Unfolding and refolding of cytochrome c driven by the interaction with lipid micelles

Binding of native cyt c to L-PG micelles leads to a partially unfolded conformation of cyt c. This micelle-bound state has no stable tertiary structure, but remains as -helical as native cyt c in solution. In contrast, binding of the acid-unfolded cyt c to L-PG micelles induces folding of the polypeptide, resulting in a similar helical state to that originated from the binding of native cyt c to L-PG micelles. Far-ultraviolet (UV) circular dichroism (CD) spectra showed that this common micelle-associated helical state (HL) has a native-like -helix content, but is highly expanded without a tightly packed hydrophobic core, as revealed by tryptophan fluorescence, near-UV, and Soret CD spectroscopy. The kinetics of the interaction of native and acid-unfolded cyt c was investigated by stopped-flow tryptophan fluorescence. Formation of HL from the native state requires the disruption of the tightly packed hydrophobic core in the native protein. This micelle-induced unfolding of cyt c occurs at a rate 0.1 s1, which is remarkably faster in the lipid environment compared with the expected rate of unfolding in solution. Refolding of acid-unfolded cyt c with L-PG micelles involves an early highly helical collapsed state formed during the burst phase (<3 ms), and the observed main kinetic event reports on the opening of this early compact intermediate prior to insertion into the lipid micelle

The interaction of the prion protein with lipid membranes and implications for prion conversion

Prion diseases are characterised by the conversion of the normal a-helical prion protein (PrPc), to the abnormal P-sheet isoform (PrPSc). Biophysical studies using recombinant prion proteins have helped our understanding of the structural events associated with the transition of PrPc to PrPSc. These studies were performed in an aqueous environment, however PrP in living cells is anchored to cholesterol/sphingomyelin rich raft-domains. Evidence suggests that the lipid environment plays’ a role in the conversion of PrPc to PrPSc. Therefore in this thesis the biophysical properties of PrP in lipid membranes were evaluated. The binding of Syrian hamster prion protein, SHaPrP (90-231) to model lipid membranes was investigated by tryptophan fluorescence spectroscopy. Membranes composed of negatively charged lipids, zwitterionic lipids and raft-like membranes containing DPPC, cholesterol and sphingomyelin, were investigated. The results show that PrP has an affinity for negatively charged and gel-phase zwitterionic membranes. Binding of PrP to raft-like membranes was also observed. The interaction of PrP to negatively charged membranes involved both electrostatic and hydrophobic lipid- protein interactions, whereas the binding of PrP to raft-like membranes was predominantly driven by hydrophobic lipid-protein interactions. CD and ATR FTIR were used to investigate the secondary structure of PrP in lipid membranes. The interaction of PrP to negatively charged membranes was accompanied by an increase in P-sheet structure and EM showed extensive aggregation of the protein. In contrast, the binding of PrP to gel-phase zwitterionic membranes and raft-like membranes induced the formation of stable a-helical structure. No evidence of aggregation was detected in the EM images. The ability of PrP to perturb lipid membranes was examined. Evidence for the partial insertion of PrP into negatively charged membranes was obtained and the resulting p-sheet state was capable of disrupting lipid membranes, leading to total release of vesicle contents. The a-helical membrane bound state of PrP did not affect the integrity of the raft-like membranes. These finding support the view that the interaction of PrP with lipid membranes may play a role in PrP conversion

Towards personalised molecular feedback for weight loss

Background Numerous diets, apps and websites help guide and monitor dietary behaviour with the goal of losing weight, yet dieting success is highly dependent on personal preferences and circumstances. To enable a more quantitative approach to dieting, we developed an integrated platform that allows tracking of life-style information alongside molecular biofeedback measurements (lactate and insulin). Methods To facilitate weight loss, participants (≥18 years) omitted one main meal from the usual three-meal routine. Daily caloric intake was restricted to ~1200KCal with one optional snack ≤250KCal. A mobile health platform (personalhealth.warwick.ac.uk) was developed and used to maintain diaries of food intake, weight, urine collection and volume. A survey was conducted to understand participants’ willingness to collect samples, motivation for taking part in the study and reasons for dropout. Results Meal skipping resulted in weight loss after a 24 h period in contrast to 3-meal control days regardless of the meal that was skipped, breakfast, lunch or dinner (p < 0.001). Common reasons for engagement were interest in losing weight and personal metabolic profile. Total insulin and lactate values varied significantly between healthy and obese individuals at p = 0.01 and 0.05 respectively. Conclusion In a proof of concept study with a meal-skipping diet, we show that insulin and lactate values in urine correlate with weight loss, making these molecules potential candidates for quantitative feedback on food intake behaviour to people dieting

Data for 'Something in the way she moves': the functional significance of flexibility in the multiple roles of protein disulfide isomerase (PDI)

Protein disulfide isomerase (PDI) has diverse functions in the endoplasmic reticulum as catalyst of redox transfer, disulfide isomerization and oxidative protein folding, as molecular chaperone and in multi-subunit complexes. It interacts with an extraordinarily wide range of substrate and partner proteins, but there is only limited structural information on these interactions. Extensive evidence on the flexibility of PDI in solution is not matched by any detailed picture of the scope of its motion. A new rapid method for simulating the motion of large proteins provides detailed molecular trajectories for PDI demonstrating extensive changes in the relative orientation of its four domains, great variation in the distances between key sites and internal motion within the core ligand-binding domain. The review shows that these simulations are consistent with experimental evidence and provide insight into the functional capabilities conferred by the extensive flexible motion of PDI

Variants in KCNQ1 increase type II diabetes susceptibility in South Asians: A study of 3,310 subjects from India and the US

<p>Abstract</p> <p>Background</p> <p>Polymorphisms in intron 15 of potassium voltage-gated channel, KQT-like subfamily member 1 (<it>KCNQ1</it>) gene have been associated with type II diabetes (T2D) in Japanese genome-wide association studies (GWAS). More recently a meta-analysis of European GWAS has detected a new independent signal associated with T2D in intron 11 of the <it>KCNQ1 </it>gene. The purpose of this investigation is to examine the role of these variants with T2D in populations of Asian Indian descent from India and the US.</p> <p>Methods</p> <p>We examined the association between four variants in the <it>KCNQ1 </it>gene with T2D and related quantitative traits in a total of 3,310 Asian Indian participants from two different cohorts comprising 2,431 individuals of the Punjabi case-control cohort from the Sikh Diabetes Study and 879 migrant Asian Indians living in the US.</p> <p>Results</p> <p>Our data confirmed the association of a new signal at the <it>KCNQ1 </it>locus (rs231362) with T2D showing an allelic odds ratio (OR) of 1.24 95%CI [1.08-1.43], p = 0.002 in the Punjabi cohort. A moderate association with T2D was also seen for rs2237895 in the Punjabi (OR 1.14; p = 0.036) and combined cohorts (meta-analysis OR 1.14; p = 0.018). Three-site haplotype analysis of rs231362, rs2237892, rs2237895 exhibited considerably stronger evidence of association of the GCC haplotype with T2D showing OR of 1.24 95%CI [1.00-1.53], p = 0.001, permutation p = 8 × 10^-4in combined cohorts. The 'C' risk allele carriers of rs2237895 had significantly reduced measures of HOMA-B in the US cohort (p = 0.008) as well as in combined cohort in meta-analysis (p = 0.009).</p> <p>Conclusions</p> <p>Our investigation has confirmed that the variation within the <it>KCNQ1 </it>locus confers a significant risk to T2D among Asian Indians. Haplotype analysis further suggested that the T2D risk associated with <it>KCNQ1 </it>SNPs may be derived from 'G' allele of rs231362 and 'C' allele of rs2237895 and this appears to be mediated through β cell function.</p

Genome-Wide Linkage Scan to Identify Loci Associated with Type 2 Diabetes and Blood Lipid Phenotypes in the Sikh Diabetes Study

In this investigation, we have carried out an autosomal genome-wide linkage analysis to map genes associated with type 2 diabetes (T2D) and five quantitative traits of blood lipids including total cholesterol, high-density lipoprotein (HDL) cholesterol, low-density lipoprotein (LDL) cholesterol, very low-density lipoprotein (VLDL) cholesterol, and triglycerides in a unique family-based cohort from the Sikh Diabetes Study (SDS). A total of 870 individuals (526 male/344 female) from 321 families were successfully genotyped using 398 polymorphic microsatellite markers with an average spacing of 9.26 cM on the autosomes. Results of non-parametric multipoint linkage analysis using Sall statistics (implemented in Merlin) did not reveal any chromosomal region to be significantly associated with T2D in this Sikh cohort. However, linkage analysis for lipid traits using QTL-ALL analysis revealed promising linkage signals with p≤0.005 for total cholesterol, LDL cholesterol, and HDL cholesterol at chromosomes 5p15, 9q21, 10p11, 10q21, and 22q13. The most significant signal (p = 0.0011) occurred at 10q21.2 for HDL cholesterol. We also observed linkage signals for total cholesterol at 22q13.32 (p = 0.0016) and 5p15.33 (p = 0.0031) and for LDL cholesterol at 10p11.23 (p = 0.0045). Interestingly, some of linkage regions identified in this Sikh population coincide with plausible candidate genes reported in recent genome-wide association and meta-analysis studies for lipid traits. Our study provides the first evidence of linkage for loci associated with quantitative lipid traits at four chromosomal regions in this Asian Indian population from Punjab. More detailed examination of these regions with more informative genotyping, sequencing, and functional studies should lead to rapid detection of novel targets of therapeutic importance

Protein disulfide-isomerase interacts with a substrate protein at all stages along its folding pathway

In contrast to molecular chaperones that couple protein folding to ATP hydrolysis, protein disulfide-isomerase (PDI) catalyzes protein folding coupled to formation of disulfide bonds (oxidative folding). However, we do not know how PDI distinguishes folded, partly-folded and unfolded protein substrates. As a model intermediate in an oxidative folding pathway, we prepared a two-disulfide mutant of basic pancreatic trypsin inhibitor (BPTI) and showed by NMR that it is partly-folded and highly dynamic. NMR studies show that it binds to PDI at the same site that binds peptide ligands, with rapid binding and dissociation kinetics; surface plasmon resonance shows its interaction with PDI has a Kd of ca. 10−5 M. For comparison, we characterized the interactions of PDI with native BPTI and fully-unfolded BPTI. Interestingly, PDI does bind native BPTI, but binding is quantitatively weaker than with partly-folded and unfolded BPTI. Hence PDI recognizes and binds substrates via permanently or transiently unfolded regions. This is the first study of PDI's interaction with a partly-folded protein, and the first to analyze this folding catalyst's changing interactions with substrates along an oxidative folding pathway. We have identified key features that make PDI an effective catalyst of oxidative protein folding – differential affinity, rapid ligand exchange and conformational flexibility

Impact of nine common type 2 diabetes risk polymorphisms in Asian Indian Sikhs: PPARG2 (Pro12Ala), IGF2BP2, TCF7L2 and FTO variants confer a significant risk

<p>Abstract</p> <p>Background</p> <p>Recent genome-wide association (GWA) studies have identified several unsuspected genes associated with type 2 diabetes (T2D) with previously unknown functions. In this investigation, we have examined the role of 9 most significant SNPs reported in GWA studies: [peroxisome proliferator-activated receptor gamma 2 (<it>PPARG2</it>; rs 1801282); insulin-like growth factor two binding protein 2 (<it>IGF2BP2</it>; rs 4402960); cyclin-dependent kinase 5, a regulatory subunit-associated protein1-like 1 (<it>CDK5</it>; rs7754840); a zinc transporter and member of solute carrier family 30 (<it>SLC30A8</it>; rs13266634); a variant found near cyclin-dependent kinase inhibitor 2A (<it>CDKN2A</it>; rs10811661); hematopoietically expressed homeobox (<it>HHEX</it>; rs 1111875); transcription factor-7-like 2 (<it>TCF7L2</it>; rs 10885409); potassium inwardly rectifying channel subfamily J member 11(<it>KCNJ11</it>; rs 5219); and fat mass obesity-associated gene (<it>FTO</it>; rs 9939609)].</p> <p>Methods</p> <p>We genotyped these SNPs in a case-control sample of 918 individuals consisting of 532 T2D cases and 386 normal glucose tolerant (NGT) subjects of an Asian Sikh community from North India. We tested the association between T2D and each SNP using unconditional logistic regression before and after adjusting for age, gender, and other covariates. We also examined the impact of these variants on body mass index (BMI), waist to hip ratio (WHR), fasting insulin, and glucose and lipid levels using multiple linear regression analysis.</p> <p>Results</p> <p>Four of the nine SNPs revealed a significant association with T2D; <it>PPARG2 </it>(Pro12Ala) [odds ratio (OR) 0.12; 95% confidence interval (CI) (0.03–0.52); p = 0.005], <it>IGF2BP2 </it>[OR 1.37; 95% CI (1.04–1.82); p = 0.027], <it>TCF7L2 </it>[OR 1.64; 95% CI (1.20–2.24); p = 0.001] and <it>FTO </it>[OR 1.46; 95% CI (1.11–1.93); p = 0.007] after adjusting for age, sex and BMI. Multiple linear regression analysis revealed significant association of two of nine investigated loci with diabetes-related quantitative traits. The 'C' (risk) allele of <it>CDK5 </it>(rs 7754840) was significantly associated with decreased HDL-cholesterol levels in both NGT (p = 0.005) and combined (NGT and T2D) (0.005) groups. The less common 'C' (risk) allele of <it>TCF7L2 </it>(rs 10885409) was associated with increased LDL-cholesterol (p = 0.010) in NGT and total and LDL-cholesterol levels (p = 0.008; p = 0.003, respectively) in combined cohort.</p> <p>Conclusion</p> <p>To our knowledge, this is first study reporting the role of some recently emerged loci with T2D in a high risk population of Asian Indian origin. Further investigations are warranted to understand the pathway-based functional implications of these important loci in T2D pathophysiology in different ethnicities.</p

A Bidirectional Mendelian Randomization Study to evaluate the causal role of reduced blood vitamin D levels with type 2 diabetes risk in South Asians and Europeans.

Context Multiple observational studies have reported an inverse relationship between 25-hydroxyvitamin D concentrations (25(OH)D) and type 2 diabetes (T2D). However, the results of short- and long-term interventional trials concerning the relationship between 25(OH)D and T2D risk have been inconsistent. Objectives and methods To evaluate the causal role of reduced blood 25(OH)D in T2D, here we have performed a bidirectional Mendelian randomization study using 59,890 individuals (5,862 T2D cases and 54,028 controls) from European and Asian Indian ancestries. We used six known SNPs, including three T2D SNPs and three vitamin D pathway SNPs, as a genetic instrument to evaluate the causality and direction of the association between T2D and circulating 25(OH)D concentration. Results Results of the combined meta-analysis of eight participating studies showed that a composite score of three T2D SNPs would significantly increase T2D risk by an odds ratio (OR) of 1.24, p = 1.82 × 10–32; Z score 11.86, which, however, had no significant association with 25(OH)D status (Beta -0.02nmol/L ± SE 0.01nmol/L; p = 0.83; Z score -0.21). Likewise, the genetically instrumented composite score of 25(OH)D lowering alleles significantly decreased 25(OH)D concentrations (-2.1nmol/L ± SE 0.1nmol/L, p = 7.92 × 10–78; Z score -18.68) but was not associated with increased risk for T2D (OR 1.00, p = 0.12; Z score 1.54). However, using 25(OH)D synthesis SNP (DHCR7; rs12785878) as an individual genetic instrument, a per allele reduction of 25(OH)D concentration (-4.2nmol/L ± SE 0.3nmol/L) was predicted to increase T2D risk by 5%, p = 0.004; Z score 2.84. This effect, however, was not seen in other 25(OH)D SNPs (GC rs2282679, CYP2R1 rs12794714) when used as an individual instrument. Conclusion Our new data on this bidirectional Mendelian randomization study suggests that genetically instrumented T2D risk does not cause changes in 25(OH)D levels. However, genetically regulated 25(OH)D deficiency due to vitamin D synthesis gene (DHCR7) may influence the risk of T2D

Association of the PHACTR1/EDN1 genetic locus with spontaneous coronary artery dissection

Background: Spontaneous coronary artery dissection (SCAD) is an increasingly recognized cause of acute coronary syndromes (ACS) afflicting predominantly younger to middle-aged women. Observational studies have reported a high prevalence of extracoronary vascular anomalies, especially fibromuscular dysplasia (FMD) and a low prevalence of coincidental cases of atherosclerosis. PHACTR1/EDN1 is a genetic risk locus for several vascular diseases, including FMD and coronary artery disease, with the putative causal noncoding variant at the rs9349379 locus acting as a potential enhancer for the endothelin-1 (EDN1) gene. Objectives: This study sought to test the association between the rs9349379 genotype and SCAD. Methods: Results from case control studies from France, United Kingdom, United States, and Australia were analyzed to test the association with SCAD risk, including age at first event, pregnancy-associated SCAD (P-SCAD), and recurrent SCAD. Results: The previously reported risk allele for FMD (rs9349379-A) was associated with a higher risk of SCAD in all studies. In a meta-analysis of 1,055 SCAD patients and 7,190 controls, the odds ratio (OR) was 1.67 (95% confidence interval [CI]: 1.50 to 1.86) per copy of rs9349379-A. In a subset of 491 SCAD patients, the OR estimate was found to be higher for the association with SCAD in patients without FMD (OR: 1.89; 95% CI: 1.53 to 2.33) than in SCAD cases with FMD (OR: 1.60; 95% CI: 1.28 to 1.99). There was no effect of genotype on age at first event, P-SCAD, or recurrence. Conclusions: The first genetic risk factor for SCAD was identified in the largest study conducted to date for this condition. This genetic link may contribute to the clinical overlap between SCAD and FMD