SpectroscopyInternational Union of CrystaSerial femtosecond crystallographyCryo-electron mMass spectrometryElectron microscopyMacromolecular crystallographyProteinMolecularFluorescenceComputationalBiochemistryDiffraction techniquesDerivativesBiomoleculesExperimentalStructural BiologyCalculationsStructuresNeutronLaboratoryRefinementMicroscopyBiology1.35Lund UniversityAtomicRissanenChemistrySynchrotronTime-resolvedAnalysesRestraintsCompoundsBespokeStructureInsightsProcessesFragmentRevealsMacromoleculesTechniquesSynthesisConformationalVersatilityBeamlineWorkHigh-resolutionDataJournal
Spectroscopy8
- While in quantum chemistry, the experimental works mainly rely on spectroscopy, in quantum crystallography the scattering techniques (X-rays, neutrons, γ-Rays, electrons) play the central role, although spectroscopy as well as atomic microscopy are also sources of information. (wikipedia.org)
- Basic principles of modern biophysical and structural methods used to interrogate macromolecules from the atomic to cellular levels, including light and electron microscopy, X-ray crystallography, NMR spectroscopy, single molecule techniques, circular dichroism, surface plasmon resonance, mass spectrometry, and molecular dynamics and systems biological simulations. (caltech.edu)
- The building includes a microscopy suite and optical spectroscopy, nuclear magnetic resonance spectroscopy and X-ray crystallography laboratories. (rutgers.edu)
- Each complex was purified and subsequently analyzed by 11 B and 13 C NMR spectroscopy, X-ray crystallography, UV-vis spectroscopy, elemental analysis, and voltammetry. (rsc.org)
- From your routine day-to-day analytical needs such as mass spectrometry, NMR and elemental analysis to more bespoke offerings such as X-ray photon spectroscopy, Circular dichromism and X-ray crystallography, we can help. (nottingham.ac.uk)
- A particular focus is laid on the structural and kinetic characterization of enzymatic reaction intermediates by high-resolution X-ray crystallography, steady-state and transient kinetic methods, NMR spectroscopy and theoretical studies. (uni-goettingen.de)
- The first symposium, which is the kick-off event for the new LINXS theme, will focus on advanced, cutting-edge research in the fields of macromolecular crystallography, Cryo-EM, small angle scattering, electron diffraction, mass-spectroscopy, NMR, and use of XFELs etc. (lu.se)
- Students joining our group will build expertise in X-ray crystallography and multinuclear NMR spectroscopy, as well as IR and UV-vis spectroscopies. (lu.se)
International Union of Crysta3
- The International Union of Crystallography has recently established a commission on Quantum Crystallography, as extension of the previous commission on Charge, Spin and Momentum density, with the purpose of coordinating research activities in this field. (wikipedia.org)
- The Erice School of crystallography (52nd course): first course on Quantum crystallography (June 2018) The XIX Sagamore Conference (July 2018) The CECAM meeting on Quantum crystallography (June 2017) The IUCr commission on Quantum crystallography The International Union of Crystallography Macchi, Piero (2020). (wikipedia.org)
- International Union of Crystallography. (wikipedia.org)
Serial femtosecond crystallography2
- Time-resolved serial femtosecond crystallography (SFX) can potentially shine light on these conformational changes. (jyu.fi)
- Of these, 26 groups were selected by an international panel of experts to carry out their research at the two instruments-the SPB/SFX instrument (Single Particles, Clusters and Biomolecules / Serial Femtosecond Crystallography) and the FXE instrument (Femtosecond X-Ray Experiments). (lightsources.org)
Cryo-electron m2
- The work in the Gouaux Lab is concentrated on developing molecular mechanisms for the function of receptors and transporters at chemical synapses by utilizing cryo-electron microscopy, x-ray crystallography, and electrophysiology. (ohsu.edu)
- We employ a multidisciplinary approach including kinase biochemistry and biology, structural biology (X-ray crystallography and cryo-electron microscopy), assay development, high-throughput screening, proteomics, imaging and chemical biology to gain high-resolution insights into kinase/pseudokinase signaling proteins. (edu.au)
Mass spectrometry3
- Mass spectrometry combined with X-ray crystallography allows the characterization of cap protein interactions. (biosyn.com)
- Using mass spectrometry in combination with X-ray crystallography, Wang et al. (biosyn.com)
- We primarily use X-ray crystallography but also work with biochemistry, microbiology, mass spectrometry and electron microscopy. (caltech.edu)
Electron microscopy2
- however, they are increasingly merging these methods with other experimental tools such as small-angle X-ray scattering, single-molecule approaches, and electron microscopy. (hopkinsmedicine.org)
- Different methods can be used to analyze the effects of cariogenic challenge on dentin-resin interfaces, such as scanning electron microscopy (SEM), polarized light microscopy, microhardness analysis, microradiography, confocal laser scanning microscopy and X-ray analytical microscopy 2-5 . (bvsalud.org)
Macromolecular crystallography1
- With the rapid progress and improvements in the fields of macromolecular crystallography, Cryo-EM, small angle scattering, electron diffraction and use of XFELs, the new LINXS theme INTEGRATIVE STRUCTURAL BIOLOGY is formed to advance cutting-edge research and to encourage new users to utilize integrative structure biology to address key scientific questions. (lu.se)
Protein10
- We wondered if these difficulties could be overcome by focussing on the antibody combining site (i.e. the part of antibody interacting with antigen) to guide the derivation of chemical compounds that would be surrogates of the antibody, because the combining site is the part relevant to the protein-protein interaction between antibody and antigen. (cancer.gov)
- The corollary is that the specific interaction interface between the antibody fragment with target protein would be mimicked by the chemical compound surrogates. (cancer.gov)
- In research published today (August 20) scientists in Chile and Canada identify the substance in spontaneous ovulators: nerve growth factor beta (NGF-beta)-a neurotrophic protein involved in nerve development, which has the same chemical structure as OIF. (the-scientist.com)
- In order to identify the chemical structure of OIF, Addams and Ratto collaborated with protein chemist Louis Delbaere at the University of Saskatchewan. (the-scientist.com)
- Our most popular diffractometer for Protein Crystallography , configured with a high-flux rotating anode X-ray source and an extremely low noise direct X-ray detection detector. (rigaku.com)
- Spectacular performance combined with dual wavelength versatility, provides the perfect answer for high-capacity Chemical Crystallography labs or for X-ray facilities that support Chemical Crystallography and Protein Crystallography . (rigaku.com)
- User-inspired data collection and data processing software for small molecule and protein crystallography. (rigaku.com)
- Facilities include those for protein-sequence analysis, peptide and oligonucleotide synthesis, access to the synchrotron at Lawrence Berkeley National Lab for X-ray crystallography, and NMR spectrometry. (berkeley.edu)
- In a first couple of examples, I will show how distance and shape restraints from SANS have helped to improve the uniqueness of structural models for two multi-protein-RNA complexes, in combination with NMR restraints and building blocks from crystallography [1, 2]. (lu.se)
- The most common strong alternative and complement to experimental methods to methods to obtain protein structures are X-ray crystallography obtain insight in biochemical processes. (lu.se)
Molecular8
- The theoretical part of quantum crystallography is based on quantum mechanical calculations of atomic/molecular/crystal wave functions, density matrices or density models, used to simulate the electronic structure of a crystalline material. (wikipedia.org)
- In the first term, topics will include the structure and chemical properties of biological macromolecules, molecular biology methods, and biological catalysis. (caltech.edu)
- Members of the institute have published in a wide range of peer-reviewed journals, including Nature, Molecular Cell, Angewandte Chemie, JACS, Science Advances, Proceedings of the National Academy of Sciences USA, Nucleic Acids Research, Chemical Science and many others. (le.ac.uk)
- Most calculations on large chemical and/or biological molecules use classical molecular dynamics up to now. (cecam.org)
- The central research topic of our department is the analysis of molecular reaction mechanisms of enzymes as nature's chemical catalysts. (uni-goettingen.de)
- This chemist and X-ray crystallographer's work is integral to the study of molecular structures of DNA, RNA, coal and graphite. (hindustantimes.com)
- Applications of quantum chemical calculations to investigations of molecular and materials properties, as well as development and applications of classical reaction dynamics simulations. (lu.se)
- The use of molecular mechanics calculations to supplement experimental data in standard X-ray crystallography and NMR refinements is discussed and it is shown that structures can be locally improved by the use of quantum chemical calculations. (lu.se)
Fluorescence2
- X-ray diffraction (XRD) and X-ray fluorescence (XRF) are established analytical methods in drug discovery and production quality control. (rigaku.com)
- They used synchrotron X-ray fluorescence microscopy (XFM) to probe the cellular uptake and distribution of TRIP and an iodo-derivative I-TRIP by looking at elemental signals. (rsc.org)
Computational2
- Like the quantum chemistry, Quantum crystallography involves both experimental and computational work. (wikipedia.org)
- I used computational modelling, X-ray crystallography and data analysis to design molecules that might become new medicines. (abpi.org.uk)
Biochemistry1
- Ulf Ryde was born in 1963 and obtained a PhD in biochemistry methods and their possible combination with quantum chemical (enzyme kinetics and control theory) at Lund University, Sweden, methods, including a number of typical applications. (lu.se)
Diffraction techniques2
- The connection between crystallography and quantum chemistry has always been very tight, after X-ray diffraction techniques became available in crystallography. (wikipedia.org)
- Many aspects of discovery, design, development and formulation processes require structural information acquired by X-ray diffraction techniques. (rigaku.com)
Derivatives2
- X-ray crystallography of two derivatives was performed. (springer.com)
- Okada, K. Detailed Differential Coefficients of Anomalous Dispersion Terms to Derivatives in Least-Squares Refinement for X-ray Crystallography. (ccp14.ac.uk)
Biomolecules2
- Chemical and biochemical techniques used to purify and determine the structures of biomolecules. (bath.ac.uk)
- X-ray crystallography of biomolecules. (bath.ac.uk)
Experimental2
- The book Modern Charge Density Analysis offers a survey of the research involving Quantum Crystallography and of the most adopted experimental or theoretical methodologies. (wikipedia.org)
- Recent technological breakthroughs, such as ultra-fast pulsed lasers, high-performance computing and crystallography of macromolecules, helped to improve the experimental tools of physicists, biologists, and chemists working, in particular, in the area of chemical and biological physics. (cecam.org)
Structural Biology3
- He is the director of the Institute for Basic Biomedical Sciences, professor of biophysics and biophysical chemistry at the Johns Hopkins University School of Medicine and co-director of the Cancer Chemical and Structural Biology Program for the Johns Hopkins Kimmel Cancer Center. (hopkinsmedicine.org)
- Faculty of this division also participate in interdepartmental programs in structural biology, chemical biology, microbiology and toxicology. (berkeley.edu)
- Dr Ivo Tews , Associate Professor in Structural Biology at the University of Southampton, said: "Our approach was to analyse the structure of the antibody in atomic detail, using the method of X-ray crystallography. (southampton.ac.uk)
Calculations3
- The term Quantum Crystallography was first introduced in revisitation articles by L. Huang, L. Massa and Nobel Prize winner Jerome Karle, who associated it with two mainstreams: a) crystallographic information that enhances quantum mechanical calculations and b) quantum mechanical approaches to improve crystallography information. (wikipedia.org)
- Quantum-chemical calculations show that the Zn 12 cluster has a metalloid character, with four-center bonding connecting the Zn atoms. (chemistryviews.org)
- improved by using quantum chemical calculations. (lu.se)
Structures4
- Furthermore, we evaluate the ability of different fits to reproduce the amplitudes of internal fluctuations in X-ray ensembles from the B-factors in the corresponding single X-ray structures. (nih.gov)
- Figure 1: Chemical structures of mRNA Cap0, Cap1, and Cap2. (biosyn.com)
- Observing alternative conformations at low levels of electron density, in addition to comparison of independently determined X-ray crystal structures, can provide mechanistic insights into conformational dynamics. (rcsb.org)
- Full borane coordination for all species was confirmed by analysis of X-ray crystallographic data (see ESI † ), with representative structures depicted in Fig. 1 . (rsc.org)
Neutron5
- Parallel to studies on wave function determination, R. F. Stewart and P. Coppens investigated the possibilities to compute models for one-electron charge density from X-ray scattering (for example by means of pseudoatoms multipolar expansion), and later of spin density from polarized neutron diffraction, that originated the scientific community of charge, spin and momentum density. (wikipedia.org)
- A team has used neutron crystallography to image all of the atoms in a radical intermediate of a copper amine oxidase enzyme. (sciencedaily.com)
- Now, in a study recently published in ACS Catalysis , a team led by researchers at Osaka Medical and Pharmaceutical University and Osaka University has used neutron crystallography to image the atom-by-atom structure of a copper amine oxidase enzyme. (sciencedaily.com)
- Neutron crystallography, which analyzes diffraction from atomic nuclei in the enzyme (all atoms have an atomic nucleus), is an alternative imaging technique that the researchers chose for their work. (sciencedaily.com)
- Neutron crystallography is well-suited for answering these questions. (sciencedaily.com)
Laboratory6
- The new home for the Department of Chemistry and Chemical Biology at Rutgers University-New Brunswick , which provides expanded teaching, laboratory and support space, is open for classes and research. (rutgers.edu)
- 10 years into my role, 40 to 50% of my time was spent in the laboratory synthesising chemical compounds. (abpi.org.uk)
- As a medicinal chemist, I started my career working predominantly in the laboratory, synthesising intermediates and novel chemical compounds. (abpi.org.uk)
- He was the head of the Laboratory of X-ray Structure Analysis and Organic Crystal Chemistry. (iucr.org)
- From 1947 to 1950, she worked with Jacques Mering at the State Chemical Laboratory in Paris, studying X-ray diffraction technology. (hindustantimes.com)
- From 1953 to 1958, she worked in the Crystallography Laboratory at Birkbeck College, London. (hindustantimes.com)
Refinement1
- Here, I present results from different biological projects where SANS has played a crucial role by providing unique restraints for structural refinement and interpretation, complementary to other techniques (NMR, EM, crystallography). (lu.se)
Microscopy1
- The PDB contains models elucidated using three different methods: nuclear magnetic resonance (NMR), X-ray crystallography and electron cryo-microscopy (cryo-EM). (iucr.org)
Biology4
- Peter March, executive dean of the School of Arts and Sciences, speaks at the ribbon cutting ceremony for the new 144,000-square-foot Chemistry and Chemical Biology building. (rutgers.edu)
- Interim Chancellor Molloy said, "Rutgers' chemistry and chemical biology research is discovering new ways to improve lives, from clean energy solutions, to potential new treatments for cancer and HIV, to high-speed computing. (rutgers.edu)
- The Department of Chemistry and Chemical Biology educates thousands of undergraduates and graduate students, and produces research that benefits health, energy, and the environment," said School of Arts and Sciences Executive Dean Peter March. (rutgers.edu)
- Graduate student Tariq Bhatti leads visitors on a tour in the new Chemistry and Chemical Biology building. (rutgers.edu)
1.351
- Here we report the room temperature crystal structure of the chromophorebinding domains of the Deinococcus radiodurans phytochrome at 2.1Å resolution.The structure was obtained by serial femtosecond X-ray crystallography from microcrystals at an X-ray free electron laser.We find overall good agreement compared to a crystal structure at 1.35Å resolution derived from conventional crystallography at cryogenic temperatures, which we also report here. (jyu.fi)
Lund University1
Atomic2
- Often atomic-level details are known from experiments in chemical and biological physics these days. (cecam.org)
- They are developing atomic-level models that explain how chemical energy is transduced into force and motion, and how dynamic assemblies control DNA replication, gene expression, chromosome superstructure, and other essential nucleic-acid transactions. (hopkinsmedicine.org)
Rissanen1
- Advanced X-Ray Crystallography: The New Frontiers (K. Rissanen, ed. (nyu.edu)
Chemistry4
- Electron density and bonding in crystals: Principles, theory and X-ray diffraction experiments in solid state physics and chemistry. (wikipedia.org)
- This work might help researchers engineer enzymes that facilitate unusual chemistry or are highly efficient at room temperature that are useful in chemical industry. (sciencedaily.com)
- ab a Beckman Institute, Division of Chemistry and Chemical Engineering, California Institute of Technology, 1200 East California Boulevard, Mail Code 139-74, Pasadena, California 91125, USA. (rsc.org)
- Nottingham Research Chemicals aims to identify, promote and sell the novel compounds that resulted from unique and high quality synthetic chemistry research in the School of Chemistry. (nottingham.ac.uk)
Synchrotron1
- In addition to work in the lab, we do a lot of research at synchrotron radiation facilities performing state-of-the-art X-ray scattering techniques. (concordia.ca)
Time-resolved1
- Here we follow the course of phosphodiester bond formation using time-resolved X-ray crystallography. (proteopedia.org)
Analyses1
- X-ray crystallographic, biochemical and in vivo analyses confirm its orthogonality. (nature.com)
Restraints1
- A library of chemical restraints is typically used to ensure consistency between the model and the prior knowledge of stereochemistry. (iucr.org)
Compounds5
- This seemed much larger than would be expected for the range of space occupied by drug-like chemical compounds, estimated at 300 to 1000 Å2 [4, 5]. (cancer.gov)
- Thus, our Abd technology identified a hit chemical series interacting with a pocket [10, 11] near the effector binding region in RAS (activated pan-RAS binding compounds) [9]. (cancer.gov)
- Using X-ray crystallography soaking of KRASQ61H crystals by compounds, we implemented a structure-based compound development programme [9, 12]. (cancer.gov)
- First that RAS is indeed druggable (as many labs have now shown, in particular KRASG12C binding compounds [13-15]) and that antibodies could indeed be used to guide the isolation of chemical matter with our Abd technology. (cancer.gov)
- A focused NMR-based search for heterocyclic isothiourea isosteres resulted in several distinct classes of BACE-1 active site directed compounds with improved chemical stability and physicochemical properties. (rcsb.org)
Bespoke1
- A bespoke, extremely high-flux diffractometer with custom enclosure and the flexibility to utilize both ports of the rotating anode X-ray source. (rigaku.com)
Structure10
- The structure of complex 3 was confirmed by X-ray crystallography. (ias.ac.in)
- Researchers commonly obtain the atom-by-atom structure of enzymes by X-ray crystallography. (sciencedaily.com)
- The structure of the cluster anion was studied using X-ray crystallography. (chemistryviews.org)
- Fragment-based NMR screening, X-ray crystallography, structure-based design, and focused chemical library design were used to identify novel inhibitors for BACE-1. (rcsb.org)
- The X-ray crystal structure (1.6 A resolution) of the complex of the inhibitor and ODCase clearly shows the covalent bond formation with the active site Lys-72 [corrected] residue. (nih.gov)
- When she took up research at King's College, very little was known about the chemical makeup or structure of DNA. (hindustantimes.com)
- Her work to make clearer X-ray patterns of DNA molecules and laid the foundation for James Watson and Francis Crick to suggest in 1953 that the structure of DNA is a double-helix polymer, a spiral consisting of two DNA strands wound around each other. (hindustantimes.com)
- The experiments range from method development to biomolecule structure determination and studies of extremely fast processes in small molecules and chemical reactions. (lightsources.org)
- metal site is extended X-ray absorption fine structure (EXAFS). (lu.se)
- The aim of the course is that the students should achieve advanced knowledge and understanding of chemical reactions in the cell with focusing on the structure and function of proteins, enzyme catalysis and the total metabolism of the cell. (lu.se)
Insights2
- X-ray crystallography misses such insights. (sciencedaily.com)
- In the future, researchers might apply these insights to designing artificial enzymes that function used in the chemical industry. (sciencedaily.com)
Processes3
- Photosynthesis, i.e. the conversion of sun light into stored chemical energy by plants and other organisms, is one of the most important global biological processes. (stanford.edu)
- But many fundamental biological processes that involve, for example, the conversion of light into energy forms that are usable for chemical transformations are quantum mechanical in their nature. (cecam.org)
- The ultimate aim is to understand biological systems and processes in terms of the underlying physical and chemical laws. (lu.se)
Fragment1
- By fragment screening using x-ray crystallography we identified four ligands revealing ligand-binding sites in conserved interfaces between SARS-CoV-2 nsp10 and nsp14/nsp16. (lu.se)
Reveals1
- Lüdtke S, Neumann P, Erixon KM, Leeper F, Kluger R, Ficner R, Tittmann K (2013) Sub-Angström resolution crystallography reveals physical distortions that enhance reactivity of a covalent enzymatic intermediate. (uni-goettingen.de)
Macromolecules1
- For example, in biological physics these details are mainly obtained by x-ray crystallography of a crystallized version of the macromolecules. (cecam.org)
Techniques1
- This powerful instrument offers a wide range of complementary techniques providing structural, chemical and magnetic sensitivities with a single-digit nanometre spatial resolution. (lu.se)
Synthesis2
- DNA synthesis has been extensively studied, but the chemical reaction itself has not been visualized. (proteopedia.org)
- Projects in our group involve chemical synthesis and discovery of new reaction types, complemented by spectroscopic and mechanistic investigations. (lu.se)
Conformational1
- There are pH-dependence, conformational change, and radical intermediate stabilization questions of our enzyme that X-ray crystallography in itself cannot fully explain," explains Takeshi Murakawa, lead author of the study. (sciencedaily.com)
Versatility1
- Meyer D, Neumann P, Koers E, Sjuts H, Lüdtke S, Sheldrick, GM, Ficner R, Tittmann K (2012) Unexpected tautomeric equilibria of the carbanion-enamine intermediate in pyruvate oxidase highlight unrecognized chemical versatility of the thiamin cofactor. (uni-goettingen.de)
Beamline1
Work1
- The chemical compound series that was developed in this work is a pan-RAS series binding to all the RAS isoforms [12] because the binding pocket is found in KRAS, HRAS and NRAS. (cancer.gov)
High-resolution1
- Here we report a new algorithm, CONTACT, that identifies contact networks of conformationally heterogeneous residues directly from high-resolution X-ray crystallography data. (rcsb.org)
Data1
- We then used mathematical models and a chemical-computing approach to analyse the data, using the Southampton High Performance Computing cluster IRIDIS. (southampton.ac.uk)
Journal4
- Journal of the American Chemical Society (2012) 134 , 16452-16455. (nyu.edu)
- Journal of the American Chemical Society (2011) 133 , 16358-16361. (nyu.edu)
- Journal of the American Chemical Society (2010) 132 , 14191-14202. (nyu.edu)
- Journal of the American Chemical Society (2010) 132 , 11566-11579. (nyu.edu)