A peptide model of the copper-binding region of lysyl oxidase☆

Ryvkin, Faina; Greenaway, Frederick T.

doi:10.1016/j.jinorgbio.2004.04.010

Cited by 18 publications

(24 citation statements)

References 31 publications

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“…A number of different approaches to overcome the lack of metal‐ligand moiety force field parameters for metalloproteins have been employed in molecular simulations. The nonbonded approach uses only electrostatic and van der Waals parameters to model the interactions between the Cu ion and coordinating protein residues . Although this approach is the easiest to incorporate into existing potential functions, the coordination site geometry may not be retained and the metal ion can bind to additional ligands or even leave the coordination site due to the lack of explicit bonds and long‐range electrostatic interactions.…”

Section: Introductionmentioning

confidence: 99%

“…The nonbonded approach uses only electrostatic and van der Waals parameters to model the interactions between the Cu ion and coordinating protein residues. [37][38][39] Although this approach is the easiest to incorporate into existing potential functions, the coordination site geometry may not be retained and the metal ion can bind to additional ligands or even leave the coordination site due to the lack of explicit bonds and long-range electrostatic interactions. Furthermore, the simulated metalloprotein structures may be differently influenced based on whether the formal charge or the partial charge model is chosen for simulating the electrostatic interactions, which in turn is one of the factors that determines the calculated energy and the structure in MM studies.…”

Section: Introductionmentioning

confidence: 99%

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New force field parameters for metalloproteins I: Divalent copper ion centers including three histidine residues and an oxygen‐ligated amino acid residue

Wise

Coskuner

2014

J Comput Chem

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Transition metal ion complexation with proteins is ubiquitous across such diverse fields as neurodegenerative and cardiovascular diseases and cancer. In this study, the structures of divalent copper ion centers including three histidine and one oxygen-ligated amino acid residues and the relative binding affinities of the oxygen-ligated amino acid residues with these metal ion centers, which are debated in the literature, are presented. Furthermore, new force field parameters, which are currently lacking for the full-length metal-ligand moieties, are developed for metalloproteins that have these centers. These new force field parameters enable investigations of metalloproteins possessing these binding sites using molecular simulations. In addition, the impact of using the atom equivalence and inequivalence atomic partial charge calculation procedures on the simulated structures of these metallopeptides, including hydration properties, is described.

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Section: Introductionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

New force field parameters for metalloproteins I: Divalent copper ion centers including three histidine residues and an oxygen‐ligated amino acid residue

Wise

Coskuner

2014

J Comput Chem

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“…For simplicity, in this report DESs refer to both DES and IDES. DESs are pyridinium-based structural isomers arising from the condensation of four lysine residues by lysyl-oxidase 4,11,12. Only a small proportion of DESs is found as a free form in biological fluids.…”

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confidence: 99%

High-Sensitivity NanoLC−MS/MS Analysis of Urinary Desmosine and Isodesmosine

et al. 2009

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Chronic obstructive pulmonary disease (COPD) is characterized by the degradation of elastin, the major insoluble protein of lung tissues. The degradation of elastin gives rise to desmosine (DES) and isodesmosine (IDES), two major urinary products typified by a hydrophilic pyridinium-based crosslinker structure. A high sensitivity method based on nanoflow liquid chromatography tandem mass spectrometry with multiple reaction monitoring was developed for the analysis of urinary DES and IDES. The analytes were derivatized with propionic anhydride and deuterated DES (D 4 -DES) was used as an internal standard. This method enables the quantification of DES and IDES in as little as 50 µL of urine and provides a detection limit of 0.10 ng/mL (0.95 fmol on-column). We report the analysis of DES and IDES in a cohort of 40 urine specimens from four groups of individuals: (a) COPD rapid decliners (11.8 ± 3.7 ng/mg creatine (crea)), (b) COPD slow decliners (16.0 ± 3.1 ng/ mg crea), (c) healthy smokers (13.2 ± 1.9 ng/mg crea), and (d) healthy nonsmokers (14.9 ± 2.9 ng/ mg crea). Our analysis reveals a statistically significant decrease in the level of urinary DES and IDES in COPD rapid decliner patients compared to healthy nonsmoker controls and COPD slow decliner patients. This methodology may be useful for monitoring DES and IDES levels in well controlled animal models for COPD or for longitudinal studies in COPD patients.Chronic obstructive pulmonary disease, or COPD, is a respiratory disorder generally caused by smoking. 1-3 Two major forms of COPD are emphysema and chronic bronchitis. 3 COPD is characterized by impaired lung function, inflammation and scarring of bronchial tubes, and degradation of elastin-containing tissues. The elastin is a major protein component of insoluble fibers providing elastic properties to tissues such as lung, skin, and blood vessels. 4 Also, elastin peptides were reported to be chemotactic for neutrophils and macrophages and could play a role in the progression of pulmonary emphysema once elastin degradation is initiated. 5,6 Most of the COPD biomarkers reported in the literature are cross-linkers 1,7,8 released during the elastin breakdown. The two most abundant and studied elastin crosslinkers are desmosine (DES) and isodesmosine (IDES) 9,10 ( Figure 1). For simplicity, in this report DESs refer to both DES and IDES. DESs are pyridinium-based structural isomers arising from the

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“…3b). The spectroscopic data for the CuHL species, the d-d transition energy at 609 nm, the EPR parameters A II = 170 G, g II = 2.264 correspond very well to the 3N coordination to the metal ion [39]. The pK value for the deprotonation of the CuHL complex (6.33, Table 2) corresponds to the deprotonation of the nonbonding to copper(II) ions histidine residue (pK 6.46, Table 1).…”

Section: Copper(ii) Complexes Of Alloferonmentioning

confidence: 71%