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1.
Foods ; 13(4)2024 Feb 14.
Article in English | MEDLINE | ID: mdl-38397559

ABSTRACT

Food is one of the factors with the highest impact on human health. Today, attention is paid not only to food properties such as energy provision and palatability but also to functional aspects including phytochemical, antioxidant properties, etc. Massaman and spicy basil leaf curries are famous Thai food dishes with a good harmony of flavor and taste, derived from multiple herbs and spices, including galangal rhizomes, chili pods, garlic bulbs, peppers, shallots, and coriander seeds, that provide an array of health benefits. The characterization of phytochemicals detected by LC-ESI-QTOF-MS/MS identified 99 components (Masaman) and 62 components (spicy basil leaf curry) such as quininic acid, hydroxycinnamic acid, luteolin, kaempferol, catechin, eugenol, betulinic acid, and gingerol. The cynaroside and luteolin-7-O-glucoside found in spicy basil leaf curry play a key role in antioxidant activities and were found at a significantly higher concentration than in Massaman curry. Phenolic and flavonoid compounds generally exhibit a bitter and astringent taste, but all the panelists scored both curries higher than 7 out of 9, confirming their acceptable flavor. Results suggest that the Massaman and spicy basil leaves contain various phytochemicals at different levels and may be further used as functional ingredients and nutraceutical products.

2.
Foods ; 13(2)2024 Jan 05.
Article in English | MEDLINE | ID: mdl-38254479

ABSTRACT

All living organisms undergo molecular damage by free radical products. Disrupting the balance between antioxidants and free radicals leads to greater risks of diabetes, hypertension, stroke, and cancer. Consumption of curries containing various herbs and spices provides antioxidant and anti-inflammatory benefits which promote health. The antioxidant and nitric oxide (NO) inhibitory properties of six popular Thai curries, including green curry (G), Panang curry (P), Massaman curry (M), spicy basil leaf curry (SB), southern sour curry (SS), and southern spicy yellow curry (SY) were determined. All six curries contained phenolic and flavonoid compounds and provided antioxidant activity based on electron transfer and hydrogen atom donor properties, as well as having the ability to reduce oxidized metal. The highest antioxidant value was found in SB, followed by M, SS, and SY. The replacement of sugar with dried stevia powder at 50% (Re) improved antioxidant activity. The ORAC assay provided five times higher results than DPPH, ABTS, and FRAP. Extracts of all curries at 1 mg/mL on the macrophage cell line RAW 264.7 showed no cytotoxicity. The highest NO inhibition was found in SB (p < 0.05). All curry extracts contained quercetin, kaempferol, luteolin, and apigenin. The six selected popular Thai curries had antioxidant and anti-inflammatory health benefits. Nutraceuticals, functional foods, and the ingredients of each raw material and curry powder should be further investigated.

3.
J Microbiol Biotechnol ; 32(10): 1315-1324, 2022 Oct 28.
Article in English | MEDLINE | ID: mdl-36198663

ABSTRACT

Fermentation is an effective process for providing various beneficial effects in functional beverages. Lactic acid bacteria and yeast fermentation-based biotransformation contribute to enhancement of nutritional value and digestibility, including lactose intolerance reduction and control of infections. In this study, the probiotic fermented fruit juice (PFJ) was produced by Lactobacillus plantarum TISTR 1465, Lactobacillus salivarius TISTR 1112, and Saccharomyces boulardii CNCM I-745 while mixed fruit juice (MFJ) was used as the basic medium for microorganism growth. The potential function, the anti-salmonella activity of PFJ, was found to be effective at 250 mg/ml of MIC and 500 mg/ml of MBC. Biofilm inhibition was performed using the PFJ samples and showed at least 70% reduction in cell attachment at the MIC concentration of Salmonella Typhi DMST 22842. The antioxidant activities of PFJ were determined and the results revealed that FSB.25 exhibited 78.40 ± 0.51 mM TE/ml by FRAP assay, while FPSB.25 exhibited 3.44 ± 0.10 mM TE/ml by DPPH assay. The volatile compounds of PFJ were characterized by GC-MS, which identified alcohol, aldehyde, acid, ester, ketone, phenol, and terpene. The most abundant organic acid and alcohol detected in PFJ were acetic acid and 2-phenylethanol, and the most represented terpene was ß-damascenone. The sensory attributes showed scores higher than 7 on a 9-point hedonic scale for the FPB.25, illustrating that it was well accepted by panelists. Taken together, our results showed that PFJ could meet current consumer demand regarding natural and functional, fruit-based fermented beverages.


Subject(s)
Lactobacillales , Probiotics , Saccharomyces boulardii , Fruit and Vegetable Juices , Antioxidants/pharmacology , Antioxidants/analysis , Saccharomyces cerevisiae , Fermentation , Biotransformation , Terpenes
4.
Int J Food Sci ; 2021: 2213814, 2021.
Article in English | MEDLINE | ID: mdl-34651043

ABSTRACT

Vascular dementia (VaD) is the second most common type of dementia following Alzheimer's disease, but the therapeutic efficacy is still not effective. This makes the searching for novel neuroprotective agents important. Therefore, we hypothesized that royal jelly, a well-known traditional medicine, could attenuate memory impairment and brain damage in vascular dementia. This study determined the effects of royal jelly hydrolysate (RJH) and possible mechanism of cell damage and cognitive-enhancing effect in animal study. An in vitro study assessed the effects of RJH on acetylcholinesterase inhibitor, cell viability, and cell damage in SH-SY5Y neuroblastoma cells. Then, an in vivo study examined vascular dementia by the occlusion of the right middle cerebral artery (Rt.MCAO); adult male Wistar rats had been orally given RJH at doses ranging from 10, 50, to 100 mg/kg for 14 days before and 14 days after the occlusion of Rt.MCAO to mimic the VaD condition. Rats' spatial memory was evaluated using Morris water maze and radial arm maze every 7 days after Rt.MCAO throughout a 14-day experimental period, and then, they were sacrificed and the acetylcholinesterase (AChE) activity in the hippocampus was determined. The results showed that RJH has no cytotoxic effect with the final concentration up to 500 µg protein/ml and reduces cell death from the H2O2- and glutamate-induced cell damage in in vitro neuroblastoma cells. Importantly, RJH significantly improved memory performance in Morris water maze test and radial arm maze and decreased the level of acetyl cholinesterase activity. In conclusion, RJH is the potential neuroprotective agent and cognitive enhancer for VaD.

5.
J Food Biochem ; 43(12): e13058, 2019 12.
Article in English | MEDLINE | ID: mdl-31608485

ABSTRACT

Angiotensin I-converting enzyme (ACE) inhibitory peptides were derived from tuna cooking juice (TCJ) hydrolysis by alcalase in the continuous enzymatic membrane reactor (cEMR) coupling with 1 kDa MWCO membrane. The permeated sample from cEMR for 510 min of hydrolysis was purified by size exclusion chromatography in Sephadex G-25 column. A fraction exhibited the highest ACE inhibitory activity was further separated by RP-HPLC, resulting two fractions showed highest ACE inhibitory activities. The molecular weight (MW) and amino acid sequences of peptides from both fractions were determined using LC-MS/MS. Two potential ACE inhibitory peptides were obtained and showed molecular weight of 959.46 and 1,141.29 Da. PRACTICAL APPLICATIONS: Tuna cooking juice (TCJ) usually was either used as protein source of feed meal or directly discharged to wastewater treatment system. However, it contains water-soluble proteins in a group of sarcoplasmic protein, which is small water-soluble proteins and easily hydrolyzed to small peptides. In this study, the active peptides, angiotensin I-converting enzyme inhibitory peptides (MW of 959.46 and 1,141.29 Da), obtained from TCJ hydrolysate and identified by LC-MS/MS would be a beneficial ingredient for nutraceuticals and functional food against hypertension.


Subject(s)
Angiotensin-Converting Enzyme Inhibitors/chemistry , Peptides/chemistry , Peptides/isolation & purification , Peptidyl-Dipeptidase A/chemistry , Amino Acid Sequence , Animals , Cooking , Hydrolysis , Tuna
6.
AIMS Biophys ; 4(1): 1-18, 2017.
Article in English | MEDLINE | ID: mdl-28050603

ABSTRACT

SMYD3 plays a key role in cancer cell viability, adhesion, migration and invasion. SMYD3 promotes formation of inducible regulatory T cells and is involved in reducing autoimmunity. However, the nearly "closed" substrate-binding site and poor in vitro H3K4 methyltransferase activity have obscured further understanding of this oncogenically related protein. Here we reveal that SMYD3 can adopt an "open" conformation using molecular dynamics simulation and small-angle X-ray scattering. This ligand-binding-capable open state is related to the crystal structure-like closed state by a striking clamshell-like inter-lobe dynamics. The two states are characterized by many distinct structural and dynamical differences and the conformational transition pathway is mediated by a reversible twisting motion of the C-terminal domain (CTD). The spontaneous transition from the closed to open states suggests two possible, mutually non-exclusive models for SMYD3 functional regulation and the conformational selection mechanism and allostery may regulate the catalytic or ligand binding competence of SMYD3. This study provides an immediate clue to the puzzling role of SMYD3 in epigenetic gene regulation.

7.
J Sci Food Agric ; 96(11): 3795-800, 2016 Aug.
Article in English | MEDLINE | ID: mdl-26676993

ABSTRACT

BACKGROUND: Fish skin has become a new source of collagen. It is usually extracted at low temperature. Increasing the extraction temperature can increase the collagen yield. However, high temperature might cause degradation of the triple helical structure of collagen, which is related to its functional biomaterial. This work thus aimed to investigate the effect of extraction temperature on the extraction efficiency and characteristics of acid-soluble collagen (ASC), particularly its triple helical structure. RESULTS: ASC was extracted at 5 ± 1, 15 ± 1 and 25 ± 1 °C for 0-24 h with 0.3 or 0.5 mol L(-1) acetic acid. The results showed that extraction with 0.5 mol L(-1) acetic acid gave a higher extraction efficiency than that in 0.3 mol L(-1) acetic acid (P < 0.5). Extraction at 25 ± 1 °C for 5 h with 0.5 mol L(-1) acetic acid gave a higher extraction efficiency (73.73 ± 1.28%), which is higher than that of 5 ± 1 °C by about 1.7-fold. All ASC obtained were identified as type I collagen and showed similar physicochemical properties. CONCLUSION: The results showed that extraction temperature strongly affected extraction efficiency. Extraction at 25 °C did not affect the triple helical structure, which was confirmed by the results of Fourier transform infrared, circular dichroism spectrum and collagen self-assembly. © 2015 Society of Chemical Industry.


Subject(s)
Cichlids , Collagen Type I/chemistry , Fish Proteins/chemistry , Industrial Waste/analysis , Skin/chemistry , Acetic Acid/chemistry , Animals , Circular Dichroism , Cold Temperature , Collagen Type I/economics , Collagen Type I/isolation & purification , Electrophoresis, Polyacrylamide Gel , Fish Proteins/economics , Fish Proteins/isolation & purification , Food-Processing Industry/economics , Hydroxyproline/analysis , Indicators and Reagents/chemistry , Industrial Waste/economics , Kinetics , Microscopy, Electron, Scanning , Protein Denaturation , Protein Folding , Protein Stability , Protein Structure, Secondary , Solubility , Spectroscopy, Fourier Transform Infrared , Thailand
8.
PLoS One ; 10(12): e0145758, 2015.
Article in English | MEDLINE | ID: mdl-26717235

ABSTRACT

SMYD proteins are an exciting field of study as they are linked to many types of cancer-related pathways. Cardiac and skeletal muscle development and function also depend on SMYD proteins opening a possible avenue for cardiac-related treatment. Previous crystal structure studies have revealed that this special class of protein lysine methyltransferases have a bilobal structure, and an open-closed motion may regulate substrate specificity. Here we use the molecular dynamics simulation to investigate the still-poorly-understood SMYD2 dynamics. Cross-correlation analysis reveals that SMYD2 exhibits a negative correlated inter-lobe motion. Principle component analysis suggests that this correlated dynamic is contributed to by a twisting motion of the C-lobe with respect to the N-lobe and a clamshell-like motion between the lobes. Dynamical network analysis defines possible allosteric paths for the correlated dynamics. There are nine communities in the dynamical network with six in the N-lobe and three in the C-lobe, and the communication between the lobes is mediated by a lobe-bridging ß hairpin. This study provides insight into the dynamical nature of SMYD2 and could facilitate better understanding of SMYD2 substrate specificity.


Subject(s)
Histone-Lysine N-Methyltransferase/chemistry , Molecular Dynamics Simulation , Motion , Principal Component Analysis , Protein Structure, Secondary
9.
Curr Drug Targets ; 16(9): 976-87, 2015.
Article in English | MEDLINE | ID: mdl-25882215

ABSTRACT

Cystic fibrosis (CF) is a deadly genetic disease that affects the lungs and digestive system. A mutation in the CF transmembrane conductance regulator (CFTR) gene is the cause of the disease. How epigenetics contributes to CFTR expression is still poorly understood. Epigenetics is a mechanism that alters gene expression without changing the underlying DNA sequence. Epigenetic mechanisms include DNA methylation and histone modification. Both mechanisms have been implicated in CFTR gene regulation. Here we review epigenetic regulation of CFTR transcription while discussing potential epigenetic targeting strategies including DNA methyltransferase, histone deacetylase, and histone methyltransferase and demethylase inhibition. Because of the reversibility of epigenetics, targeting epigenetic mechanisms has been an attractive therapeutic approach. However, epigenetic targeting of CF disease is still at its infant stage.


Subject(s)
Cystic Fibrosis Transmembrane Conductance Regulator/genetics , Cystic Fibrosis/drug therapy , Enzyme Inhibitors/pharmacology , Epigenesis, Genetic/drug effects , Cystic Fibrosis/enzymology , Cystic Fibrosis/genetics , DNA Modification Methylases/antagonists & inhibitors , Enzyme Inhibitors/therapeutic use , Histone Deacetylases , Histone Methyltransferases , Histone-Lysine N-Methyltransferase , Humans , Mutation
10.
Int J Mol Sci ; 16(1): 1406-28, 2015 Jan 08.
Article in English | MEDLINE | ID: mdl-25580534

ABSTRACT

SET (Suppressor of variegation, Enhancer of Zeste, Trithorax) and MYND (Myeloid-Nervy-DEAF1) domain-containing proteins (SMYD) have been found to methylate a variety of histone and non-histone targets which contribute to their various roles in cell regulation including chromatin remodeling, transcription, signal transduction, and cell cycle control. During early development, SMYD proteins are believed to act as an epigenetic regulator for myogenesis and cardiomyocyte differentiation as they are abundantly expressed in cardiac and skeletal muscle. SMYD proteins are also of therapeutic interest due to the growing list of carcinomas and cardiovascular diseases linked to SMYD overexpression or dysfunction making them a putative target for drug intervention. This review will examine the biological relevance and gather all of the current structural data of SMYD proteins.


Subject(s)
DNA-Binding Proteins/chemistry , Histones/chemistry , Transcription Factors/chemistry , Binding Sites , DNA-Binding Proteins/metabolism , Histone-Lysine N-Methyltransferase/chemistry , Histone-Lysine N-Methyltransferase/metabolism , Histones/metabolism , Humans , Muscle, Skeletal/cytology , Muscle, Skeletal/metabolism , Protein Structure, Tertiary , Substrate Specificity , Transcription Factors/metabolism , Zinc Fingers
11.
Curr Drug Targets ; 16(9): 988-92, 2015.
Article in English | MEDLINE | ID: mdl-25418859

ABSTRACT

Cystic fibrosis (CF) is a genetic disorder that can lead to death at an early age. CF is characterized by respiratory infection, airway obstruction, inflammation, and eventually end-stage lung failure. CF also damages pancreatic exocrine function resulting in serious complications such as nutritional deficiencies. Current therapy to this multisystem disease requires the practice of both pharmacological and nutritional approaches. Growing evidence shows that bioactive food components, such as polyunsaturated fatty acids, phytochemicals, and antioxidants, have beneficial effects in the management of CF disease. This review will summarize the current status of bioactive compounds in CF therapy.


Subject(s)
Antioxidants/therapeutic use , Cystic Fibrosis/diet therapy , Fatty Acids, Unsaturated/therapeutic use , Phytochemicals/therapeutic use , Cystic Fibrosis/pathology , Dietary Supplements , Functional Food , Humans , Nutritional Status
12.
Biochem Biophys Res Commun ; 448(2): 169-74, 2014 May 30.
Article in English | MEDLINE | ID: mdl-24768637

ABSTRACT

The formation of CXCR2-NHERF1-PLCß2 macromolecular complex in neutrophils regulates CXCR2 signaling and plays a key role in neutrophil chemotaxis and transepithelial neutrophilic migration. However, NHERF1 by itself, with only two PDZ domains, has a limited capacity in scaffolding the multiprotein-complex formation. Here we report the crystal structure of the NHERF1 PDZ2 domain in complex with the C-terminal CXCR2 sequence. The structure reveals that the PDZ2-CXCR2 binding specificity is achieved by numerous hydrogen bonds and hydrophobic contacts with the last four CXCR2 residues contributing to specific interactions. The structure also reveals two probable modes of PDZ2 dimerization where the two canonical ligand-binding pockets are well separated and orientated in a unique parallel fashion. This study provides not only the structural basis for the PDZ-mediated NHERF1-CXCR2 interaction, but also an additional example of how PDZ domains may dimerize, which both could prove valuable in understanding NHERF1 complex-scaffolding function in neutrophils.


Subject(s)
Phosphoproteins/chemistry , Phosphoproteins/metabolism , Receptors, Interleukin-8B/chemistry , Receptors, Interleukin-8B/metabolism , Sodium-Hydrogen Exchangers/chemistry , Sodium-Hydrogen Exchangers/metabolism , Amino Acid Sequence , Binding Sites , Crystallography, X-Ray , Humans , Models, Molecular , Molecular Sequence Data , PDZ Domains , Protein Conformation , Protein Multimerization
13.
Biochem Biophys Res Commun ; 446(1): 399-403, 2014 Mar 28.
Article in English | MEDLINE | ID: mdl-24613836

ABSTRACT

The formation of CFTR-NHERF2-LPA2 macromolecular complex in airway epithelia regulates CFTR channel function and plays an important role in compartmentalized cAMP signaling. We previously have shown that disruption of the PDZ-mediated NHERF2-LPA2 interaction abolishes the LPA inhibitory effect and augments CFTR Cl(-) channel activity in vitro and in vivo. Here we report the first crystal structure of the NHERF2 PDZ1 domain in complex with the C-terminal LPA2 sequence. The structure reveals that the PDZ1-LPA2 binding specificity is achieved by numerous hydrogen bonds and hydrophobic contacts with the last four LPA2 residues contributing to specific interactions. Comparison of the PDZ1-LPA2 structure to the structure of PDZ1 in complex with a different peptide provides insights into the diverse nature of PDZ1 substrate recognition and suggests that the conformational flexibility in the ligand binding pocket is involved in determining the broad substrate specificity of PDZ1. In addition, the structure reveals a small surface pocket adjacent to the ligand-binding site, which may have therapeutic implications. This study provides an understanding of the structural basis for the PDZ-mediated NHERF2-LPA2 interaction that could prove valuable in selective drug design against CFTR-related human diseases.


Subject(s)
Cystic Fibrosis Transmembrane Conductance Regulator/chemistry , Cystic Fibrosis Transmembrane Conductance Regulator/metabolism , Phosphoproteins/chemistry , Phosphoproteins/metabolism , Receptors, Lysophosphatidic Acid/chemistry , Receptors, Lysophosphatidic Acid/metabolism , Sodium-Hydrogen Exchangers/chemistry , Sodium-Hydrogen Exchangers/metabolism , Amino Acid Sequence , Binding Sites , Crystallography, X-Ray , Cystic Fibrosis/drug therapy , Cystic Fibrosis/genetics , Cystic Fibrosis/metabolism , Cystic Fibrosis Transmembrane Conductance Regulator/genetics , Drug Design , Humans , Hydrogen Bonding , Hydrophobic and Hydrophilic Interactions , Ligands , Models, Molecular , Molecular Sequence Data , Multiprotein Complexes/chemistry , Multiprotein Complexes/genetics , Multiprotein Complexes/metabolism , PDZ Domains , Phosphoproteins/genetics , Protein Structure, Quaternary , Receptors, Lysophosphatidic Acid/genetics , Recombinant Proteins/chemistry , Recombinant Proteins/genetics , Recombinant Proteins/metabolism , Sequence Homology, Amino Acid , Sodium-Hydrogen Exchangers/genetics , Thiocyanates/metabolism
14.
J Mol Biol ; 426(20): 3413-25, 2014 Oct 09.
Article in English | MEDLINE | ID: mdl-24594358

ABSTRACT

Estrogen receptor (ER) signaling plays a pivotal role in many developmental processes and has been implicated in numerous diseases including cancers. We recently showed that direct ERα methylation by the multi-specificity histone lysine methyltransferase SMYD2 regulates estrogen signaling through repressing ERα-dependent transactivation. However, the mechanism controlling the specificity of the SMYD2-ERα interaction and the structural basis of SMYD2 substrate binding diversity are unknown. Here we present the crystal structure of SMYD2 in complex with a target lysine (Lys266)-containing ERα peptide. The structure reveals that ERα binds SMYD2 in a U-shaped conformation with the binding specificity determined mainly by residues C-terminal to the target lysine. The structure also reveals numerous intrapeptide contacts that ensure shape complementarity between the substrate and the active site of the enzyme, thereby likely serving as an additional structural determinant of substrate specificity. In addition, comparison of the SMYD2-ERα and SMYD2-p53 structures provides the first structural insight into the diverse nature of SMYD2 substrate recognition and suggests that the broad specificity of SMYD2 is achieved by multiple molecular mechanisms such as distinct peptide binding modes and the intrinsic dynamics of peptide ligands. Strikingly, a novel potentially SMYD2-specific polyethylene glycol binding site is identified in the CTD domain, implicating possible functions in extended substrate binding or protein-protein interactions. Our study thus provides the structural basis for the SMYD2-mediated ERα methylation, and the resulting knowledge of SMYD2 substrate specificity and target binding diversity could have important implications in selective drug design against a wide range of ERα-related diseases.


Subject(s)
Estrogen Receptor alpha/metabolism , Estrogens/metabolism , Histone-Lysine N-Methyltransferase/metabolism , Signal Transduction , Amino Acid Sequence , Binding Sites/genetics , Crystallography, X-Ray , Electrophoresis, Polyacrylamide Gel , Estrogen Receptor alpha/chemistry , Estrogen Receptor alpha/genetics , Ethylene Glycol/chemistry , Ethylene Glycol/metabolism , Histone-Lysine N-Methyltransferase/chemistry , Histone-Lysine N-Methyltransferase/genetics , Humans , Lysine/chemistry , Lysine/metabolism , Methylation , Models, Molecular , Mutation , Protein Binding , Protein Structure, Tertiary , Sequence Homology, Amino Acid , Substrate Specificity
15.
Biochem Biophys Res Commun ; 446(2): 638-43, 2014 Apr 04.
Article in English | MEDLINE | ID: mdl-24642259

ABSTRACT

The formation of CXCR2-NHERF1-PLCß3 macromolecular complex in pancreatic cancer cells regulates CXCR2 signaling activity and plays an important role in tumor proliferation and invasion. We previously have shown that disruption of the NHERF1-mediated CXCR2-PLCß3 interaction abolishes the CXCR2 signaling cascade and inhibits pancreatic tumor growth in vitro and in vivo. Here we report the crystal structure of the NHERF1 PDZ1 domain in complex with the C-terminal PLCß3 sequence. The structure reveals that the PDZ1-PLCß3 binding specificity is achieved by numerous hydrogen bonds and hydrophobic contacts with the last four PLCß3 residues contributing to specific interactions. We also show that PLCß3 can bind both NHERF1 PDZ1 and PDZ2 in pancreatic cancer cells, consistent with the observation that the peptide binding pockets of these PDZ domains are highly structurally conserved. This study provides an understanding of the structural basis for the PDZ-mediated NHERF1-PLCß3 interaction that could prove valuable in selective drug design against CXCR2-related cancers.


Subject(s)
Pancreatic Neoplasms/metabolism , Phospholipase C beta/metabolism , Phospholipase C beta/ultrastructure , Phosphoproteins/metabolism , Phosphoproteins/ultrastructure , Receptors, Interleukin-8B/metabolism , Sodium-Hydrogen Exchangers/metabolism , Sodium-Hydrogen Exchangers/ultrastructure , Binding Sites , Cell Line, Tumor , Crystallography/methods , Humans , Models, Chemical , Models, Molecular , Pancreatic Neoplasms/chemistry , Pancreatic Neoplasms/ultrastructure , Phospholipase C beta/chemistry , Phosphoproteins/chemistry , Protein Binding , Protein Conformation , Receptors, Interleukin-8B/ultrastructure , Signal Transduction , Sodium-Hydrogen Exchangers/chemistry
16.
PLoS One ; 8(12): e81904, 2013.
Article in English | MEDLINE | ID: mdl-24339979

ABSTRACT

NHERF1 is a PDZ adaptor protein that scaffolds the assembly of diverse signaling complexes and has been implicated in many cancers. However, little is known about the mechanism responsible for its scaffolding promiscuity or its ability to bind to multiple targets. Computational studies have indicated that PDZ promiscuity may be attributed to its conformational dynamics, but experimental evidence for this relationship remains very limited. Here we examine the conformational flexibility of the NHERF1 PDZ1 domain using crystal lattice trapping via solving PDZ1 structure of a new crystal form. The structure, together with prior PDZ1 structures of a different space group, reveals that 4 of 11 ligand-interacting residues undergo significant crystal packing-induced structural changes. Most of these residues correspond to the residues involved in allosteric transition when a peptide ligand binds. In addition, a subtle difference in ligand conformations causes the same peptide to bind in slightly different modes in different crystal forms. These findings indicate that substantial structural flexibility is present in the PDZ1 peptide-binding pocket, and the structural substate trapped in the present crystal form can be utilized to represent the conformational space accessible to the protein. Such knowledge will be critical for drug design against the NHERF1 PDZ1 domain, highlighting the continued need for experimentally determined PDZ1-ligand complexes.


Subject(s)
Molecular Dynamics Simulation , Multiprotein Complexes/chemistry , Phosphoproteins/chemistry , Receptors, Interleukin-8B/chemistry , Signal Transduction , Sodium-Hydrogen Exchangers/chemistry , Crystallography, X-Ray , Humans , Multiprotein Complexes/genetics , Phosphoproteins/genetics , Protein Structure, Quaternary , Receptors, Interleukin-8B/genetics , Sodium-Hydrogen Exchangers/genetics
17.
PLoS One ; 8(10): e76219, 2013.
Article in English | MEDLINE | ID: mdl-24098448

ABSTRACT

Neutrophil plays an essential role in host defense against infection, but uncontrolled neutrophilic infiltration can cause inflammation and severe epithelial damage. We recently showed that CXCR2 formed a signaling complex with NHERF1 and PLC-2, and that the formation of this complex was required for intracellular calcium mobilization and neutrophilic transepithelial migration. To uncover the structural basis of the complex formation, we report here the crystal structure of the NHERF1 PDZ1 domain in complex with the C-terminal sequence of CXCR2 at 1.16 Å resolution. The structure reveals that the CXCR2 peptide binds to PDZ1 in an extended conformation with the last four residues making specific side chain interactions. Remarkably, comparison of the structure to previously studied PDZ1 domains has allowed the identification of PDZ1 ligand-specific interactions and the mechanisms that govern PDZ1 target selection diversities. In addition, we show that CXCR2 can bind both NHERF1 PDZ1 and PDZ2 in pulldown experiments, consistent with the observation that the peptide binding pockets of these two PDZ domains are highly structurally conserved. The results of this study therefore provide structural basis for the CXCR2-mediated neutrophilic migration and could have important clinical applications in the prevention and treatment of numerous neutrophil-dependent inflammatory disorders.


Subject(s)
PDZ Domains , Phosphoproteins/chemistry , Receptors, Interleukin-8B/chemistry , Sodium-Hydrogen Exchangers/chemistry , Amino Acid Motifs , Amino Acid Sequence , Binding Sites , Drug Design , Humans , Ligands , Models, Molecular , Molecular Sequence Data , Neutrophils/immunology , Neutrophils/metabolism , Phosphoproteins/metabolism , Protein Binding , Protein Conformation , Receptors, Interleukin-8B/metabolism , Sequence Alignment , Sodium-Hydrogen Exchangers/metabolism
18.
PLoS One ; 6(6): e21640, 2011.
Article in English | MEDLINE | ID: mdl-21738746

ABSTRACT

SmyD2 belongs to a new class of chromatin regulators that control gene expression in heart development and tumorigenesis. Besides methylation of histone H3 K4, SmyD2 can methylate non-histone targets including p53 and the retinoblastoma tumor suppressor. The methyltransferase activity of SmyD proteins has been proposed to be regulated by autoinhibition via the intra- and interdomain bending of the conserved C-terminal domain (CTD). However, there has been no direct evidence of a conformational change in the CTD. Here, we report two crystal structures of SmyD2 bound either to the cofactor product S-adenosylhomocysteine or to the inhibitor sinefungin. SmyD2 has a two-lobed structure with the active site located at the bottom of a deep crevice formed between the CTD and the catalytic domain. By extensive engagement with the methyltransferase domain, the CTD stabilizes the autoinhibited conformation of SmyD2 and restricts access to the catalytic site. Unexpectedly, despite that the two SmyD2 structures are highly superimposable, significant differences are observed in the first two helices of the CTDs: the two helices bend outwards and move away from the catalytic domain to generate a less closed conformation in the sinefungin-bound structure. Although the overall fold of the individual domains is structurally conserved among SmyD proteins, SmyD2 appear to be a conformational "intermediate" between a close form of SmyD3 and an open form of SmyD1. In addition, the structures reveal that the CTD is structurally similar to tetratricopeptide repeats (TPR), a motif through which many cochaperones bind to the heat shock protein Hsp90. Our results thus provide the first evidence for the intradomain flexibility of the TPR-like CTD, which may be important for the activation of SmyD proteins by Hsp90.


Subject(s)
Crystallography, X-Ray/methods , Histone-Lysine N-Methyltransferase/chemistry , Histone-Lysine N-Methyltransferase/metabolism , Histones/chemistry , Histones/metabolism , Humans , Protein Structure, Tertiary
19.
J Mol Biol ; 406(1): 149-59, 2011 Feb 11.
Article in English | MEDLINE | ID: mdl-21167177

ABSTRACT

The SmyD family represents a new class of chromatin regulators that is important in heart and skeletal muscle development. However, the critical questions regarding how they are regulated posttranslationally remain largely unknown. We previously suggested that the histone methyltransferase activity of SmyD1, a vital myogenic regulator, appears to be regulated by autoinhibition and that the possible hinge motion of the conserved C-terminal domain (CTD) might be central to the maintenance and release of the autoinhibition. However, the lack of direct evidence of the hinge motion has limited our further understanding of this autoinhibitory mechanism. Here, we report the crystal structure of full-length SmyD3 in complex with the methyltransferase inhibitor sinefungin at 1.7 Å. SmyD3 has a two-lobed structure with the substrate binding cleft located at the bottom of a  15-Å-deep crevice formed between the N- and C-terminal lobes. Comparison of SmyD3 and SmyD1 clearly suggests that the CTD can undergo a large hinge-bending motion that defines two distinct conformations: SmyD3 adopts a closed conformation with the CTD partially blocking the substrate binding cleft; in contrast, SmyD1 appears to represent an open form, where the CTD swings out by ∼12 Å from the N-terminal lobe, forming an open cleft with the active site completely exposed. Overall, these findings provide novel structural insights into the mechanism that modulates the activity of the SmyD proteins and support the observation that a posttranslational activation, such as by molecular chaperon Hsp90, is required to potentiate the proteins.


Subject(s)
Adenosine/analogs & derivatives , Enzyme Inhibitors/chemistry , Histone-Lysine N-Methyltransferase/chemistry , Protein Processing, Post-Translational , Adenosine/chemistry , Amino Acid Sequence , Catalytic Domain , Histone-Lysine N-Methyltransferase/antagonists & inhibitors , Humans , Molecular Sequence Data , Protein Conformation , X-Ray Diffraction
20.
J Biol Chem ; 285(52): 40635-44, 2010 Dec 24.
Article in English | MEDLINE | ID: mdl-20943667

ABSTRACT

SmyD1 is a cardiac- and muscle-specific histone methyltransferase that methylates histone H3 at lysine 4 and regulates gene transcription in early heart development. The unique domain structure characterized by a "split" SET domain, a conserved MYND zinc finger, and a novel C-terminal domain (CTD) distinguishes SmyD1 from other SET domain containing methyltransferases. Here we report the crystal structure of full-length SmyD1 in complex with the cofactor analog sinefungin at 2.3 Å. The structure reveals that SmyD1 folds into a wrench-shaped structure with two thick "grips" separated by a large, deep concave opening. Importantly, our structural and functional analysis suggests that SmyD1 appears to be regulated by an autoinhibition mechanism, and that unusually spacious target lysine-access channel and the presence of the CTD domain both negatively contribute to the regulation of this cardiovascularly relevant methyltransferase. Furthermore, our structure also provides a structural basis for the interaction between SmyD1 and cardiac transcription factor skNAC, and suggests that the MYND domain may primarily serve as a protein interaction module and cooperate SmyD1 with skNAC to regulate cardiomyocyte growth and maturation. Overall, our data provide novel insights into the mechanism of SmyD1 regulation, which would be helpful in further understanding the role of this protein in heart development and cardiovascular diseases.


Subject(s)
DNA-Binding Proteins/chemistry , Histone-Lysine N-Methyltransferase/chemistry , Muscle Proteins/chemistry , Myocardium/enzymology , Myocytes, Cardiac/enzymology , Transcription Factors/chemistry , Animals , Catalytic Domain , Crystallography, X-Ray , DNA-Binding Proteins/genetics , DNA-Binding Proteins/metabolism , Histone Methyltransferases , Histone-Lysine N-Methyltransferase/genetics , Histone-Lysine N-Methyltransferase/metabolism , Mice , Molecular Chaperones/chemistry , Molecular Chaperones/genetics , Molecular Chaperones/metabolism , Muscle Proteins/genetics , Muscle Proteins/metabolism , Transcription Factors/genetics , Transcription Factors/metabolism
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