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Citric acid-modified pH-sensitive bone-targeted delivery of estrogen for the treatment of postmenopausal osteoporosis. Mater Today Bio 2023; 22:100747. [PMID: 37576873 PMCID: PMC10415756 DOI: 10.1016/j.mtbio.2023.100747] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2023] [Revised: 06/20/2023] [Accepted: 07/24/2023] [Indexed: 08/15/2023] Open
Abstract
Bone targeted delivery of estrogen offers great promise for the clinical application of estrogen in the treatment of postmenopausal osteoporosis (PMOP). However, the current bone-targeted drug delivery system still has several issues that need to be solved, such as the side effects of bone-targeted modifier molecules and the failure of the delivery system to release rapidly in the bone tissue. It is important to aggressively search for new bone-targeted modifier molecules and bone microenvironment-responsive delivery vehicles. Inspired by the distribution of citric acid (CA) mainly in bone tissue and the acidic bone resorption microenvironment, we constructed a CA-modified diblock copolymer poly(2-ethyl-2-oxazoline)-poly(ε-caprolactone) (CA-PEOz) drug delivery system. In our study, we found that the CA modification significantly increased the bone targeting of this drug delivery system, and the delivery system was able to achieve rapid drug release under bone acidic conditions. The delivery system significantly reduced bone loss in postmenopausal osteoporotic mice with a significant reduction in estrogenic side effects on the uterus. In summary, our study shows that CA can act as an effective bone targeting modifier molecule and provides a new option for bone targeting modifications. Our study also provides a new approach for bone-targeted delivery of estrogen for the treatment of PMOP.
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Comments on ''Efficacy of Topical Losartan in Management of Mammoplasty and Abdominoplasty Scars: A Randomized, Double-Blind Clinical Trial''. Aesthetic Plast Surg 2023; 47:114-115. [PMID: 35943541 DOI: 10.1007/s00266-022-03046-8] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2022] [Accepted: 07/26/2022] [Indexed: 12/16/2022]
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Physiological functions of podosomes: From structure and function to therapy implications in osteoclast biology of bone resorption. Ageing Res Rev 2023; 85:101842. [PMID: 36621647 DOI: 10.1016/j.arr.2023.101842] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2022] [Revised: 12/09/2022] [Accepted: 01/03/2023] [Indexed: 01/07/2023]
Abstract
With increasing age, bone tissue undergoes significant alterations in composition, architecture, and metabolic functions, probably causing senile osteoporosis. Osteoporosis possess the vast majority of bone disease and associates with a reduction in bone mass and increased fracture risk. Bone loss is on account of the disorder in osteoblast-induced bone formation and osteoclast-induced bone resorption. As a unique bone resorptive cell type, mature bone-resorbing osteoclasts exhibit dynamic actin-based cytoskeletal structures called podosomes that participate in cell-matrix adhesions specialized in the degradation of mineralized bone matrix. Podosomes share many of the same molecular constitutions as focal adhesions, but they have a unique structural organization, with a central core abundant in F-actin and encircled by scaffolding proteins, kinases and integrins. Here, we conclude recent advancements in our knowledge of the architecture and the functions of podosomes. We also discuss the regulatory pathways in osteoclast podosomes, providing a reference for future research on the podosomes of osteoclasts and considering podosomes as a therapeutic target for inhibiting bone resorption.
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LEP and LEPR are possibly a double-edged sword for wound healing. J Cell Physiol 2023; 238:355-365. [PMID: 36571294 DOI: 10.1002/jcp.30936] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2022] [Revised: 12/05/2022] [Accepted: 12/13/2022] [Indexed: 12/27/2022]
Abstract
Wound healing is a complex and error-prone process. Wound healing in adults often leads to the formation of scars, a type of fibrotic tissue that lacks skin appendages. Hypertrophic scars and keloids can also form when the wound-healing process goes wrong. Leptin (Lep) and leptin receptors (LepRs) have recently been shown to affect multiple stages of wound healing. This effect, however, is paradoxical for scarless wound healing. On the one hand, Lep exerts pro-inflammatory and profibrotic effects; on the other hand, Lep can regulate hair follicle growth. This paper summarises the role of Lep and LepRs on cells in different stages of wound healing, briefly introduces the process of wound healing and Lep and LepRs, and examines the possibility of promoting scarless wound healing through spatiotemporal, systemic, and local regulation of Lep levels and the binding of Lep and LepRs.
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Circadian clock genes as promising therapeutic targets for bone loss. Biomed Pharmacother 2023; 157:114019. [PMID: 36423544 DOI: 10.1016/j.biopha.2022.114019] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2022] [Revised: 11/11/2022] [Accepted: 11/13/2022] [Indexed: 11/22/2022] Open
Abstract
The circadian clock regulates many key physiological processes such as the sleep-wake cycle, hormone release, cardiovascular health, glucose metabolism and body temperature. Recent evidence has suggested a critical role of the circadian system in controlling bone metabolism. Here we review the connection between bone metabolism and the biological clock, and the roles of these mechanisms in bone loss. We also analyze the regulatory effects of clock-related genes on signaling pathways and transcription factors in osteoblasts and osteoclasts. Additionally, osteocytes and endothelial cells (ECs) regulated by the circadian clock are also discussed in our review. Furthermore, we also summarize the regulation of circadian clock genes by some novel modulators, which provides us with a new insight into a potential strategy to prevent and treat bone diseases such as osteoporosis by targeting circadian genes.
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The ASIC3-M-CSF-M2 macrophage-positive feedback loop modulates fibroblast-to-myofibroblast differentiation in skin fibrosis pathogenesis. Cell Death Dis 2022; 13:527. [PMID: 35661105 PMCID: PMC9167818 DOI: 10.1038/s41419-022-04981-9] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2021] [Revised: 05/23/2022] [Accepted: 05/26/2022] [Indexed: 01/21/2023]
Abstract
Inflammation is one of the main pathological features leading to skin fibrosis and a key factor leading to the progression of skin fibrosis. Acidosis caused by a decrease in extracellular pH is a sign of the inflammatory process. Acid-sensing ion channels (ASICs) are ligand-gated ion channels on the cell membrane that sense the drop in extracellular pH. The molecular mechanisms by which skin fibroblasts are regulated by acid-sensing ion channel 3 (ASIC3) remain unknown. This study investigated whether ASIC3 is related to inflammation and skin fibrosis and explored the underlying mechanisms. We demonstrate that macrophage colony-stimulating factor (M-CSF) is a direct target of ASIC3, and ASIC3 activation promotes M-CSF transcriptional regulation of macrophages for M2 polarization. The polarization of M2 macrophages transduced by the ASIC3-M-CSF signal promotes the differentiation of fibroblasts into myofibroblasts through transforming growth factor β1 (TGF-β1), thereby producing an ASIC3-M-CSF-TGF-β1 positive feedback loop. Targeting ASIC3 may be a new treatment strategy for skin fibrosis.
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[Interleukin 33 inhibits lipopolysaccharide-induced high permeability of cardiac microvascular endothelial cells]. ZHONGHUA NEI KE ZA ZHI 2022; 61:559-564. [PMID: 35488608 DOI: 10.3760/cma.j.cn112138-20210625-00444] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
Objective: To investigate the effect of interleukin-33 (IL-33) on lipopolysaccharide (LPS)-induced permeability of rat cardiac microvascular endothelial cells (RCMECs). Methods: RCMECs were cultured in vitro to be divided into control group, LPS group, IL-33 group and LPS+IL-33 group. The effect of IL-33 on the proliferation of RCMECs was detected by cell counting reagent (CCK8). Fluorescein isothiocyanate (FITC)-dextran assay was used to evaluate the permeability of RCMECs. The expression of vascular endothelial calmodulin, ras homologous gene family (Rho) member A (RhoA) and phosphorylated Rho-associated coiled-coil-containing protein kinase (p-ROCK2) proteins were tested by western blot. High-throughput sequencing and gene ontology (GO) were performed for gene expression in LPS and LPS+IL-33 groups. Results: No significant effect of IL-33 at 10-50 ng/ml on the proliferation of RCMECs was observed (P>0.05). Compared with the control group, the permeability of RCMECs (permeability coefficient ratio 1.404±0.029 vs. 1.000±0.200, P<0.05) was significantly increased in LPS group and the expression of vascular endothelial calmodulin (relative gray value 0.429 5±0.012 9 vs. 0.594 9±0.014 2, P<0.05) was down-regulated, while the permeability of monolayers (permeability coefficient ratio, 0.948±0.013, P<0.01) was decreased in LPS+IL-33 group and the expression of vascular endothelial calmodulin (relative grayscale value 0.549 1±0.012 0, P<0.005) was up-regulated compared with the LPS group. High-throughput sequencing data revealed that the differential genes downregulated in the LPS and LPS+IL-33 groups were associated with cytoskeleton and Rho signaling pathway. Compared with the control group, RhoA (relative gray value 0.211 4±0.009 9 vs. 0.135 0±0.007 6, P<0.000 1) and p-ROCK (relative gray value 0.656 3±0.013 2 vs. 0.503 6±0.036 2, P<0.000 1) protein expression was upregulated in the LPS group. When compared with LPS group, RhoA (relative gray value 0.157 7±0.010 7, P=0.000 2), p-ROCK (relative gray value 0.427 7±0.003 8, P<0.000 1) protein expression was decreased in LPS+IL-33 group. Conclusion: IL-33 may improve LPS-induced hyperpermeability of RCMECs by inhibiting RhoA and p-ROCK protein expression in Rho/Rho-associated coiled-coil-containing protein kinase signaling pathway.
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Measurement of the Cosmic Ray Helium Energy Spectrum from 70 GeV to 80 TeV with the DAMPE Space Mission. PHYSICAL REVIEW LETTERS 2021; 126:201102. [PMID: 34110215 DOI: 10.1103/physrevlett.126.201102] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/05/2021] [Revised: 03/25/2021] [Accepted: 04/06/2021] [Indexed: 06/12/2023]
Abstract
The measurement of the energy spectrum of cosmic ray helium nuclei from 70 GeV to 80 TeV using 4.5 years of data recorded by the Dark Matter Particle Explorer (DAMPE) is reported in this work. A hardening of the spectrum is observed at an energy of about 1.3 TeV, similar to previous observations. In addition, a spectral softening at about 34 TeV is revealed for the first time with large statistics and well controlled systematic uncertainties, with an overall significance of 4.3σ. The DAMPE spectral measurements of both cosmic protons and helium nuclei suggest a particle charge dependent softening energy, although with current uncertainties a dependence on the number of nucleons cannot be ruled out.
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Factors Affecting the Enhancement Patterns of Intrahepatic Cholangiocarcinoma (ICC) on Contrast-Enhanced Ultrasound (CEUS) and their Pathological Correlations in Patients with a Single Lesion. ULTRASCHALL IN DER MEDIZIN (STUTTGART, GERMANY : 1980) 2016; 37:609-618. [PMID: 25919414 DOI: 10.1055/s-0034-1399485] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
Purpose: To investigate the factors that influence the enhancement patterns of intrahepatic cholangiocarcinomas (ICC) on contrast-enhanced ultrasound (CEUS) and analyze the correlations between the enhancement patterns on CEUS and pathological findings. Materials and Methods: Ninety-six patients with 96 pathologically confirmed ICCs underwent CEUS. CEUS images were retrospectively evaluated for tumor enhancement patterns in the arterial, portal and late phases. The arterial enhancement patterns were correlated with clinicopathological factors. The possible influencing factors were correlated with pathologic findings. Results: Thirty-six patients with ICC demonstrated rim-like enhancement, and 60 exhibited non-rim-like enhancement in the arterial phase on CEUS. The incidence of non-rim-like-enhancing ICCs was higher in patients with cirrhosis and chronic viral hepatitis than patients with no chronic liver disease (p = 0.001). The sizes of the ICCs with homogeneous hyper-enhancement were significantly smaller than those with inhomogeneous hyper-enhancement (p = 0.007). Arterial non-rim-like-enhancing ICCs showed higher microvessel density (MVD) and arterial density (AD) and less fibrous stroma and necrosis than rim-like-enhancing ICCs. Arterial inhomogeneous-enhancing ICCs had lower MVD and AD and much more fibrous stroma and necrosis than homogeneous-enhancing ICCs. Conclusion: The enhancement pattern of ICCs in the arterial phase on CEUS was affected by a liver cirrhosis and chronic viral hepatitis and tumor size. The amount of MVD, AD, fibrous stroma and necrosis in ICC tumors may be responsible for the difference in the enhancement patterns.
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Characterization and comparison of EST-SSR and TRAP markers for genetic analysis of the Japanese persimmon Diospyros kaki. GENETICS AND MOLECULAR RESEARCH 2013; 12:2841-51. [PMID: 23359055 DOI: 10.4238/2013.january.9.3] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
Abstract
We developed and characterized expressed sequence tags (ESTs)-simple sequence repeats (SSRs) and targeted region amplified polymorphism (TRAP) markers to examine genetic relationships in the persimmon genus Diospyros gene pool. In total, we characterized 14 EST-SSR primer pairs and 36 TRAP primer combinations, which were amplified across 20 germplasms of 4 species in the genus Diospyros. We used various genetic parameters, including effective multiplex ratio (EMR), diversity index (DI), and marker index (MI), to test the utility of these markers. TRAP markers gave higher EMR (24.85) but lower DI (0.33), compared to EST-SSRs (EMR = 3.65, DI = 0.34). TRAP gave a very high MI (8.08), which was about 8 times than the MI of EST-SSR (1.25). These markers were utilized for phylogenetic inference of 20 genotypes of Diospyros kaki Thunb. and allied species, with a result that all kaki genotypes clustered closely and 3 allied species formed an independent group. These markers could be further exploited for large-scale genetic relationship inference.
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Microwave absorption of gamma'-Fe2.6 Ni1.4N nanoparticles derived from nitriding counterpart precursor. JOURNAL OF NANOSCIENCE AND NANOTECHNOLOGY 2012; 12:3040-3047. [PMID: 22849063 DOI: 10.1166/jnn.2012.5842] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/01/2023]
Abstract
Gamma-Fe2.6Ni1.4 nanoparticles were prepared by the arc-discharge method as the precursor and its nitride counterpart of gamma'-Fe2.6Ni14N nanoparticles was synthesized directly through a thermal ammonolysis reaction at the temperature of 673 K for two hours. The resultant product was identified as a homogeneous ternary nitride with nearly spherical shape and average size of about 60.0 nm. The electromagnetic characteristics of gamma'-Fe2.6Ni1.4N derivant and gamma-Fe2.6Ni1.4 precursor have been studied in the frequency range of 2-18 GHz. Compared with the precursor, gamma'-Fe2.6Ni1.4N nanoparticles exhibits an enhanced electromagnetic absorption property resulted from the increased dielectric loss by nitriding process. The optimal reflection loss (RL) of gamma'-Fe2.6Ni1.4N nanoparticles/paraffin composite can reach -39.9 dB at 5.2 GHz in a thickness of 2.29 mm, and the frequency band corresponding RL < -10 dB is over 2.6-18 GHz in the thickness range of 0.78-4.20 mm.
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Distinct mechanism of small-for-size fatty liver graft injury--Wnt4 signaling activates hepatic stellate cells. Am J Transplant 2010; 10:1178-88. [PMID: 20420630 DOI: 10.1111/j.1600-6143.2010.03102.x] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Abstract
In this study, we aimed to investigate the significance of hepatic stellate cells (HSCs) activation in small-for-size fatty liver graft injury and to explore the underlying molecular mechanism in a rat liver transplantation model. A rat orthotopic liver transplantation model using fatty grafts (40% of fatty changes) and cirrhotic recipients was applied. Intragraft gene expression profiles, ultrastructure features and HSCs activation were compared among the rats received different types of grafts (whole vs. small-for-size, normal vs. fatty). The distinct molecular signature of small-for-size fatty graft injury was identified by cDNA microarray screening and confirmed by RT-PCR detection. In vitro functional studies were further conducted to investigate the direct effect of specific molecular signature on HSCs activation. HSCs activation was predominantly present in small-for-size fatty grafts during the first 2 weeks after transplantation, and was strongly correlated with progressive hepatic sinusoidal damage and significant upregulation of intragraft Wnt4 signaling pathway. In vitro suppression of Wnt4 expression could inhibit HSC activation directly. In conclusion, upregulation of Wnt4 signaling led to direct HSC activation and subsequently induced small-for-size fatty liver grafts injury. Discovery of this distinct mechanism may lay the foundation for prophylactic treatment for marginal graft injury in living donor liver transplantation.
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Algebraic direct methods for few-atoms structure models. Acta Crystallogr A 2002; 58:361-9. [PMID: 12089459 DOI: 10.1107/s0108767302005597] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2001] [Accepted: 03/26/2002] [Indexed: 11/10/2022] Open
Abstract
As a basis for direct-methods phasing at very low resolution for macromolecular crystal structures, normalized structure-factor algebra is presented for few-atoms structure models with N = 1, 2, 3, em leader equal atoms or polyatomic globs per unit cell. Main results include: [see text]. Triplet discriminant Delta(hk) and triplet weight W(hk) parameters, a approximately 4.0 and b approximately 3.0, respectively, were determined empirically in numerical error analyses. Tests with phases calculated for few-atoms 'super-glob' models of the protein apo-D-glyceraldehyde-3-phosphate dehydrogenase (approximately 10000 non-H atoms) showed that low-resolution phases from the new few-atoms tangent formula were much better than conventional tangent formula phases for N = 2 and 3; phases from the two formulae were essentially the same for N > or = 4.
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[Electro physiological characteristics of single potassium channel in isolated habenula neurons]. ZHONGGUO YING YONG SHENG LI XUE ZA ZHI = ZHONGGUO YINGYONG SHENGLIXUE ZAZHI = CHINESE JOURNAL OF APPLIED PHYSIOLOGY 2001; 17:239-270. [PMID: 21189619] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 05/30/2023]
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Globbic approximation in low-resolution direct-methods phasing. ACTA CRYSTALLOGRAPHICA SECTION D: BIOLOGICAL CRYSTALLOGRAPHY 2000; 56:1148-55. [PMID: 10957633 DOI: 10.1107/s0907444900008362] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/03/2000] [Accepted: 06/09/2000] [Indexed: 11/10/2022]
Abstract
Probabilistic direct-methods phasing theory, originally based on a uniform atomic distribution hypothesis, is shown to be adaptable to a non-uniform bulk-solvent-compensated globbic approximation for protein crystals at low resolution. The effective number n(g) of non-H protein atoms per polyatomic glob increases with decreasing resolution; low-resolution phases depend on the positions of only N(g) = N(a)/n(g) globs rather than N(a) atoms. Test calculations were performed with measured structure-factor data and the refined structural parameters from a protein crystal with approximately 10 000 non-H protein atoms per molecule and approximately 60% solvent volume. Low-resolution data sets with d(min) ranging from 15 to 5 A gave n(g) = ad(min) + b, with a = 1.0 A(-1) and b = -1.9 for the test case. Results of tangent-formula phase-estimation trials emphasize that completeness of the low-resolution data is critically important for probabilistic phasing.
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Bulk-solvent correction in direct-methods phasing. ACTA CRYSTALLOGRAPHICA SECTION D: BIOLOGICAL CRYSTALLOGRAPHY 2000; 56:451-7. [PMID: 10739918 DOI: 10.1107/s0907444900000573] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Abstract
It is shown that for crystals of large proteins at low diffraction resolution, with N approximately 10 000 independent non-H protein atoms and d(min) approximately 8 A, a simple bulk-solvent correction yields the Sayre equation in its classical form, F(h) = q summation operator(k)F(k)F(h - k). In the low-resolution protein case, the proportionality factor becomes q = 1/[(<rho(P) > - rho(S))V], where V is the unit-cell volume, rho(S) is the assumed constant electron density in the solvent regions of the crystal and <rho(P)> is the average electron density in the protein regions. The classical form of the tangent formula follows from the bulk-solvent-corrected Sayre equation and its validity at low resolution is verified in empirical calculations.
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On 'globbicity' of low-resolution protein structures. ACTA CRYSTALLOGRAPHICA SECTION D: BIOLOGICAL CRYSTALLOGRAPHY 1999; 55:230-7. [PMID: 10089414 DOI: 10.1107/s0907444998008208] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/30/1997] [Accepted: 06/10/1998] [Indexed: 11/10/2022]
Abstract
Using Harker's [Harker (1953). Acta Cryst. 6, 731-736] idea of spherically averaged polyatomic groups or 'globs' as the units of structure suitable for analyzing low-resolution diffraction data from protein crystals, 'globbic' scattering factors have been calculated for main-chain peptide units and amino-acid side-chain groups to 3 A resolution via Debye's [Debye (1915). Ann. Phys. (Leipzig), 46, 809-823] scattering formula. It is shown that the scattering factors are insensitive to intra-globbic conformational variation and can be approximated fairly well by a single-Gaussian formula, i.e. fg(s) = Zg exp(-1.7Zgs2), where s = (sin theta)/lambda and Zg is the total electron count for the atoms of the glob. Phase errors due to the globbic approximation and their effect on electron-density maps at 3.5 A resolution have been assessed via calculations for the crambin structure; this analysis indicates that the globbic scattering factors will be useful in efforts to develop procedures for direct-methods phasing of diffraction data to approximately 3.5 A resolution from protein crystals.
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On integrating the techniques of direct methods with anomalous dispersion. IV. A simplified perturbation treatment for SAS phasing. Acta Crystallogr A 1997; 53 ( Pt 1):74-83. [PMID: 9037748 DOI: 10.1107/s0108767396011993] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023] Open
Abstract
Results from probabilistic theory for the single-wavelength anomalous-scattering (SAS) Friedel pair, two-phase structure invariants, psi H = phi H + phi-H, are used to show that the SAS three-phase structure invariants, psi HK = phi H + phi K + phi-H-K, tend to positive values that are easily estimated. Appropriate averages of the estimates provide SAS perturbation corrections in the form of positive origin shifts for the probability distribution of psi HK values and for the tangent formula. The theoretical probabilistic results are verified by empirical statistical analyses of model-calculated phases and experimentally measured structure-factor magnitudes for a small-molecule and a protein crystal structure.
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Statistical Expectation Value of the Debye–Waller Factor and E(hkl) Values for Macromolecular Crystals. ACTA CRYSTALLOGRAPHICA SECTION D: BIOLOGICAL CRYSTALLOGRAPHY 1996; 52:257-66. [PMID: 15299698 DOI: 10.1107/s0907444995014053] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Abstract
If the unit-cell distribution of atomic mean-square displacement parameters B = 8pi(2)<u(2)> is assumed to be normal, with mean micro = <B> and variance sigma(2) = <(B-<B >)(2)>, the statistical expectation value of the Debye-Waller factor W(2) = exp(-2Bs(2)), where s = (sin theta)/lambda, is <W(2)> = exp[-2( micro - sigma(2)s(2))s(2)]. This result has been incorporated into procedures for scaling and normalizing measured Bragg intensities to their Wilson expectation values. The procedures can determine both isotropic micro (B) and sigma(B) and anisotropic micro (U(ij)) and sigma(U(ij) distribution parameters. Tests with experimental data and refined structural models for several protein crystals show that the procedures yield reliable normalized structure-factor amplitudes for direct-methods applications, with values of R = summation operator (h)||E(o)| - |E(c)||/ summation operator (h)|E(o)| averaging approximately 5%.
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Abstract
At 3 to 4 A resolution, the electron density of a protein may be modeled by a continuous chain of 'globs' representing the amide region of the peptide backbone and the side-chain residues. Group scattering factors are derived from a trans planar C alpha C = ONC alpha backbone segment and most favored side-chain conformer for 18 different amino acids. Trial calculations indicate that the phase error and crystallographic residual comparing the atomic and 'globic' models rapidly decrease from high to low resolution. At 3 A resolution, the phase error is approximately 80 degrees. These results indicate that the electron density of a protein composed of N amino acid residues may be adequately modeled by 2N globs at low resolution.
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On integrating the techniques of direct methods with anomalous dispersion. III. Estimation of two-wavelength two-phase structure invariants. Acta Crystallogr A 1994; 50 ( Pt 3):307-11. [PMID: 8024726 DOI: 10.1107/s0108767393009778] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023] Open
Abstract
For diffraction data at two wavelengths from a crystal with anomalous scatterers, there are six types of two-phase structure invariants for Friedel pairs. Two of the six are single-wavelength invariants; the other four are mixed-wavelength invariants. It is shown that the latter can be estimated by a straightforward extension of results from the probabilistic direct-methods theory for the single-wavelength anomalous scattering case described in paper I [Hauptman (1982). Acta Cryst. A38, 632-641]. Statistical tests of the mixed-wavelength estimates are reported for small-molecule and macro-molecular examples.
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On integrating the techniques of direct methods with anomalous dispersion. II. Statistical properties of the two-phase structure invariants. Acta Crystallogr A 1991; 47 ( Pt 4):340-5. [PMID: 1910634 DOI: 10.1107/s0108767391000892] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022] Open
Abstract
Results of a statistical study of probabilistic estimates of two-phase structure invariants (TPSI) for Friedel pairs in the case of single-wavelength anomalous scattering are reported. Numerical analysis of the TPSI sign, magnitude and error distributions shows that the concise formula for TPSI by probability theory [Hauptman (1982). Acta Cryst. A38, 632-641; Giacovazzo (1983). Acta Cryst. A39, 585-592] has desirable statistical properties. Computational results for the known structures of cocaine methiodide (N-methylcocaine iodide) and of cytochrome c550 and its PtCl2-4 derivative show that when [E[ values are large most of the signs of the TPSI are correctly determined - for [E[ greater than 1.0, 90% or more of the TPSI signs are positive as predicted - and the errors in the estimated TPSI magnitudes do not exceed approximately 10% for [E[ greater than 1.0 in the small-molecule case or approximately 50% for [E[ greater than 1.5 in the macromolecular case. These results suggest that the theory will be useful for estimating the TPSI for unknown structures.
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