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NMR Molecular Replacement Provides New Insights into Binding Modes to Bromodomains of BRD4 and TRIM24. J Med Chem 2022; 65:5565-5574. [PMID: 35357834 PMCID: PMC9017284 DOI: 10.1021/acs.jmedchem.1c01703] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Structure-based drug discovery (SBDD) largely relies on structural information from X-ray crystallography because traditional NMR structure calculation methods are too time consuming to be aligned with typical drug discovery timelines. The recently developed NMR molecular replacement (NMR2) method dramatically reduces the time needed to generate ligand-protein complex structures using published structures (apo or holo) of the target protein and treating all observed NOEs as ambiguous restraints, bypassing the laborious process of obtaining sequence-specific resonance assignments for the protein target. We apply this method to two therapeutic targets, the bromodomain of TRIM24 and the second bromodomain of BRD4. We show that the NMR2 methodology can guide SBDD by rationalizing the observed SAR. We also demonstrate that new types of restraints and selective methyl labeling have the potential to dramatically reduce "time to structure" and extend the method to targets beyond the reach of traditional NMR structure elucidation.
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NMR Reporter Assays for the Quantification of Weak-Affinity Receptor-Ligand Interactions. SLAS DISCOVERY : ADVANCING LIFE SCIENCES R & D 2021; 26:1020-1028. [PMID: 33899548 DOI: 10.1177/24725552211009782] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
Biophysical methods are widely employed in academia and the pharmaceutical industry to detect and quantify weak molecular interactions. Such methods find broad application in fragment-based drug discovery (FBDD). In an FBDD campaign, a suitable affinity determination method is key to advancing a project beyond the initial screening phase. Protein-observed (PO) nuclear magnetic resonance (NMR) finds widespread use due to its ability to sensitively detect very weak interactions at residue-level resolution. When there are issues precluding the use of PO-NMR, ligand-observed (LO) NMR reporter assays can be a useful alternative. Such assays can measure affinities in a similar range to PO-NMR while offering some distinct advantages, especially with regard to protein consumption and compound throughput. In this paper, we take a closer look at setting up such assays for routine use, with the aim of getting high-quality, accurate data and good throughput. We assess some of the key characteristics of these assays in the mathematical framework established for fluorescence polarization assays with which the readers may be more familiar. We also provide guidance on setting up such assays and compare their performance with other affinity determination methods that are commonly used in drug discovery.
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Abstract
Fragment-based drug discovery (FBDD) has come of age in the last decade with the FDA approval of four fragment-derived drugs. Biophysical methods are at the heart of hit discovery and validation in FBDD campaigns. The three most commonly used methods, thermal shift, surface plasmon resonance, and nuclear magnetic resonance, can be daunting for the novice user. We aim here to provide the nonexpert user of these methods with a summary of problems and challenges that might be faced, but also highlight the potential gains that each method can contribute to an FBDD project. While our view on FBDD is slightly biased toward enabling structure-guided drug discovery, most of the points we address in this review are also valid for non-structure-focused FBDD.
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The Solution Structure and Dynamics of Cd-Metallothionein from Helix pomatia Reveal Optimization for Binding Cd over Zn. Biochemistry 2019; 58:4570-4581. [DOI: 10.1021/acs.biochem.9b00830] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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5
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Abstract
Cotranslational protein folding is a vectorial process, and for membrane proteins, N-terminal helical segments are the first that become available for membrane insertion. While structures of many G-protein coupled receptors (GPCRs) in various states have been determined, the details of their folding pathways are largely unknown. The seven transmembrane (TM) helices of GPCRs often contain polar residues within the hydrophobic core, and some of the helices in isolation are predicted to be only marginally stable in a membrane environment. Here we review our efforts to describe how marginally hydrophobic TM helices of GPCRs integrate into the membrane in the absence of all compensating interhelical contacts, ideally capturing early biogenesis events. To this end, we use truncated GPCRs, here referred to as fragments. We present data from the human Y4 and the yeast Ste2p receptors in detergent micelles derived from solution NMR techniques. We find that the secondary structure in the fragments is similar to corresponding parts of the entire receptors. However, uncompensated polar or charged residues destabilize the helices, and prevent proper integration into the lipid bilayer, in agreement with the biophysical scales from Wimley and White for the partitioning of amino acids into the membrane-interior. We observe that the stability and integration of single TM helices is improved by adding neighboring helices. We describe a topology study, in which all possible forms of the Y4 receptor were made so that the entire receptor is truncated from the N-terminus by one TM helix at a time. We discover that proteins with an increasing number of helices assume a more defined topology. In a parallel study, we focused on the role of extracellular loops in ligand recognition. We demonstrate that transferring all loops of the human Y1 receptor onto the E. coli outer membrane protein OmpA in a suitable topology results in a chimeric receptor that displays, albeit reduced, affinity and specificity for the cognate ligand. Our data indicate that not all TM helices will spontaneously insert into the helix, and we suggest that at least for some GPCRs, N-terminal segments might remain associated with the translocon until their interacting partners are biosynthesized. Cotranslational protein folding is a vectorial process, and for membrane proteins, N-terminal helical segments are the first that become available for membrane insertion. Here fragments corresponding to these segments are investigated by NMR.![]()
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Backbone resonance assignments for the PHD-Bromo dual-domain of the human chromatin reader TRIM24. BIOMOLECULAR NMR ASSIGNMENTS 2016; 10:207-211. [PMID: 26878853 DOI: 10.1007/s12104-016-9668-9] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/19/2015] [Accepted: 02/05/2016] [Indexed: 06/05/2023]
Abstract
Plant homeodomains (PHD) and Bromo domains are both chromatin reader domains that recognise histone methylation degree and acetylation state, respectively. The tripartite motif protein TRIM24 is a multidomain protein carrying a PHD-Bromo motif at its C-terminus, through which it is able to bind to histone 3 (H3) N-terminal tails with a specific modification pattern, namely unmethylated at K4 and acetylated at K23 (H3-K4me0K23ac). Here we report the 1H, 13C and 15N backbone resonance assignment of this 23 kDa motif, which we have obtained by heteronuclear multidimensional NMR spectroscopy. Furthermore we show that the secondary Cα and Cβ chemical shifts are in good agreement with a previously published crystal structure.
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Long-range conformational transition of a photoswitchable allosteric protein: molecular dynamics simulation study. J Phys Chem B 2014; 118:13468-76. [PMID: 25365469 DOI: 10.1021/jp506873y] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
A local perturbation of a protein may lead to functional changes at some distal site. An example is the PDZ2 domain of human tyrosine phosphatase 1E, which shows an allosteric transition upon binding to a peptide ligand. Recently Buchli et al. presented a time-resolved study of this transition by covalently linking an azobenzene photoswitch across the binding groove and using a femtosecond laser pulse that triggers the cis-trans photoisomerization of azobenzene. To aid the interpretation of these experiments, in this work seven microsecond runs of all-atom molecular dynamics simulations each for the wild-type PDZ2 in the ligand-bound and -free state, as well as the photoswitchable protein (PDZ2S) in the cis and trans states of the photoswitch, in explicit water were conducted. First the theoretical model is validated by recalculating the available NMR data from the simulations. By comparing the results for PDZ2 and PDZ2S, it is analyzed to what extent the photoswitch indeed mimics the free-bound transition. A detailed description of the conformational rearrangement following the cis-trans photoisomerization of PDZ2S reveals a series of photoinduced structural changes that propagate from the anchor residues of the photoswitch via intermediate secondary structure segments to the C-terminus of PDZ2S. The changes of the conformational distribution of the C-terminal region is considered as the distal response of the isolated allosteric protein.
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β-Barrel scaffolds for the grafting of extracellular loops from G-protein-coupled receptors. Biol Chem 2014; 393:1341-55. [PMID: 23109547 DOI: 10.1515/hsz-2012-0234] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2012] [Accepted: 07/15/2012] [Indexed: 11/15/2022]
Abstract
Owing to the difficulties in production and purification of G-protein-coupled receptors (GPCRs), relatively little structural information is available about this class of receptors. Here we aim at developing small chimeric proteins, displaying the extracellular ligand-binding motifs of a human GPCR, the Y receptor. This allows the study of ligand-receptor interactions in simplified systems. We present comprehensive information on the use of transmembrane (OmpA) and soluble (Blc) β-barrel scaffolds. Whereas Blc appeared to be not fully compatible with our approach, owing to problems with refolding of the hybrid constructs, loop-grafted versions of OmpA delivered encouraging results. Previously, we described a chimeric construct based on OmpA displaying all three extracellular Y1 receptor loops in different topologies and showing moderate affinity to one of the natural ligands. Now, we present detailed data on the interaction of these constructs with several Y receptor ligands along with data on new constructs. Our findings suggest a common binding mode for all ligands, which is mediated through the C-terminal residues of the peptide ligand, supporting the functional validity of these hybrid receptors. The observed binding affinities, however, are well below those observed for the natural receptors, clearly indicating limitations in mimicking the natural systems.
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Abstract
Cell spheroids represent attractive building units for bone tissue engineering, because they provide a three-dimensional environment with intensive direct cell-cell contacts. Moreover, they allow for co-culture of both osteoblasts and vessel-forming cells, which may markedly increase their survival and vascularisation after transplantation. To test this hypothesis, we generated co-culture spheroids by aggregating different combinations of primary human osteoblasts (HOB), human dermal microvascular endothelial cells (HDMEC) and normal human dermal fibroblasts (NHDF) using the liquid overlay technique. Mono-culture spheroids consisting either of HOB or HDMEC served as controls. After in vitro characterisation, the different spheroids were transplanted into dorsal skinfold chambers of CD1 nu/nu mice to study in vivo their viability and vascularisation over a 2-week observation period by means of repetitive intravital fluorescence microscopy and immunohistochemistry. In vitro, co-culture spheroids containing HDMEC rapidly formed dense tubular vessel-like networks within 72 h and exhibited a significantly decreased rate of apoptotic cell death when compared to mono-culture HDMEC spheroids. After transplantation, these networks interconnected to the host microvasculature by external inosculation. Of interest, this process was most pronounced in HOB-HDMEC spheroids and could not further be improved by the addition of NHDF. Accordingly, HOB-HDMEC spheroids were larger when compared to the other spheroid types. These findings indicate that HOB-HDMEC spheroids exhibit excellent properties to preserve viability and to promote proliferation and vascularisation. Therefore, they may be used as functional vascularisation units in bone tissue engineering for the seeding of scaffolds or for the vitalisation of non-healing large bone defects.
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Prolyl isomerase PIN1 regulates DNA double-strand break repair by counteracting DNA end resection. Mol Cell 2013; 50:333-43. [PMID: 23623683 DOI: 10.1016/j.molcel.2013.03.023] [Citation(s) in RCA: 61] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2012] [Revised: 02/02/2013] [Accepted: 03/22/2013] [Indexed: 10/26/2022]
Abstract
The regulation of DNA double-strand break (DSB) repair by phosphorylation-dependent signaling pathways is crucial for the maintenance of genome stability; however, remarkably little is known about the molecular mechanisms by which phosphorylation controls DSB repair. Here, we show that PIN1, a phosphorylation-specific prolyl isomerase, interacts with key DSB repair factors and affects the relative contributions of homologous recombination (HR) and nonhomologous end-joining (NHEJ) to DSB repair. We find that PIN1-deficient cells display reduced NHEJ due to increased DNA end resection, whereas resection and HR are compromised in PIN1-overexpressing cells. Moreover, we identify CtIP as a substrate of PIN1 and show that DSBs become hyperresected in cells expressing a CtIP mutant refractory to PIN1 recognition. Mechanistically, we provide evidence that PIN1 impinges on CtIP stability by promoting its ubiquitylation and subsequent proteasomal degradation. Collectively, these data uncover PIN1-mediated isomerization as a regulatory mechanism coordinating DSB repair.
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11
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Interferometry with Bose-Einstein condensates in microgravity. PHYSICAL REVIEW LETTERS 2013; 110:093602. [PMID: 23496709 DOI: 10.1103/physrevlett.110.093602] [Citation(s) in RCA: 78] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/22/2013] [Indexed: 06/01/2023]
Abstract
Atom interferometers covering macroscopic domains of space-time are a spectacular manifestation of the wave nature of matter. Because of their unique coherence properties, Bose-Einstein condensates are ideal sources for an atom interferometer in extended free fall. In this Letter we report on the realization of an asymmetric Mach-Zehnder interferometer operated with a Bose-Einstein condensate in microgravity. The resulting interference pattern is similar to the one in the far field of a double slit and shows a linear scaling with the time the wave packets expand. We employ delta-kick cooling in order to enhance the signal and extend our atom interferometer. Our experiments demonstrate the high potential of interferometers operated with quantum gases for probing the fundamental concepts of quantum mechanics and general relativity.
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12
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Ligand Binding Studied by 2D IR Spectroscopy Using the Azidohomoalanine Label. J Phys Chem B 2012; 116:13705-12. [DOI: 10.1021/jp3095209] [Citation(s) in RCA: 66] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
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13
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Approaches towards Structures of Y Receptors, Examples of Human G-Protein Coupled Receptors, by Solution NMR. Chimia (Aarau) 2012; 66:781-6. [DOI: 10.2533/chimia.2012.781] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
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A chimeric GPCR model mimicking the ligand binding site of the human Y1 receptor studied by NMR spectroscopy. Chembiochem 2011; 12:1690-3. [PMID: 21695755 DOI: 10.1002/cbic.201100244] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2011] [Indexed: 01/23/2023]
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Studies of the structure of the N-terminal domain from the Y4 receptor - a G protein-coupled receptor - and its interaction with hormones from the NPY family. Chembiochem 2009; 9:2276-84. [PMID: 18767100 DOI: 10.1002/cbic.200800221] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Abstract
Binding of peptide hormones to G protein-coupled receptors is believed to be mediated through formation of contacts of the ligands with residues of the extracellular loops of family 1 GPCRs. Here we have investigated whether additional binding sites exist within the N-terminal domain, as studied in the form of binding of peptides from the neuropeptide Y (NPY) family to the N terminus of the Y4 receptor (N-Y4). The N-terminal domain of the Y4 receptor has been expressed in isotopically enriched form and studied by solution NMR spectroscopy. The peptide is unstructured in solution, whereas a micelle-associated helical segment is formed in the presence of dodecylphosphocholine (DPC) or sodium dodecylsulfate (SDS). As measured by surface plasmon resonance (SPR) spectroscopy, N-Y4 binds with approximately 50 microM affinity to the pancreatic polypeptide (PP), a high-affinity ligand to the Y4 receptor, whereas binding to neuropeptide Y (NPY) and peptide YY (PYY) is much weaker. Residues critical for binding in PP and in N-Y4 have been identified by site-directed mutagenesis. The data indicate that electrostatic interactions dominate and that this interaction is mediated by acidic ligand and basic receptor residues. Residues of N-Y4 are likely to contribute to the binding of PP, and in addition might possibly also help to transfer the hormone from the membrane-bound state into the receptor binding pocket.
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Properties of the N
-terminal domains from Y receptors probed by NMR spectroscopy. J Pept Sci 2009; 15:184-91. [DOI: 10.1002/psc.1102] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
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18
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Abstract
In this review a structural approach developed to answer the question whether hormones from the neuropeptide Y (NPY) family are recognized directly from solution or from the membrane-bound state is described. The chosen strategy is built onto a comparison of a set of peptides with well-known pharmacology and investigates whether similarities of structures of pharmacologically related peptides are higher in solution or in the membrane-bound state. Moreover, we have established the membrane-association mode of these peptides and contributed to our understanding of the structural features of these hormones both when placed in bulk solution and when bound to membranes. As a result we propose a receptor recognition pathway that includes initial association with the membrane and requires the peptides to come off the membrane to diffuse into the binding pocket of the receptor. This review also presents methodology recently developed by us to simulate the structural transition the peptides undergo when diffusing from bulk solution onto the membrane.
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Cover Picture: Studies of the Structure of the N-Terminal Domain from the Y4 Receptor-a G Protein-Coupled Receptor-and its Interaction with Hormones from the NPY Family (ChemBioChem 14/2008). Chembiochem 2008. [DOI: 10.1002/cbic.200890053] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
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A Minimal Transmembrane β-Barrel Platform Protein Studied by Nuclear Magnetic Resonance†,‡. Biochemistry 2007; 46:1128-40. [PMID: 17260943 DOI: 10.1021/bi061265e] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
In this study, we were concerned with the structural role of the surface-exposed extracellular loops of the N-terminal transmembrane (TM) domain of OmpA. A variant of the TM domain of outer membrane protein A (OmpA) with all four such loops shortened, which we call the beta-barrel platform (BBP), was successfully refolded. This indicates that the removed parts of the surface-exposed loops indeed do not contain amino acid sequences critical for this membrane protein's refolding in vitro. BBP has the potential to be used as a template beta-barrel membrane protein structure for the development of novel functions, although our results also highlight the potential difficulties that can arise when functionality is being engineered into the loop regions of membrane proteins. We have used solution nuclear magnetic resonance spectroscopy to determine the global fold of BBP+EF, BBP with a metal ion-binding EF-hand inserted in one of the shortened loops. BBP and BBP+EF in dihexanoylphosphatidylcholine micelles are eight-stranded antiparallel beta-barrels, and BBP represents the smallest beta-structured integral membrane protein known to date.
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Die Komplexe der Hexamine «penten» und «ptetraen» Thermodynamik ihrer Bildung in wässeriger Lösung. Helv Chim Acta 2004. [DOI: 10.1002/hlca.19710540121] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
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22
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Resonance superfluidity in a quantum degenerate Fermi gas. PHYSICAL REVIEW LETTERS 2001; 87:120406. [PMID: 11580493 DOI: 10.1103/physrevlett.87.120406] [Citation(s) in RCA: 38] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/22/2001] [Indexed: 05/23/2023]
Abstract
We consider the superfluid phase transition that arises when a Feshbach resonance pairing occurs in a dilute Fermi gas. We apply our theory to consider a specific resonance in potassium ((40)K), and find that for achievable experimental conditions, the transition to a superfluid phase is possible at the high critical temperature of about 0.5T(F). Observation of superfluidity in this regime would provide the opportunity to experimentally study the crossover from the superfluid phase of weakly coupled fermions to the Bose-Einstein condensation of strongly bound composite bosons.
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Comparison of different schemes to treat long-range electrostatic interactions in molecular dynamics simulations of a protein crystal. Proteins 2001; 43:509-19. [PMID: 11340666 DOI: 10.1002/prot.1062] [Citation(s) in RCA: 49] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Eight molecular dynamics simulations of a ubiquitin crystal unit cell were performed to investigate the effect of different schemes to treat the long-range electrostatic interactions as well as the need to include counter ions. A crystal system was chosen as the test system, because the higher charge density compared with a protein in solution makes it more sensitive to the way of treating the electrostatic interactions. Three different schemes of treating the long-range interactions were compared: straight cutoff, reaction-field approximation, and a lattice-sum method (P3M). For each of these schemes, two simulations were performed, one with and one without the counter ions. Two additional simulations with a reaction-field force and different initial placements of the counter ions were performed to examine the effect of the initial positions of the ions. The inclusion of long-range electrostatic interactions using either a reaction-field or a lattice-sum method proved to be necessary for the simulation of crystals. These two schemes did not differ much in their ability to reproduce the crystallographic structure. The inclusion of counter ions, on the other hand, seems not necessary for obtaining a stable simulation. The initial positions of the ions have a visible but small effect on the simulation.
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Formation of pairing fields in resonantly coupled atomic and molecular bose-einstein condensates. PHYSICAL REVIEW LETTERS 2001; 86:1915-1918. [PMID: 11289819 DOI: 10.1103/physrevlett.86.1915] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/03/2000] [Indexed: 05/23/2023]
Abstract
We show that pair correlations may play an important role in the dynamical properties of a Bose-Einstein condensed gas composed of an atomic field resonantly coupled with a condensed field of molecular dimers. Specifically, pair correlations in this system can dramatically modify the coherent and incoherent transfers between the atomic and molecular fields.
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Viscosity dependence of protein dynamics. Proteins 2001; 42:414-21. [PMID: 11151012] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/18/2023]
Abstract
The influence of solvent viscosity on protein dynamics was investigated with molecular dynamics simulations of factor Xa in two solvents differing only in viscosity, by a factor of 10. We obtained this viscosity change by changing the masses of the solvent atoms by a factor of 100. Equilibrium properties of the protein, that is, the average structure, its fluctuations, and the secondary structure, show no significant dependence on the solvent viscosity. The dynamic properties of the protein, that is, the atom-positional correlation times and torsional angle transitions, however, depend on the solvent viscosity. The protein appears to be much more mobile in the solvent of lower viscosity. It feels the influence of the solvent not only on the surface but even in its core. With increasing solvent viscosity, the positional relaxation times of atoms in the protein core increase as much as those of atoms on the protein surface, and the relative increase in the core is even larger than on the surface.
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On the temperature and pressure dependence of a range of properties of a type of water model commonly used in high-temperature protein unfolding simulations. Biophys J 2000; 78:2752-60. [PMID: 10827960 PMCID: PMC1300865 DOI: 10.1016/s0006-3495(00)76820-2] [Citation(s) in RCA: 33] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022] Open
Abstract
Molecular dynamics simulations of protein folding and unfolding are often carried out at temperatures (400-600 K) that are much higher than physiological or room temperature to speed up the (un)folding process. Use of such high temperatures changes both the protein and solvent properties considerably, compared to physiological or room temperature. Water models designed for use in conjunction with biomolecules, such as the simple point charge (SPC) model, have generally been calibrated at room temperature and pressure. To determine the distortive effect of high simulation temperatures on the behavior of such "room temperature" water models, the structural, dynamic, and thermodynamic properties of the much-used SPC water model are investigated in the temperature range from 300 to 500 K. Both constant pressure and constant volume conditions, as used in protein simulations, were analyzed. We found that all properties analyzed change markedly with increasing temperature, but no phase transition in this temperature range was observed.
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The arterial blood supply of the human patella. Its clinical importance for the operating technique in vascularized knee joint transplantations. Surg Radiol Anat 1998; 19:345-51. [PMID: 9479707 DOI: 10.1007/bf01628498] [Citation(s) in RCA: 20] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
The architecture of the arteries supplying the patellar rete was examined in 14 anatomic specimens in order to develop an optimized operating technique for knee joint transplantation. The specimens were fixed in Jores Solution and exarticulated from the hip joint. The lower limbs were injected with Berliner-Blau-Gelatin, and the arteries were dissected macroscopically. Five to six main arteries entered the patellar rete at 1, 3, 5, 7 and 11 o'clock forming an arterial circle. These arteries were the same main arteries which supply the distal end of the femur and the proximal part of the tibia. From an anatomic perspective, they provide the complete arterial blood supply to a whole knee joint being transplanted including the patella. Based on these anatomic results, we transplanted two allogenic vascularized human knee joints preserving the patella, the capsule, and the patellar ligament. Up to six months after surgery we demonstrated the perfusion and viability of all three transplanted bones, particularly the patella, by 99mTc DPD scintigraphy. We compared these findings with knee joint arthroscopy and with histologic results from biopsies taken from the patella. The postoperative examinations clearly indicated the viability of the transplanted patella employing this new operating technique. The results of the entire study demonstrate that it is technically feasible to transplant a whole knee joint which remains clinically viable.
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[201Tl myocardial SPECT. First experiences with a simultaneous transmission-emission acquisition protocol for patient-specific attenuated correction]. Nuklearmedizin 1996; 35:78-85. [PMID: 8710529] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
Abstract
AIM In this study our first clinical experiences with simultaneous transmission and emission acquisition in 201 TI myocardial SPECT (T/E-SPECT) are discussed. METHODS The non-uniform attenuation (AK) was carried out with a triple-head camera (PRISM 3000, Picker Inc.) correction equipped with fanbeam collimators. A line source of 750 MBq 99mTc was used to construct the transmission profile. Prior to investigation patients got 80-120 MBq 201TI-chloride intravenously injected. RESULTS The study comprises the evaluation of 40 patients, derived from the clinical routine. The investigation followed an usual one day protocol. Our results using T/E-SPECT reveal an almost equilibrated activity distribution between anterior and posterior myocardial wall. CONCLUSION For this reason it is to be expected that T/E-SPECT provides more reliable information about the posterior myocardial wall, than the usual SPECT technique without attenuation correction.
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Motion tomography of a single trapped ion. PHYSICAL REVIEW. A, ATOMIC, MOLECULAR, AND OPTICAL PHYSICS 1996; 53:R1966-R1969. [PMID: 9913226 DOI: 10.1103/physreva.53.r1966] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/22/2023]
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31
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201T1-Myokard-SPECT. Nuklearmedizin 1996. [DOI: 10.1055/s-0038-1629833] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/17/2022]
Abstract
Zusammenfassung
Ziel: In dieser Studie werden unsere ersten klinischen Erfahrungen mit der simultanen Akquisition von Transmissions- und Emissionsdaten bei der 201TI-Myokard-SPECT (T/E-SPECT) zur nichthomogenen, patientenspezifischen Abschwächungskorrektur (AK) vorgestellt. Methoden: Die Untersuchungen wurden mit einer Dreikopf-Rotationsgammakamera (Prism 3000, Fa. Picker) durchgeführt, die mit speziellen Fanbeam (Cardiofan) Kollimatoren ausgerüstet war. Das Transmissionsprofil wurde mit Hilfe einer Linienquelle, gefüllt mit 750 MBq 99mTc, erstellt. Die Myokardszintigraphien wurden nach i.v Applikation von 80-120 MBq 201TI-Chlorid nach dem gängigen Eintagesprotokoll durchgeführt. Ergebnisse: Die Studie umfaßt die Auswertung von insgesamt 40 Patienten, die zur Abklärung einer koronaren Herzerkrankung untersucht wurden. Als - für die klinische Routine maßgebliches - Ergebnis zeigte sich, daß mit der Methode der T/E-SPECT eine weitgehend ausgeglichene, anatomiekonformere Aktivitätsverteilung zwischen Herzvorderwand (VW) und -hinterwand (HW) zu erzielen ist. Schlußfolgerung: Damit ist zu erwarten, daß T/E-SPECT gegenüber den konventionellen Verfahren ohne Schwächungskorrektur zu einer zuverlässigeren Beurteilung von Hinterwandbefunden führt.
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Saturated absorption spectroscopy using diode-laser phase noise. PHYSICAL REVIEW. A, ATOMIC, MOLECULAR, AND OPTICAL PHYSICS 1994; 50:4303-4309. [PMID: 9911406 DOI: 10.1103/physreva.50.4303] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/22/2023]
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33
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Laser-noise-induced polarization fluctuations as a spectroscopic tool. PHYSICAL REVIEW. A, ATOMIC, MOLECULAR, AND OPTICAL PHYSICS 1994; 49:5067-5077. [PMID: 9910827 DOI: 10.1103/physreva.49.5067] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/22/2023]
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Abstract
We report on spectra obtained by measuring the laser intensity noise after a broad-bandwidth diode-laser beam passes through a rubidium vapor cell. The atomic resonance converts laser frequency fluctuations into intensity fluctuations. We compare our experimental spectra with numerically calculated spectra based on a phase-diffusion model of the laser field and find good agreement.
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Laser-noise-induced population fluctuations in two-level systems: Complex and real Gaussian driving fields. PHYSICAL REVIEW. A, ATOMIC, MOLECULAR, AND OPTICAL PHYSICS 1992; 45:468-476. [PMID: 9906746 DOI: 10.1103/physreva.45.468] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/22/2023]
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Does noradrenaline influence the extracellular accumulation of potassium, sodium, calcium, and hydrogen ions ([K+]e, [Na+]e, [Ca2+]e, [H+]e) during global ischemia in isolated rat hearts? Basic Res Cardiol 1991; 85 Suppl 1:283-92. [PMID: 1965401 DOI: 10.1007/978-3-662-11038-6_23] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
The influence of noradrenaline (NA) on net cation fluxes during global ischemia (gI) was investigated in isolated rat hearts. The hearts were perfused according to the Langendorff technique and left ventricular pressure (LVP), the first derivative of the LVP (dP/dtmax, dP/dtmin), coronary perfusion pressure (CPP), and heart rate (HF) were measured. In the control group, the perfusion medium was either Krebs-Henseleit's solution (KHS), or KHS and tetramethylammonium-chloride (TMA; 100 microM). In this study TMA was used as a marker to determine changes in the extracellular space (ECS) size during gI. The hearts were subjected to 40 min of gI. Changes in the size of the ECS, and net cation movements were calculated during the first 20 min of gI. In treated hearts, NA (50 nM) was added to the perfusate 15 min before the onset of gI. Extracellular concentrations of K+, Na+, Ca2+, H+, and TMA were measured using double-barreled polyvinyl-chloride (PVC) mini-electrodes. Relative changes in the ECS size and net cation movements were calculated from the extracellular TMA and cation concentrations. In separate experiments, the hemodynamics and lactate overflow of treated hearts were compared with control hearts prior to and following a brief period (1 min) of gI. Addition of NA to the perfusate significantly: 1) increased CPP, LVP, dP/dtmax, dP/dtmin, and HF prior to the onset of gI, and increased cell swelling during gI; 2) diminished K(+)-release from the cells, but significantly increased the influx of sodium and calcium into the intracellular space (ICS); 3) increased lactate overflow prior to and following 1 min of gI. We assume that catecholamines increase ECS shrinkage before and during gI, probably by increased lactate production. NA stimulates the Na+/K+ pump, thereby reducing [K+]e accumulation. The increased [Ca2+]i and intracellular acidification promote sodium entry into the cells during gI.
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The influence of administered mass on the subcellular distribution and binding of mercury in rat liver and kidney. Arch Toxicol 1985; 56:242-6. [PMID: 3994506 DOI: 10.1007/bf00295161] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
The influence of the administered mass on the tissue and sub-cellular distribution of mercury (Hg) was investigated in rats, using 203Hg. The fraction of the dose deposited in liver increased threefold over the dose range 0.17-1.65 mg Hg X kg-1, while the retention in the kidney decreased by a factor of 2. The uptake in other organs, lung, spleen, brain, thymus, salivary glands showed no dose-dependent variation. Subcellular fractionation studies showed a dose-dependent increase in the Hg content of the liver cytosol, with corresponding decreases in the deposition in the lysosomal and nuclei-cell debris fractions. In contrast, no clear changes in the distribution of Hg amongst the subcellular organelles of the kidney were observed. The amount of Hg bound to metallothionein in the liver cytosol rose steeply with increasing dose. However, in the kidney cytosol the mass of Hg bound to metallothionein increased with dose up to 0.55 mg Hg X kg-1, thereafter remaining approximately constant. These observations suggest that the Hg-binding metallothionein in the kidney was saturated by administered doses greater than 0.55 mg Hg X kg-1, whereas in liver saturation levels of the metal were not reached even at the highest dose tested, 1.65 mg Hg X kg-1.
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Note on the metabolism of the mercury chelating agent sodium 2,3-dimercaptopropane-1-sulfonate. JOURNAL OF TOXICOLOGY AND ENVIRONMENTAL HEALTH 1979; 5:759-64. [PMID: 490684 DOI: 10.1080/15287397909529785] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Chromatographic analysis of the radioactive urine obtained after injection into rats of [1,3-(14)C] dimercaptopropane sodium sulfonate (DMPS, Dimaval) showed that part of the administered chelating agent is excreted unchanged. This was confirmed by the results of studies of sulfur excretion in the different fractions of the urine as well as by titration of the excreted thiol groups. The results show that, at least in rats, DMPS is not involved in important metabolic reactions.
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Abstract
The epidemiology of peptic ulcer was investigated in 1105 endoscopy patients in a Zurich city hospital and in a random nongastroenterological hospital population. A raised susceptibility for duodenal ulcer was found in young, mainly unskilled, foreign labourers. There was no raised susceptibility in female foreign workers who also suffered less often from gastric ulcer than Swiss women. A tendency to ulceration in certain other diseases previously incriminated and in alcohol and nicotine consumers was not observed. A connection between susceptibility to ulceration and migration is assumed.
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[Epidemiology of ulcer disease (proceedings)]. ZEITSCHRIFT FUR GASTROENTEROLOGIE 1977; 15:625. [PMID: 930207] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
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[Diagnosis of ulcer and hiatal hernia using endoscopy and radiology (proceedings)]. ZEITSCHRIFT FUR GASTROENTEROLOGIE 1977; 15:621-2. [PMID: 930205] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
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Tumor volume, luxury perfusion, and regional blood volume changes in man visualized by subtraction computerized tomography. J Neurosurg 1976; 44:449-57. [PMID: 768416 DOI: 10.3171/jns.1976.44.4.0449] [Citation(s) in RCA: 20] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Computer and photographic methods for producing subtractions of computerized axial tomographic (CAT) scans have been developed. By subtracting point for point a normal scan from one taken after intravenous infusion of contrast material, a picture of the contrast in the cerebral vessels is created. By this method, tumor size and degree of vascularity may be assessed. Furthermore, abnormalities in perfusion and changes in blood volume due to mass effects and edema may be detected. Subtracting scans should add to the diagnostic potential of CAT and provide a noninvasive way to study vascular changes in cerebral disease.
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Cerebral blood volume in man. Computer analysis of a computerized brain scan. JAMA 1975; 234:1154-5. [PMID: 1102735] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
Cerebral blood volume in man can be measured by subtracting computerized axial tomogram density measurements taken before from those taken after an intravascular marker is infused into the blood. The average blood volume is 3.0 ml/100 ml of brain tissue, with a range of 2.4 to 4.25. This method can be applied in studying cerebral pathologic conditions. Areas of cerebral edema, surrounding a tumor, have a decreased blood volume.
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Infectious DNA from coliphage TI. 3. The occurrence of single-strand breaks in stored, thermally-treated, and U.V.-irradiated molecules. INTERNATIONAL JOURNAL OF RADIATION BIOLOGY AND RELATED STUDIES IN PHYSICS, CHEMISTRY, AND MEDICINE 1971; 19:519-36. [PMID: 5315436 DOI: 10.1080/09553007114550711] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
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On the mechnaism of radiosensitization by 5-bromouracil. The occurrence of DNA strand breaks in U.V.-irradiated phage T4 as influenced by cysteamine. Photochem Photobiol 1970; 12:207-18. [PMID: 5498540 DOI: 10.1111/j.1751-1097.1970.tb06052.x] [Citation(s) in RCA: 29] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
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Novel analgesics and molecular rearrangements in the morphine--thebaine group. IX. A novel aromatisation during Hofmann degradation. JOURNAL OF THE CHEMICAL SOCIETY. PERKIN TRANSACTIONS 1 1969; 17:2225-8. [PMID: 5390119 DOI: 10.1039/j39690002225] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
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