparison of the Structures and Activities of Cg10062 with other 4-OT Enzymes
Authors: Hackert Marvin , Guo Youzhong , Johnson, Jr. William , Whitman Christian
Published: November 2015

The tautomerase superfamily is a broad family of proteins represented by 4-oxalocrotonate tautomerase (4-OT), 5-(carboxymethyl)-2-hydroxymuconate isomerase (CHMI), cis-3-chloroacrylic acid dehalogenase (cis-CaaD), malonate semialdehyde decarboxylase (MSAD), and macrophage migration inhibitory factor (MIF). 4-OT and many of its homologues are homo- or heterohexamers composed of small (60-75 a.a. residue) subunits while CHMI, MSAD, cis-CaaD and MIF are nearly twice that size and form trimers. The subunits of this family share two distinguishing features – one or two beta-alpha-beta structural motifs and a catalytically important N-terminal Pro residue. Several different catalytic activities are known to utilize this same structural motif - tautomerase, isomerase, decarboxylase, dehalogenase, etc. Cg10062 is a homologue of cis-CaaD, however, it differs from cis-CaaD in several respects. In addition to being able to process cis-3-chloroacrylic acid, it also displays multiple other functions such as the capability to process trans-3-chloroacrylic acid (like CaaD), to process phenylpyruvate (like PPT/MIF) and 2-oxo-3-pentynoate (like CaaD, cis-CaaD and MSAD). Furthermore, Cg10062 is inactivated by both (R) and (S)-oxirane-2-carboxylate. However, cis-CaaD is only inactivated by the (R)- isomer. The X-ray structures of native Cg10062, and its inactivated complexes have been determined and the results of comparing these structures and activities with CaaD, cis-CaaD, PPT/MIF and MSAD will be reported. This work was supported in part by The Welch Foundation ( F1334).
Nanoencapsulation of Silver-Based Antimicrobial Drugs
Authors: Gagnon Jacinthe , Caruso Rachel , Fromm Katharina
Published: November 2015

Implant-associated infections still remain an issue in medicine and can cause various medical complications. In order to ensure proper host-cell integration and biocompatibility to an implant, it is essential to prevent bacterial adhesion during the critical period of 6 hours after surgery. Moreover, as the implants are increasingly used in medicine, bacteria are becoming more resistant to antibiotics, in such a way that new developments in preventing and curing infections are more than ever needed. Silver compounds and nanoparticles are gaining more interest from the scientific society as a replacement to antibiotics. However, silver compounds may be too soluble and even toxic for the host. Encapsulation might be very advantageous in order to increase the stability and biocompatibility of silver drugs. In addition, it allows a more controllable release of antimicrobial agents. In this study, ceria nanocapsules with integrated silver nanoparticles (Ag/CeO2 NCs) were synthesized according to the method depicted in the figure below. The capsules were then characterized using XRD, TEM, SEM, and FT-IR. Silver nanoparticles (Ag NPs) are visible on the surface as well as in the cavity of Ag/CeO2 NCs, suggesting that they were integrated within the ceria shell. This system can release silver during a period exceeding 3 months, which demonstrates a good release control of the antimicrobial agent. The Ag/CeO2 NCs have a low cytotoxicity towards human alveolar epithelial cells, but allow only a poor cell attachment. In order to improve the cell attachment on the nanocapsules, as well as to reduce the silver being released, a TiO2 coating around the Ag/CeO2 NCs was added to this system. This resulted in the so-called Ag/CeO2/TiO2 NCs. These novel nanocontainers were also characterized in order to evaluate the cytotoxicity and antimicrobial activity.
Truncated Human ATP-Specific Succinyl-CoA Synthetase
Authors: Fraser Marie , Yu Chelsea , Hayakawa Koto , Hayakawa Koto
Published: November 2015

Two isoforms of the heterodimeric enzyme succinyl-CoA synthetase (SCS) exist in the mitochondria of humans. One is specific for ATP, while the other is specific for GTP. Both catalyze the reversible reaction: succinate + CoA + NTP ⇌ succinyl-CoA + NDP + Pi, where N denotes adenosine or guanosine. SCS is best known as an enzyme of the citric acid cycle where the reaction generates NTP. In the reverse direction, SCS replenishes succinyl-CoA required for the catabolism of ketone bodies and for heme synthesis. Nucleotide-specific forms are thought to be required for SCS to serve its different metabolic roles. The nucleotide specificity lies in the β-subunit [1], and the β-subunit of human ATP-specific SCS has been shown to interact with the C-terminus of erythroid-specific aminolevulinic acid synthase (ALAS2) [2]. ALAS2 catalyzes the committed step in heme synthesis: succinyl-CoA + Gly ⇌ 5-aminolevulinate + CoA + CO2. An interaction between SCS and ALAS2 makes biological sense, since this could provide channeling of succinyl-CoA from SCS to ALAS2. We hypothesize that the interaction is with the carboxy-terminus of the β-subunit of ATP-specific SCS because sequence comparisons show that the β-subunit of ATP-specific SCS has a carboxy-terminal extension when compared to other SCSs' β-subunits. To test this hypothesis, we added a carboxy-terminal His8-tag to the α-subunit of human ATP-specific SCS and mutated the codon for Thr 396β to a stop codon. This truncated version of human ATP-specific SCS has been produced in E. coli and purified. As well as testing to see if truncated human ATP-specific SCS interacts with ALAS2, we are using the truncated version in crystallization trials. Crystals of full-length human ATP-specific SCS diffract to only 3.2 Å and our goal is to obtain better-diffracting crystals of the complex of ATP with truncated human ATP-specific SCS.
Inhibitor Binding Mode Differences Within the AGC Subfamily
Authors: Delker Silvia , Robinson Dale , Bahmanyar Sami , Pagarigan Barbra , Fang Wei , Abbasian Mahan , Mahmoudi Afshin , Cashion Daniel , Cathers Brian , Chamberlain Philip
Published: November 2015

Designing potent selective kinase inhibitors is an ongoing challenge due to the high level of homology within the protein kinome. The AGC family comprises ~12% of the kinome and includes many important drug targets. We compared the binding mode of two inhibitors within the catalytic domain of a set of AGC kinase family members: PKC related kinase (PRK), p90 ribosomal s6 kinase N terminal domain (RSKn), and protein kinase A (PKA). We observed that even within the closely related AGC kinase subfamily, the two ligands can bind in alternate orientations. Alternative binding modes can be attributed to specific sequence variations and structural differences, however the observation of multiple inhibitor binding modes within a subfamily highlights the difficulties in predicting the activity spectrum of kinase inhibitors. The crystal structures described herein may help in the design of potent, selective kinase inhibitors to these or related kinases.
Crystal Structure of BRP39 protein expressed during Mammary Gland Apoptosis
Authors: Choudhary Suman , Mohanty Ashok , Fisher Andrew
Published: November 2015

Breast regression protein (BRP39) from mice is a 39 kDa protein which is a member of chitolectin class of GH18 family. High levels of expression of BRP39 have been detected in breast carcinoma. It has been proposed that this may act as a protecting signalling factor and also help in proliferation of cells during breast cancer. It can act as a potential candidate for rational structure based drug design against breast cancer. Here, we report the crystal structure of recombinant BRP39 in a deglycosylated form which was expressed in a heterologous system i.e E.Coli. To understand the role of sugar moiety, crystal structure of a deglycosylated chitolectin is an essential requirement. The structure was solved by molecular replacement method of phase determination and refined to a 2.6 A0resolution. The overall structure of BRP39 consists of two globular domains: a large (β/α)8 TIM barrel domain and a small (α+β) domain. The most striking observation from BRP39 structure is the conformation of critical Trp 100 residue into the β-barrel of carbohydrate binding groove of BRP39. The structure reveals that the glycan moiety plays an important role in the orientation of critical Trp100 in the β-barrel. In deglycosylated BRP39, it orients away from the barrel and resembles the conformation as seen in non-glycosylated chitinases. In contrast to this, the corresponding Trp is oriented into the barrel in case of other glycosylated homologues of BRP39 which may have its implications in sugar binding. Furthermore, in MGP-40, the altered conformation of loop is stabilized by H-bonding and stacking interactions whereas in BRP39, no hydrogen bond was observed between any of the residues of this loop except for Trp100 which interacts with a water molecule may be to stabilize its conformation. Another important observation in the sugar binding groove of BRP39 structure is the mutation of two important residues, one in TIM barrel domain and another in a part of α+β domain which is also involved in sugar binding. Asn100 and Arg263 in Hcgp39 and other chitinase- like proteins (SPX-40 structures) are replaced by Lys101 and Lys264 in BRP39. Both of these residues i.e. Asn100 and Arg 263 in HCgp39 have been reported to be involved in stabilizing the binding of GlcNAc inside the groove. Possibly, there is a significant distortion in the shape of sugar binding groove due to these mutations in BRP39.
Structural and Functional Analysis of the interaction between PCNA and ATAD5
Authors: Bui Tam , Xing Guangxin , McConkey Haley , Jha Vikash , Ling Hong
Published: November 2015

Proliferating cell nuclear antigen (PCNA) is a DNA sliding clamp that coordinates DNA replication and repair. PCNA is loaded on and unloaded off of DNA during replication. It is loaded onto DNA by the replication factor C (RFC) complex. The mechanism of PCNA unloading is not fully understood however. ATPase family AAA domain containing protein 5 (ATAD5) interacts with subunits of RFC to form a RFC-like complex that functions in unloading PCNA. Reduced expression of ATAD5 extends the life of replication factories by retaining PCNA and other repliosome proteins on chromatin. ATAD5 also plays a role in maintaining genomic stability, as mutations to ATAD5 cause genomic instability in mice and human cells. The region of ATAD5 that interacts with PCNA had yet to be determined. Proteins interacting with PCNA usually have a PCNA-interaction protein (PIP) motif termed the PIP-box. Through sequence analysis, we identified a putative PIP-box in ATAD5. Using GST pull-down experiments, we found that the putative PIP-box bound to PCNA. Mutation of the key residues in the PIP-box abolished the binding. The interaction was also confirmed by isothermal titration calorimetry (ITC) analysis of PCNA and a synthetic peptide containing the PIP-box. The binding constant (Kd) of the PCNA-peptide interaction is 6.2μM, determined by the ITC assays. To further characterize the interaction, we co-crystallized PCNA and the ATAD5 peptide. The complex crystals diffracted to a resolution of 3.5Å. The crystals belong to the space group H3, with unit-cell parameters a = 83.6Å and c = 211.4Å. Our molecular replacement solution indicates that the peptide binds on PCNA at the conserved PIP-box binding pocket. Taken together, our work demonstrates that ATAD5 does contain a PIP motif that directly interacts with PCNA. The structure-function studies on the interaction will provide insights into the molecular mechanism of PCNA unloading and the role of ATAD5 in DNA replication and repair.
Solid-to-solid polymorphic transitions in amino acid crystals
Authors: van den Ende Joost , Cuppen Herma
Published: November 2015

The properties of crystals are related to their structure and therefore they can be different for different polymorphs. For example, the pharmaceutical characteristics bioavailability and shelf life can depend on the formed polymorph and its stability. We aim to understand transitions between polymorphs that occur in the solid phase, with the ultimate goal to induce or inhibit these transitions. We apply Molecular Dynamics (MD) simulations as a computational microscope to study these processes at the molecular level. Our used model systems for polymorphic behavior of molecular crystals in a pharmaceutical context are amino-acid crystals, in particular DL-norleucine. The polymorphs of DL-norleucine consist of tightly packed hydrogen-bonded bilayers with straight side chains that are weakly bound through Van-der-Waals interactions. When DL-norleucine undergoes a polymorphic transition, the bilayers shift with respect to each other. In the simulations of the enantiotropically-related beta and alpha polymorph, we observe that the transformed lattice parameters and molecular properties behave identically with temperature for both polymorphs. Consequently, the polymorphs only differ in the orientation of the molecular bilayers in the a'c' and the b'c'-plane, which explains the ease of transitions between them. Moreover, in simulations of the beta polymorph at 350 K we observe partial phase transitions which we could follow with the help of specifically designed order parameters. The transitions are exclusively occurring in the b'c'-plane. This indicates a possible transformation mechanism in which first shifts of bilayers occur in this plane, followed by shifts in the a'c'-plane. Interestingly, the region of highest flexibility of the molecule shifts from the middle to the end of the carbon chain at the highest studied temperature.
Theoretical Prediction of Crystal Polymorphs for Organic Molecules
Authors: Obata Shigeaki , Sato Mitsuaki , Goto Hitoshi
Published: November 2015

Crystal structure prediction is one of the useful theoretical tools for designing and synthesizing new materials in pharmaceutical therapeutics and industrial electronics. Furthermore, the prediction can provide immense valuable scientific knowledge on a crystal growth, polymorphism and many properties of organic molecular crystals. Therefore, we have started the development of high-speed and high-accurate prediction method for organic molecular crystal structures [1,2]. In this work, we demonstrate the theoretical predictions of crystal structures of fourteen target molecules that were used in the international competitions known as CSP blind tests hosted by CCDC [3]. All strategies required for crystal lattice construction expanded to a given effective crystal radius, crystal energy calculation with the reliable molecular force field (MMFF94s) and exhaustive geometry search included a variety of crystal polymorphism are implemented into CONFLEX program [1]. As the results of the applications, we confirmed in all cases of target molecules that, at least, one calculated crystal structure in agreement with the corresponding observed ones can be found. Essential ability required for the prediction method to survive the CSP competitions is that the experimental crystal structure can computationally reproduce within top 3 of most stable structures in crystal energy evaluation. In these tests, only three applications to the target I (Orth. polymorph), II and VIII can successfully satisfy the demand. Details will be discussed in this conference.
Exploring frontiers of crystalline porous materials
Authors: Haranczyk Maciej , Martin Richard
Published: November 2015

We present a computational framework for the rapid identification and characterization of high surface area materials from within the vast chemical space of crystalline porous materials such as metal-organic frameworks (MOFs) or covalent organic frameworks (COFs). MOFs and COFs have been the subject of intense research interest due largely to their highly tunable structural properties and record-breaking internal surface areas; gravimetric surface area is one of the most addressed properties of porous materials, and has seen improvement by approximately a factor of twenty since the first reports. However, the design of MOFs with optimum chemical and geometrical properties remains a great challenge, due to the vast combinatorial space of building blocks and topologies in which they can be arranged. Efforts to identify high-performance materials have involved trial-and-error, observation-based design, computational enumeration and screening of large combinatorial libraries as well as optimization-based approaches. In our presentation, we will give an overview of techniques under development in our group, in particular, algorithms for 3D structure model assembly and material characterization. We will also present how these tools can be employed in both enumeration and optimization-based discovery of novel materials.
Interpreting computed crystal energy landscapes for pharmaceutical molecules
Authors: Price Sarah
Published: November 2015

Crystal Structure Prediction (CSP) algorithms aim to generate the thermodynamically feasible crystal structures of a molecule from the chemical diagram, ranking their relative stability by a necessarily approximate estimate of the crystal energy. Such calculations are becoming feasible for molecules of a size and flexibility of small molecule pharmaceuticals. Contrasting the crystal energy landscape, the computer generated structures that are thermodynamically plausible as polymorphs, with the results of experimental polymorph screening, shows that CSP studies are not limited to being a search for the most thermodynamically stable crystal structure but can play a valuable role in understanding polymorphism and the potential complexity of crystallisation behaviour.[1] This presentation will illustrate the use of CSP as a complement to industrial-type solid form screening activities. Examples will include olanzapine, [2] tazofelone, two closely related 5-HT2a agonists and 6-[(5-chloro-2-([(4-chloro-2-fluorophenyl)methyl]oxy)phenyl)methyl]-2-pyridinecarboxylic acid (GSK269984B).[3] This illustrates the use of the crystal energy landscape to understand disorder, help structurally characterise metastable polymorphs and suggest whether there are additional polymorphs to be targeted. Since crystal energy landscapes usually include a wider range of crystal structures than known polymorphs, it raises the scientific question as to what determines which structures can be observed as metastable polymorphs. Thus both scientific as well as technological challenges need to be overcome before we can predict polymorphs.
Direct Atomic Imaging of Oxide Surfaces
Authors: Yu Rong , Zhan Wei , He Mo-Rigen , Lu Sirong , Zhu Jing
Published: November 2015

Surfaces of metal oxides are of crucial importance for a variety of technological applications such as heterogeneous catalysis, thin film growth, gas sensing, and corrosion prevention [1]. Due to the complexities of oxides in crystal structure and electronic structure, however, the surface science of oxides lags far behind that of metals or semiconductors. Conventional surface-science techniques, typically scanning tunneling microscopy (STM) and low energy electron diffraction (LEED), are usually limited to surfaces of single crystals with relatively simple structures. Metal oxides are usually good insulators, either band insulators or Mott insulators, making them not suitable for STM, LEED, and most of spectroscopic methods using low energy electrons as probes. On the other hand, the complex atomic structures of oxides results in too many structural parameters to be determined by spectroscopy or diffraction methods. Recent developments in high-resolution transmission electron microscopy (TEM) provide us opportunities to overcome the above difficulties. With the realization of aberration-correction, the point resolution of TEM has been improved into the milestone 1 Angstrom scale. In addition, the correction of the spherical aberration has almost eliminated the contrast delocalization in high-resolution images. Therefore, high resolution TEM becomes an even more powerful tool than before for materials research at a truly atomic-scale. Here, we will present our recent works on atomic and electronic structure of oxide surfaces [2-3]. We will show that the structure and dynamics of oxide surfaces can be directly imaged and measured at the sub-angstrom scale with an accuracy of picometers, comparable to that obtained by conventional surface science techniques on single crystals.
TRHEPD rocking curve analyses of Pt/Ge(001) and TiO2(110) surfaces
Authors: Mochizuki Izumi , Fukaya Yuki , Ariga Hiroko , Wada Ken , Hyodo Toshio , Shidara Tetsuo , Maekawa Masaki , Kawasuso Atsuo , Asakura Kiyotaka
Published: November 2015

Recently, we developed new total reflection high-energy positron diffraction (TRHEPD) apparatus [1] on a beam line of the linac-based intense positron beam of the Slow Positron Facility at KEK, Japan. The high intensity allows us to install a brightness-enhancement section, which to observation of clear positron diffraction patterns for crystal surfaces under total reflection condition. In this work, we investigated the atomic configuration of Pt-induced nanowires formed on a Ge(001) surface [2] using the apparatus. By means of the diffraction intensity analysis based on the dynamical diffraction theory, or TRHEPD rocking curve analysis, a previously proposed theoretical model [D. E. P. Vanpoucke et al., Phys. Rev. B 77, 241308(R) (2008)], composed of Ge dimers on the top layer and buried Pt arrays in the second and fourth layers, was confirmed to be the fundamental structure of the nanowire. We also investigated the atomic configuration of a rutile-TiO2(110) surface. It is well known that the structure of this surface transforms its periodicity from (1×1) to (1×2) by elevating the sample temperature above ~1100 K, whereas the detailed structure is yet to be revealed. There is a longstanding controversy between the structure models proposed by scanning tunneling microscopy, low energy electron diffraction, surface X-ray diffraction, first-principles calculation with density functional theory results, etc. To solve the problem, we have measured TRHEPD rocking curves and determined the atomic arrangements of the topmost crystal surface [3].
Surface sensitivity of total reflection high-energy positron diffraction
Authors: Hyodo Toshio , Fukaya Yuki , Mochizuki Izumi , Maekawa Masaki , Wada Ken , Shidara Tetsuo , Ichimiya Ayahiko , Kawasuso Atsuo
Published: November 2015

"Reflection high-energy positron diffraction (RHEPD) is the positron counterpart of reflection high-energy electron diffraction (RHEED). RHEPD was proposed in 1992 [1], and first demonstrated in 1998 [2]. Unlike the case of the electron, the potential energy of the positron inside a crystal is positive, and hence positrons incident on a crystal surface with a glancing angle smaller than a certain critical angle are totally reflected. This feature makes the positrons a tool extremely sensitive to the topmost layer of the crystal surface. Recent development of a brightness-enhanced intense positron beam at KEK [K. Wada, et al., J. Phys.: Conf. Ser. 443, 012082 (2013)] has made it possible to obtain clear RHEPD patterns. We rename the technique with a refined beam as ""total reflection high-energy positron diffraction (TRHEPD)"". Here we demonstrate that the TRHEPD pattern from the Si(111)-7x7 DAS surface taken with a glancing angle smaller than the critical angle for the total reflection is essentially determined only by the atoms exposed on the surface (adatoms and the atoms in the first surface layer) [3]. The technical details of the positron beam preparation [M. Maekawa, et al., to be published in Eur. Phys. J. D (2014)], results on the Pt/Ge(001) nano-wire surface[I. Mochizuki, et al., Phys. Rev. B 85, 245438 (2012)], TiO2(110)-1x2 surface, and silicene on Ag(111) surface [Y. Fukaya, et al., Phys. Rev. B 88 205413 (2013)] are also presented in this conference. "
Advances in Crystallographic Image Processing for Scanning Probe Microscopy
Authors: Moeck Peter , Bilyeu Taylor , Mainzer Koenig Axel , Straton Jack
Published: November 2015

Crystallographic image processing (CIP) is well established in the electron microscopy community, where it is used for the analysis and enhancement of high-resolution transmission electron microscope images of crystals and two-dimensional (2D) arrays of membrane proteins. The technique has recently been adapted to the processing of 2D periodic images from scanning probe microscopes (SPMs) [1]. Within this context, a procedure for the unambiguous identification of the underlying Bravais lattice of an experimental or theoretical image of a 2D periodic array of objects (e.g. molecules or atoms and their respective electron density distribution functions, ...) has been developed [2]. This procedure constitutes a partial solution to a longstanding but unresolved issue in CIP. The unresolved issue itself is the complete quantification of the deviations of 2D periodic images from the plane symmetry groups. A complete solution to this problem will allow for unambiguous decisions as to which plane symmetry best models experimental data when all systematic errors in the acquiring and processing of the image data have been accounted for at a level that systematic rest errors are negligible. Our 2D Bravais lattice identification procedure is independent of which type of microscope has been utilized for the recording of the images. It is based on classification procedures for non-disjoint models from the robotics community and is particularly useful for the correction of scanning tunneling microscope (STM) images that suffer from a blunt scanning probe tip artifact [2]. With the crystallographic processing of two molecular resolution STM images of periodic arrays of tetraphenoxyphthalocyanine on graphite, it is demonstrated how the classical CIP plane symmetry estimation procedures are augmented by our unambiguous translation symmetry identification method. We also apply CIP to an artificial SPM image that features a blunt scanning probe tip artifact, see the figure below.
Structure determination of two-dimensional atomic sheet of silicene using TRHEPD
Authors: Fukaya Yuki , Mochizuki Izumi , Maekawa Masaki , Wada Ken , Hyodo Toshio , Matsuda Iwao , Kawasuso Atsuo
Published: November 2015

This study reports determination of the atomic coordinates of a two-dimensional atomic sheet, silicene, by using total reflection high-energy positron diffraction (TRHEPD) [1]. TRHEPD method, formerly called as RHEPD, is a surface-sensitive tool owing to the total reflection of positrons. Since the sign of the potential energy for positrons in crystals is positive, opposite to that for the electrons, the positron beam at a grazing incidence are totally reflected at a crystal surface. The penetration depth of the positron beam in the total reflection region is estimated to be approximately a few Å, which corresponds to the thickness of 1-2 atomic layers. Thus, the positron beam selectively sees the topmost surface layer and hence the TRHEPD method is very useful for structure determinations of crystal surface and two-dimensional atomic sheet on the substrate. Silicene is a two-dimensional atomic sheet of silicon. Since the silicene has an intriguing property such as a Dirac cone like a graphene, it attracts increasing attention as a candidate for future devices. Recently, the synthesis of silicene on a Ag(111) surface was successfully performed [2]. Although the atomic coordinates of the silicene in this system was theoretically calculated, they were not confirmed experimentally. It is very important to experimentally determine the magnitude of the buckling in silicene and the spacing between the bottom of the silicene and the substrate because the dispersion of the Dirac cone is closely related to these structure parameters. We thus investigated the atomic positions of the silicene on the Ag(111) surface using the TRHEPD [3]. From the rocking curve analysis based on the dynamical diffraction theory of positrons (see figure), the existence of the buckling (0.83 Å) in silicene was verified experimentally. Moreover, the spacing between the silicene and the substrate was determined as 2.17 Å. The structural difference with the graphene will be also discussed.
Conformational changes in human Norovirus polymerase
Authors: Ng Kenneth , Zamyatkin Dmitry , Rho Hayeong , Hoffarth Elesha , Jurca Gabriela , Cottle Andrew , Lang Dean , Sohal Vinay , Savtchouk Julia , Parra Francisco
Published: November 2015

Human Noroviruses (NV) belong in the Caliciviridae family and are a major cause of gastroenteritis outbreaks throughout the world. Crystal structures of the RNA-dependent RNA polymerase from the human Norovirus have been determined in over ten different crystal forms in the presence and absence of divalent metal cations, nucleoside triphosphates, inhibitors and primer-template duplex RNA. These structures show how the polymerase enzyme can adopt a range of conformations in which the thumb, fingers and palm domains change orientations depending on the step of the enzymatic cycle trapped in different crystal forms. We discuss how the evidence from crystallographic and biochemical experiments combine to better understand how viral RNA polymerase enzymes from human Norovirus and related positive-strand RNA viruses can adopt a range of conformational states to facilitate RNA binding, NTP binding, catalysis, RNA translocation and pyrophosphate release. The detailed structural and mechanistic understanding of these conformational changes is important for providing a sound basis for understanding viral replication in general, as well as for the design of novel inhibitors capable of trapping the enzyme in specific conformational states.
The crystal structure of the C-terminal domain of the Ebola virus nucleoprotein
Authors: Derewenda Zygmunt , Dziubanska Paulina , Derewenda Urszula , Ellena Jeffrey , Haley Krystal , Engel Daniel
Published: November 2015

Ebola virus (EBOV) and Marburg virus are members of the family Filoviridae. Both are highly pathogenic and cause hemorrhagic fever, lethal in 90% of infected people. There is fear that the viruses can be used as bioterrorism agents. There are no approved vaccines, and intense effort is underway to discover drugs targeting these viruses. The EBOV genome encodes seven proteins, two of which have no known structures: RNA polymerase (L) and nucleoprotein (NP). NP is essential for packaging viral genomic RNA into the nucleocapsid. Other viruses also contain nucleoproteins, but only the Ebola and Marburg NP proteins contain two distinct domains. The C-terminal domain (Ct; ~100 residues) has no homologues; it acts as a hub for protein-protein interactions important for the assembly of the nucleocapsid and for the interaction with the VP40 matrix protein, embedded in the viral membrane. We obtained three distinct crystal forms of the Ct domain of NP from EBOV, and solved the structures using anomalous scattering from Se, and Molecular Replacement. High-quality NMR data were also collected. The models were refined at 1.6-2.0 Å resolution to R factors ~20%. The protein has a novel fold, with topology distantly related to the β-grasp fold. In spite of its small size, the Ct domain shows high melting temperature of ~60°C. Our efforts focus on the identification of how the C-terminal domain of NP binds to its partners. As part of an effort towards anti-filovirus drug discovery, proteins NP, VP24, VP35 and VP40 are being targeted for small molecule inhibition using a yeast-based phenotypic assay. Each protein, when expressed in budding yeast, produces a slow-growth phenotype. Chemical suppressors of the slow-growth phenotype will be identified and used in viral growth assays to confirm their antiviral activity. The structure of NP will be used to complement small molecule screening methods.
The C. Elegans fusion protein EFF-1 is homologous to viral class II proteins
Authors: Rey Félix
Published: November 2015

Class II proteins are viral membrane fusogenic molecules folded essentially as β-sheet and having an internal fusion peptide. In particular, they lack the characteristic central alpha-helical coiled coil present in the post-fusion conformation of all other viral fusion proteins. The regular, icosahedrally symmetric enveloped viruses that have been studied so far, such as flaviviruses, alphaviruses and phleboviruses have been shown to have class II fusion proteins, which in their pre-fusion conformation make an icosahedral shell surrounding the viral membrane. Yet despite having very similar envelope proteins, these viruses belong to three different viral families with totally different genome replication machineries. We have recently identified the rubella virus fusion a belonging to class II, although the virus particles appear pleomorphic and lack icosahedral symmetry. In spite of the lack of any detectable sequence conservation, the available structures indicate that class II proteins have undergone divergent evolution from a distal, ancestral gene. We have now discovered that the cellular fusion protein EFF-1, involved in syncytium formation during the genesis of the skin in nematodes (C. elegans) and in other multicellular organisms, is also folded as a class II viral fusion protein, thereby indicating common ancestry, highlighting an unprecedented amount of exchange of genetic information between viruses and cells. My talk will discuss the implications of this finding, which highlights the intricate exchange of genetic information that has taken place between viruses and cells during evolution. This analysis also suggests a mechanism for the homotypic cell-cell fusion process, which has not been studied so far.
Histone mimicry and hijacking of host proteins by influenza virus protein NS1
Authors: Qin Su , Liu Yanli , Tempel Wolfram , Eram Mohammad , Bian Chuanbing , Liu Ke , Senisterra Guillermo , Crombet Lissete , Vedadi Masoud
Published: November 2015

Pathogens can interfere with vital biological processes of their host by mimicking host proteins. The NS1 protein of the influenza A H3N2 subtype possesses a histone H3K4-like sequence at its carboxyl terminus and has been reported to use this mimic to hijack host proteins. However, this mimic lacks a free N-terminus that is essential for binding to many known H3K4 readers. Here we show that the double chromodomains of CHD1adopt an 'open pocket' to interact with the free N-terminal amine of H3K4, and the open pocket permits the NS1 mimic to bind in a distinct conformation. We also explored the possibility that NS1 hijacks other cellular proteins and found that the NS1 mimic has access to only a subset of chromatin-associated factors, such as WDR5. Moreover, methylation of the NS1 mimic can not be reversed by the H3K4 demethylase LSD1. Overall, we thus conclude that the NS1 mimic is an imperfect histone mimic.
Structure study of UHRF1, recoginition of epigenetic marks.
Authors: Arita Kyohei , Ariyoshi Mariko , Sugita Kazuya , Tochio Hidehito , Shirakawa Masahiro
Published: November 2015

Two major epigenetic traits, histone modifications and DNA methylation, regulate various chromatin-template processes in mammals. The pattern of these epigenetic traits is cooperatively established in early embryogenesis and cell development, and inherited during the cell cycle. UHRF1 (also known as Np95 or ICBP90) is believed to play an important role in linking the two major epigenetic traits. UHRF1 has five functional domains, UBL, Tandem Tudor (TTD), pland homeo domain (PHD), SET and RING-associated doain (SRA) and RING finger. To maintain DNA methylation pattern, UHRF1 recognizes hemi-methylated DNA generated during DNA replication through interactions with its SRA domain, and recruit maintenance of DNA methyltransferase Dnmt1 to the site [1], [2]. UHRF1 also recognizes histone H3 containing tri-methylated Lys9 (H3K9me3) via its TTD-PHD moiety. [3]. To obtain the structural basis for recognition of epigenetic marks by UHRF1, we determined the crystal structure of the SRA domain in complex with hemi-methylated DNA. The structure showed that the DNA binding caused a loop and an N-terminal tail of the SRA domain. Interestingly, the methyl-cytosine base at the hemi-methylation site was flipped out from the DNA helix, which has not observed in other DNA binding proteins. These results suggest that the Base flip out mechanism is important event for maintenance of DNA methylation. We also determined the crystal structure of TTD-PHD region of UHRF1 in complex with H3K9me3 peptide. To our surprise, the linker region between the reader modules, which is predicted as an intrinsically disorder, was formed a stable structure with binding to the groove of TTD and plays an essential role in the formation of histone H3 binding hole between the reader modules. The structure revealed how multiple histone modifications were simultaneously decoded by the linked histone reader modules of UHRF1.
Structure of the Human Telomeric Stn1-Ten1 Complex
Authors: Bryan Christopher , Rice Cory , Harkisheimer Michael , Schultz David , Skordalakes Emmanuel
Published: November 2015

The telomeric CST complex plays a central role in chromosome end capping and replication in budding yeast, and homologues of CST were identified recently in higher eukaryotes. The human CST (Ctc1, hStn1, hTen1) has been shown to play a role in telomere maintenance, but the extent of conservation across species has been in question because of low sequence identity (below 10% for Ctc1, the core subunit of the CST complex) and data suggesting subtle differences in function between complexes. We solved the high-resolution crystal structure of the human Stn1-Ten1 complex, which revealed striking structural similarity between the yeast and human CST complexes. We also showed using southern blots and fluorescence in situ hybridization experiments that disruption of the hStn1-Ten1 binding interface in vivo produces elongated telomeres and telomere defects in accordance with what has been previously observed for the yeast CST complex. Our results support structural and functional conservation of telomeric CST across species.
Structural Profiles of Nanocrystals from ASAXS and Crystallographic Techniques
Authors: Lechner Rainer , Fritz-Popovski Gerhard , Yarema Maksym , Heiss Wolfgang , Hoell Armin , Schuelli Tobias , Paris Oskar
Published: November 2015

The chemical synthesis of core/shell colloidal nanocrystals (NCs) have lead to an pronounced improvement in the optical properties and the chemical stability of semiconducting NCs [1]. The main topic of this work is the structural characterisation of core/shell NCs with anomalous small angle x-ray scattering (ASAXS) in combination with diffraction techniques (XRD) at laboratory- and synchrotron sources (HZB-BESSY and ESRF). Furthermore we complete these findings with complementary microscopy techniques (TEM). The detailed knowledge of the structural properties of the core/shell NCs allows to study the impact of the nanometer sized dimensions on their optical properties. The infrared emission of lead chalcogenide nanocrystals (NCs) in the size range of 5 - 10 nm can be drastically increased stabilising the core with a hard protective shell [1,2]., e.g., PbS/CdS NCs shows a higher efficiency and stability [2] with respect to pure PbS-NCs. In contrast to a shell growth on top of a core, we investigated in this study the CdS-shell growth on PbS NCs driven by Cd for Pb cation exchange [2]. Especially, we studied three different final shell thicknesses of 0.9, 1.5 and 2 nm. The chemical composition profile of the CdS-shell as a function of reaction time are derived from ASAXS experiments in sub-nanomter resolution. The crystal structure of the shell was derived by XRD combined with TEM measurements, respectively. We relate the chemical and structural information to the measured PL intensities of the core/shell NCs. We reveal the existence of two different crystalline phases, i.e. the metastable rock salt and the equilibrium zinc blende phase within the chemically pure CdS-shell. The highest improvement in the PL emission was achieved for 0.9 nm shells depicting a large metastable rock salt phase fraction matching the crystal structure of the PbS core. These results could be only achieved using ASAXS that gieves a mean chemical profile of a large ensemble of single core/shell NCs, but in sub-nanometer resolution [3].