Effect of Urea on Peptide Conformation in Water: Molecular Dynamics and Experimental Characterization

Caballero-Herrera, Ana; Nordstrand, Kerstin; Berndt, Kurt D.; Nilsson, Lennart

doi:10.1529/biophysj.105.061978

Cited by 142 publications

(130 citation statements)

References 91 publications

(140 reference statements)

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“…In the samples without denaturant, the values of HSA do not show significant changes when the ibuprofen is added, and an R h value, in agreement with that reported in literature for free albumins, is observed. 45,53,54 Starting from this value, by increasing the denaturant concentration, an increment of the protein size is observed.…”

Section: Comparison Between Saxs and Dlsmentioning

confidence: 88%

Human serum albumin binding ibuprofen: A 3D description of the unfolding pathway in urea

Galantini¹,

Leggio²,

Konarev³

et al. 2010

Biophysical Chemistry

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This is a PDF file of an unedited manuscript that has been accepted for publication. As a service to our customers we are providing this early version of the manuscript. The manuscript will undergo copyediting, typesetting, and review of the resulting proof before it is published in its final form. Please note that during the production process errors may be discovered which could affect the content, and all legal disclaimers that apply to the journal pertain. A C C E P T E D M A N U S C R I P T ACCEPTED MANUSCRIPT A C C E P T E D M A N U S C R I P T ACCEPTED MANUSCRIPT2 AbstractSmall angle X-ray scattering (SAXS) technique, supported by light scattering measurements and spectroscopic data (circular dichroism and fluorescence) allowed us to restore the 3D structure at low resolution of defatted human serum albumin (HSA) in interaction with ibuprofen. The data were carried out on a set of HSA solutions with urea concentrations between 0.00 and 9.00 M. The SingularValue Decomposition method, applied to the complete SAXS data set allowed us to distinguish three different states in solution. In particular a native conformation N (at 0.00 M urea), an intermediate I1(at 6.05 M urea) and an unfolded structure U (at 9.00 M urea) were recognized. The low resolution structures of these states were obtained by exploiting both ab initio and rigid body fitting methods. In particular, for the protein without denaturant, a conformation recently described (Leggio & al., PCCP, 2008, 10, 6741-6750), very similar to the crystallographic heart shape, with only a slight reciprocal movement of the three domains, was confirmed. The I1 structure was instead characterized by only a closed domain (domain III) and finally, the recovered structure of the U state revealed the characteristic feature of a completely open state. A direct comparison with the free HSA pointed out that the presence of the ibuprofen provokes a shift of the equilibrium towards higher urea concentrations without changing the unfolding sequence. The work represents a type of analysis which could be exploited in future investigations on proteins in solution, in the binding of drugs or endogenous compounds and in the pharmacokinetic properties as well as in the study of allosteric effects, cooperation or anticooperation mechanisms.

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Section: Comparison Between Saxs and Dlsmentioning

confidence: 88%

Human serum albumin binding ibuprofen: A 3D description of the unfolding pathway in urea

Galantini¹,

Leggio²,

Konarev³

et al. 2010

Biophysical Chemistry

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“…The denaturing properties of urea have been studied extensively (52)(53)(54)(55). The evidence suggests that urea denaturation likely occurs through two possible pathways (56). Urea can act "indirectly" by altering the water structure and orienting the distribution of water molecules and perturbing hydrophobic interactions (57)(58)(59).…”

Section: Discussionmentioning

confidence: 99%

Naturally Occurring Osmolytes Modulate the Nanomechanical Properties of Polycystic Kidney Disease Domains

Oberhauser

2010

Journal of Biological Chemistry

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Polycystin-1 (PC1) is a large membrane protein that is expressed along the renal tubule and exposed to a wide range of concentrations of urea. Urea is known as a common denaturing osmolyte that affects protein function by destabilizing their structure. However, it is known that the native conformation of proteins can be stabilized by protecting osmolytes that are found in the mammalian kidney. PC1 has an unusually long ectodomain with a multimodular structure including 16 Ig-like polycystic kidney disease (PKD) domains. Here, we used single-molecule force spectroscopy to study directly the effects of several naturally occurring osmolytes on the mechanical properties of PKD domains. This experimental approach more closely mimics the conditions found in vivo. We show that upon increasing the concentration of urea there is a remarkable decrease in the mechanical stability of human PKD domains. We found that protecting osmolytes such as sorbitol and trimethylamine N-oxide can counteract the denaturing effect of urea. Moreover, we found that the refolding rate of a structurally homologous archaeal PKD domain is significantly slowed down in urea, and this effect was counteracted by sorbitol. Our results demonstrate that naturally occurring osmolytes can have profound effects on the mechanical unfolding and refolding pathways of PKD domains. Based on these findings, we hypothesize that osmolytes such as urea or sorbitol may modulate PC1 mechanical properties and may lead to changes in the activation of the associated polycystin-2 channel or other intracellular events mediated by PC1. Polycystin-1 (PC1)2 is a large transmembrane protein, which, when mutated, cause autosomal dominant polycystic kidney disease (PKD), one of the most common lifethreatening genetic diseases, which is a leading cause of kidney failure (1). The available evidence suggests that PC1 acts as a mechanosensor, receiving signals from the primary (luminal) cilia, neighboring cells, and extracellular matrix and transduces them into cellular responses that regulate proliferation, adhesion, and differentiation that are essential for the control of renal tubules and kidney morphogenesis (1-4).PC1 is expressed along the renal tubule, where it is exposed to a wide range of concentrations of urea, from 5 mM in the proximal tubule to up to ϳ1 M in the collecting duct (5-7). Urea is known as a common denaturant that affects protein function by perturbing their structure (8). Several osmolytes have been found in the mammalian kidney that are known to counteract the effects of urea on proteins (9 -15). Among epithelial cells of the kidney medulla, the principal organic osmolytes include the polyols sorbitol and inositol, the methylamines betaine and glycerophosphocholine, and the amino acid taurine. Protecting osmolytes are found in all taxa (11,14). For example, cartilaginous fish concentrate trimethylamine N-oxide (TMAO), to offset the damaging effects of urea on protein function, and it is one of the best studied protecting osmolytes (e.g. 16 -20).The mecha...

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“…• an indirect mechanism which involves the effect of urea on the solvent structure itself to weaken hydrophobic interactions and improve solvation of hydrophobic groups on the protein [16][17][18][19][20][21] • a direct mechanism which involves the interaction of urea with a variety of groups on the protein, such as hydrogen bonding with the protein backbone and electrostatic interactions with polar and charged groups [22][23][24][25][26] • a combination of both [20,23,27].…”

Section: Introductionmentioning

confidence: 99%

The Effect of Aqueous Urea on the Processing, Structure and Properties of CGM

Pickering¹,

Verbeek²,

Viljoen³

2012

J Polym Environ

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Corn gluten meal (CGM) is potentially a costeffective raw material for producing a bioderivable thermoplastic. However, CGM disintegrates to a powder subsequent to processing with polar plasticisers, such as water. The hypothesis of this study was that aqueous urea could be used to denature protein within CGM and therefore encourage protein-protein interactions leading to consolidated bioplastics when using water as a plasticiser. To assess this, the effects of aqueous urea on structure and properties of CGM with particular focus on storage were assessed. Processing of CGM with aqueous urea produced consolidated materials. FTIR analysis showed secondary structure was modified during processing, leading to increased amounts of a-helices and random coils and reduction of the amount of intermolecular b-sheets and turns. Above 6 wt% free water, the plasticising efficiency of water in processed CGM increased as the amount of denatured proteins increased. Below 6 wt% free water, protein secondary structure did not have a significant influence on thermal and flexural properties. It was found that storage environment and urea concentration influenced the rate of drying, however, the final water content was constant relative to CGM, and not urea. The materials were resistant to cracking at urea concentrations above 8 M, provided the mass loss during storage did not exceed 15 wt%.

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Effect of Urea on Peptide Conformation in Water: Molecular Dynamics and Experimental Characterization

Cited by 142 publications

References 91 publications

Human serum albumin binding ibuprofen: A 3D description of the unfolding pathway in urea

Human serum albumin binding ibuprofen: A 3D description of the unfolding pathway in urea

Naturally Occurring Osmolytes Modulate the Nanomechanical Properties of Polycystic Kidney Disease Domains

The Effect of Aqueous Urea on the Processing, Structure and Properties of CGM

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