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protein hydration

Vaida Juozapaitienė, Brigita Bartkutė, Vilma Michailovienė, Audrius Zakšauskas, Lina Baranauskienė, Sandra Satkūnė, Daumantas Matulis
Human carbonic anhydrase XIV (CA XIV), a transmembrane protein, highly expressed in the central nervous system, is difficult to recombinantly express and purify in large scale for the measurements of inhibitor binding and drug design. CA XIV belongs to the family of twelve catalytically active CA isoforms in the human body. Disorders in the expression of CA XIV cause serious diseases and CA XIV has been described as a possible drug target for the treatment of epilepsy, some retinopathies, and skin tumors. In this study, the effect of different promoters, E...
October 20, 2016: Journal of Biotechnology
Van-Chien Bui, Thi-Huong Nguyen
Knowledge about the mechanism by which some antibodies can block HIV-1 entry is critical to our understanding of their function and may offer new avenues for controlling the adhesion of HIV-1 to the host cells. While much progress has been made, this mechanism remains unclear. Here, atomic force microscopy, isothermal titration calorimetry (ITC), and circular dichroism spectroscopy were used to measure some biophysical characteristics of the interaction of four-domains (D1-D4) membrane protein CD4 with anti-D3 antibody OKT4 and with HIV-1 entry blocking anti-D1 antibody Leu3a...
October 17, 2016: Immunobiology
Yong Zhou, Tian Liu, Jia-Xi Duan, Ping Li, Guo-Ying Sun, Yong-Ping Liu, Jun Zhang, Liang Dong, Kin Sing Stephen Lee, Bruce D Hammcok, Jian-Xin Jiang, Cha-Xiang Guan
Acute lung injury (ALI) is characterized by rapid alveolar injury, vascular leakage, lung inflammation, neutrophil accumulation, and induced cytokines production leading to lung edema. The mortality rate of patients suffering from ALI remains high. Epoxyeicosatrienoic acids (EETs) are cytochrome P450-dependent derivatives of polyunsaturated fatty acid (PUFA) with anti-hypertensive, profibrinolytic and anti-inflammatory functions. EETs are rapidly hydrated by soluble epoxide hydrolase (sEH) to their less potent diols...
October 6, 2016: Shock
Karan Kapoor, Michael R Duff, Amit Upadhyay, Joel C Bucci, Arnold M Saxton, Robert J Hinde, Elizabeth E Howell, Jerome Yves Baudry
The dynamics of anion-quadrupole (or anion-) interactions formed between negatively charged (Asp/Glu) and aromatic (Phe) side chains are for the first time computationally characterized in RmlC (PDB: 1EP0), a homodimeric epimerase. Empirical force field-based molecular dynamics simulations predict anion-quadrupole pairs and triplets (anion-anion-anion--) are formed by the protein during the simulated trajectory which suggests that the anion-quadrupole interactions may provide a significant contribution to the overall stability of the protein, with an average of -1...
October 18, 2016: Biochemistry
Amanda L Mansouri, Laura N Grese, Erica L Rowe, James C Pino, S Chakra Chennubhotla, Arvind Ramanathan, Hugh M O'Neill, Valerie Berthelier, Christopher B Stanley
Proteins imparted with intrinsic disorder conduct a range of essential cellular functions. To better understand the folding and hydration properties of intrinsically disordered proteins (IDPs), we used osmotic stress to induce conformational changes in nuclear co-activator binding domain (NCBD) and activator for thyroid hormone and retinoid receptor (ACTR) separate from their mutual binding. Osmotic stress was applied by the addition of small and polymeric osmolytes, where we discovered that water contributions to NCBD folding always exceeded those for ACTR...
October 18, 2016: Molecular BioSystems
Singkome Tima, Siriporn Okonogi, Chadarat Ampasavate, Chad Pickens, Cory Berkland, Songyot Anuchapreeda
This study aimed at developing a curcumin (CM) nanoparticle targeted to Feline McDonough Sarcoma (FMS)-like tyrosine kinase 3 (FLT3) protein on the surface of leukemic cells and at evaluating their properties, specificity, cytotoxicity, and inhibitory effect on FLT3 protein level in FLT3-overexpressing leukemic cells, EoL-1, and MV-4-11 cells. FLT3-specific peptides were conjugated onto modified poloxamer 407 using the copper-catalyzed azide-alkyne cycloaddition reaction. The thin film hydration method was performed for FLT3-specific CM-loaded polymeric micelles (FLT3-CM-micelles) preparation...
October 14, 2016: Journal of Pharmaceutical Sciences
Ricardo J S Costa, Rhiannon Snipe, Vera Camões-Costa, Volker Scheer, Andrew Murray
BACKGROUND: Debilitating gastrointestinal symptoms (GIS) and dermatological injuries (DI) are common during and after endurance events and have been linked to performance decrements, event withdrawal, and issues requiring medical attention. The study aimed to determine whether GIS and DI affect food and fluid intake, and nutritional and hydration status, of ultramarathon runners during multi-stage (MSUM) and 24-h continuous (24 h) ultramarathons. METHODS: Ad libitum food and fluid intakes of ultramarathon runners (MSUM n = 54; 24 h n = 22) were recorded throughout both events and analysed by dietary analysis software...
December 2016: Sports Medicine—Open
Chung Eui You, Seok Hoon Moon, Kwang Hoon Lee, Kyu Han Kim, Chun Wook Park, Seong Joon Seo, Sang Hyun Cho
BACKGROUND: Atopic dermatitis (AD) is a common, complex disease that follows a chronic relapsing course and significantly affects the quality of life of patients. Skin barrier dysfunction and inflammatory processes induce and aggravate this skin condition. Proper use of an emollient for hydration is a keystone of AD treatment. Bee venom is known to have anti-inflammatory effects and has been widely used in traditional medicine to treat various inflammatory disorders. OBJECTIVE: To find out the beneficial effect of an emollient containing bee venom in the treatment of patients with AD...
October 2016: Annals of Dermatology
Ohgi Takahashi, Ryota Kirikoshi, Noriyoshi Manabe
In proteins and peptides, d-aspartic acid (d-Asp) and d-β-Asp residues can be spontaneously formed via racemization of the succinimide intermediate formed from l-Asp and l-asparagine (l-Asn) residues. These biologically uncommon amino acid residues are known to have relevance to aging and pathologies. Although nonenzymatic, the succinimide racemization will not occur without a catalyst at room or biological temperature. In the present study, we computationally investigated the mechanism of succinimide racemization catalyzed by dihydrogen phosphate ion, H₂PO₄(-), by B3LYP/6-31+G(d,p) density functional theory calculations, using a model compound in which an aminosuccinyl (Asu) residue is capped with acetyl (Ace) and NCH₃ (Nme) groups on the N- and C-termini, respectively (Ace-Asu-Nme)...
October 10, 2016: International Journal of Molecular Sciences
Aristeidis Papagiannopoulos, Anastasia Meristoudi, Stergios Pispas, Aurel Radulescu
We investigate the potential of self-assembled nanostructures of the PnBA-b-PAA amphiphilic diblock polyelectrolyte as candidates for protein nanocarriers. Three PnBA-b-PAA copolymers with different molecular weights and PnBA/PAA weight ratios are tested. The system with the most well-defined core-shell micellar structure is chosen for complexation with lysozyme. Its solutions are found to contain well-defined core-shell micelles that are stable upon increase of solution salt content to physiological levels...
October 12, 2016: Biomacromolecules
Madhulika Gupta, Charusita Chakravarty, Sanjoy Bandyopadhyay
The sensitivity of protein glass transition temperature and dynamics of Trp-cage mini-protein to the choice of water models have been investigated by performing molecular dynamics simulations at different temperatures between 130 K and 300 K using mTIP3P, TIP4P and TIP4P-Ew water models with CHARMM22 force field. Analysis of the structure of the protein and the ordering of the hydration shell water molecules revealed correlated dynamic crossovers of the protein and its hydration water. It is demonstrated that the parameterization of different water models is robust enough to probe the onset temperatures for the two dynamic crossovers of the peptide, the first one around 150~K which is attributed to active methyl group rotations, and the second one around 200-230~K specifically pertaining to glass transition of the protein...
October 11, 2016: Journal of Chemical Theory and Computation
Emmy C Wijaya, Frances Separovic, Calum J Drummond, Tamar L Greaves
Improving protein stabilisation is important for the further development of many applications in the pharmaceutical, specialty chemical, consumer product and agricultural sectors. However, protein stabilization is highly dependent on the solvent environment and, hence, it is very complex to tailor protein-solvent combinations for stable protein maintenance. Understanding solvent features that govern protein stabilization will enable selection or design of suitable media with favourable solution environments to retain protein native conformation...
September 21, 2016: Physical Chemistry Chemical Physics: PCCP
Po-Shuen Lin, Hsiao-Hua Chang, Chien-Yang Yeh, Mei-Chi Chang, Chiu-Po Chan, Han-Yueh Kuo, Hsin-Cheng Liu, Wan-Chuen Liao, Po-Yuan Jeng, Sin-Yuet Yeung, Jiiang-Huei Jeng
BACKGROUND/PURPOSE: In order to clarify the role of transforming growth factor beta 1 (TGF-β1) in pulp repair/regeneration responses, we investigated the differential signaling pathways responsible for the effects of TGF-β1 on collagen turnover, matrix metalloproteinase-3 (MMP-3), and tissue inhibitor of metalloproteinase-1 (TIMP-1) production in human dental pulp cells. METHODS: Pulp cells were exposed to TGF-β1 with/without pretreatment and coincubation by 1,4-diamino-2,3-dicyano-1,4-bis(o-aminophenyl mercapto)butadiene (U0126; a mitogen-activated protein kinase kinase [MEK]/extracellular signal-regulated kinase [ERK] inhibitor) and 4-(5-benzol[1,3]dioxol-5-yl-4-pyrldin-2-yl-1H- imidazol-2-yl)-benzamide hydrate (SB431542; an activin receptor-like kinase-5/Smad signaling inhibitor)...
October 6, 2016: Journal of the Formosan Medical Association, Taiwan Yi Zhi
Aneta Panuszko, Piotr Bruździak, Emilia Kaczkowska, Janusz Stangret
The stability of proteins in aqueous solution can be modified by the presence of osmolytes. The hydration sphere of stabilizing osmolytes is strikingly similar to the enhanced hydration sphere of protein. This similarity leads to the increase of the protein stability. Moreover, destabilizing osmolytes' hydration sphere is significantly different. These solutes generate in their surrounding so-called "structurally different water". The addition of such osmolytes causes a "dissolution" of the specific protein hydration sphere and destabilizes its folded form...
October 7, 2016: Journal of Physical Chemistry. B
Suchit Sahai, Marysuna Wilkerson, Ana Maria Zaske, Scott D Olson, Charles S Cox, Fabio Triolo
Immobilizing hydrated soft tissue specimens for atomic force microscopy (AFM) is a challenge. Here, we describe a simple and very cost-effective immobilization method, based on the use of transglutaminase in an aqueous environment, and successfully apply it to AFM characterization of human native Wharton's Jelly (nWJ), the gelatinous connective tissue matrix of the umbilical cord. A side-by-side comparison with a widely used polyphenolic protein-based tissue adhesive (Corning Cell-Tak), which is known to bind strongly to virtually all inorganic and organic surfaces in aqueous environments, shows that both adhesives successfully immobilize nWJ in its physological hydrated state...
October 1, 2016: BioTechniques
Sara Del Galdo, Andrea Amadei
In this paper we apply the computational analysis recently proposed by our group to characterize the solvation properties of a native protein in aqueous solution, and to four model aqueous solutions of globular proteins in their unfolded states thus characterizing the protein unfolded state hydration shell and quantitatively evaluating the protein unfolded state partial molar volumes. Moreover, by using both the native and unfolded protein partial molar volumes, we obtain the corresponding variations (unfolding partial molar volumes) to be compared with the available experimental estimates...
October 12, 2016: Physical Chemistry Chemical Physics: PCCP
A Tomić, B Kovačević, S Tomić
Human dipeptidyl-peptidase III (h.DPP III) is a zinc-exopeptidase that hydrolyses dipeptides from the N-terminus of its substrates. Its mechanism of action was assumed to be similar to that of thermolysin, but was never thoroughly investigated. This study presents the first insight into the reaction mechanism of h.DPP III, determined on the model and real (hydrated enzyme with Leu-enkephalin bound in the active site) systems. The Glu451-assisted water addition on amide carbon atoms and nitrogen inversion (i...
October 5, 2016: Physical Chemistry Chemical Physics: PCCP
Supriyo Bhattacharya, Romelia Salomon-Ferrer, Sangbae Lee, Nagarajan Vaidehi
GPCRs are transmembrane receptors involved in diverse biological functions. Despite the diversity in their amino acid sequences, class A GPCRs exhibit a conserved structural topology and possibly common mechanism of receptor activation. To understand how this high sequence diversity translates to a conserved functional mechanism, we have compared the dynamic behavior of eight class A GPCRs comprising of six biogenic amine receptors, and the adenosine A2A and a peptide receptor protease activated receptor 1...
October 6, 2016: Journal of Chemical Theory and Computation
Alysha Dicke, Tata Gopinath, Yingjie Wang, Gianluigi Veglia
Water plays a central role in membrane protein folding and function. It not only catalyzes lipid membrane self-assembly, but it is also affects the structural integrity and conformational dynamics of membrane proteins. Magic angle spinning (MAS) solid-state NMR is the technique of choice for measuring water accessibility of membrane proteins in a site-specific manner, providing a ruler for membrane protein topology and insertion within lipid bilayers. However, sensitivity and resolution of membrane protein samples for MAS experiments is often dictated by hydration levels, which affect membrane proteins structural dynamics...
October 5, 2016: Journal of Physical Chemistry. B
Yangzhong Qin, Menghui Jia, Jin Yang, Dihao Wang, Lijuan Wang, Jianhua Xu, Dongping Zhong
The fluctuations of hydration water and the protein are coupled together at the protein surface and often such water-protein dynamic interactions are controlled presumably by hydration water motions. However, direct evidence is scarce and it requires measuring the dynamics of hydration water and protein sidechain simultaneously. Here, we use a unique protein with a single tryptophan to directly probe interfacial water and related sidechain relaxations with temperature dependence. With systematic mutations to change local chemical identity and structural flexibility, we found that the sidechain relaxations are always slower than hydration water motions and the two dynamic processes are linearly correlated with the same energy barriers, indicating the same origin of both relaxations...
October 4, 2016: Journal of Physical Chemistry Letters
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