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1.  Deficiency Mutations of Alpha-1 Antitrypsin. Effects on Folding, Function, and Polymerization 
Misfolding, polymerization, and defective secretion of functional alpha-1 antitrypsin underlies the predisposition to severe liver and lung disease in alpha-1 antitrypsin deficiency. We have identified a novel (Ala336Pro, Baghdad) deficiency variant and characterized it relative to the wild-type (M) and Glu342Lys (Z) alleles. The index case is a homozygous individual of consanguineous parentage, with levels of circulating alpha-1 antitrypsin in the moderate deficiency range, but is a biochemical phenotype that could not be classified by standard methods. The majority of the protein was present as functionally inactive polymer, and the remaining monomer was 37% active relative to the wild-type protein. These factors combined indicate an 85 to 95% functional deficiency, similar to that seen with ZZ homozygotes. Biochemical, biophysical, and computational studies further defined the molecular basis of this deficiency. These studies demonstrated that native Ala336Pro alpha-1 antitrypsin could populate the polymerogenic intermediate—and therefore polymerize—more readily than either wild-type alpha-1 antitrypsin or the Z variant. In contrast, folding was far less impaired in Ala336Pro alpha-1 antitrypsin than in the Z variant. The data are consistent with a disparate contribution by the “breach” region and “shutter” region of strand 5A to folding and polymerization mechanisms. Moreover, the findings demonstrate that, in these variants, folding efficiency does not correlate directly with the tendency to polymerize in vitro or in vivo. They therefore differentiate generalized misfolding from polymerization tendencies in missense variants of alpha-1 antitrypsin. Clinically, they further support the need to quantify loss-of-function in alpha-1 antitrypsin deficiency to individualize patient care.
PMCID: PMC4742932  PMID: 26091018
alpha-1 antitrypsin deficiency; polymerization; mutation; unfolding; serpinopathies
2.  Neurocognitive Improvement in Patients Undergoing Carotid Endarterectomy for Atherosclerotic Occlusive Carotid Artery Disease 
Annals of Vascular Diseases  2016;9(4):307-311.
Objectives: To assess the improvement in neurocognitive functions after carotid endarterectomy (CEA) under local anesthesia (LA) in patients with carotid bifurcation occlusive disease.
Place and duration of study: Department of Vascular Surgery, Combined Military Hospital Lahore from January 2013 to January 2015.
Patients and Methods: A total of 79 patients with carotid artery occlusive disease, having no history of major stroke, depression, or dementia underwent CEA under LA. Cognitive functions were assessed 3 days before surgery and then 4 weeks and 12 weeks after the surgery using the Addenbrookes cognitive examination (ACE) score and General Practitioner Assessment of Cognition (GPCOG) Score.
Results: In ACE score, Attention, Memory, Fluency, Language, and Visuospatial orientation improved by 33.3%, 30.7%, 21.4%, 38.4%, and 31.2%, respectively, by the end of 12 weeks. An overall improvement in neurocognition was 32% (P = 0.03). In GPCOG score, Orientation, Recall, and Memory improved by 33%, 20%, and 100%, respectively, with an overall improvement of 33.3% at the end of 12 weeks (P = 0.02).
Conclusion: Both scoring systems show an overall improvement in neurocognition as well as improvements in all the subcategories in each system. Hence, we conclude statistically significant improvement in neurocognitive functions after CEA.
PMCID: PMC5174991  PMID: 28018503
cognition; endarterectomy; carotid; local anesthesia
3.  An integrative approach combining ion mobility mass spectrometry, X-ray crystallography, and nuclear magnetic resonance spectroscopy to study the conformational dynamics of α1-antitrypsin upon ligand binding 
Native mass spectrometry (MS) methods permit the study of multiple protein species within solution equilibria, whereas ion mobility (IM)-MS can report on conformational behavior of specific states. We used IM-MS to study a conformationally labile protein (α1-antitrypsin) that undergoes pathological polymerization in the context of point mutations. The folded, native state of the Z-variant remains highly polymerogenic in physiological conditions despite only minor thermodynamic destabilization relative to the wild-type variant. Various data implicate kinetic instability (conformational lability within a native state ensemble) as the basis of Z α1-antitrypsin polymerogenicity. We show the ability of IM-MS to track such disease-relevant conformational behavior in detail by studying the effects of peptide binding on α1-antitrypsin conformation and dynamics. IM-MS is, therefore, an ideal platform for the screening of compounds that result in therapeutically beneficial kinetic stabilization of native α1-antitrypsin. Our findings are confirmed with high-resolution X-ray crystallographic and nuclear magnetic resonance spectroscopic studies of the same event, which together dissect structural changes from dynamic effects caused by peptide binding at a residue-specific level. IM-MS methods, therefore, have great potential for further study of biologically relevant thermodynamic and kinetic instability of proteins and provide rapid and multidimensional characterization of ligand interactions of therapeutic interest.
PDB Code(s): 4PYW
PMCID: PMC4534181  PMID: 26011795
ion mobility mass spectrometry; protein dynamics; drug discovery; α1-antitrypsin; protein unfolding; mass spectrometry/methods; nuclear magnetic resonance; biomolecular; X-ray crystallography
4.  An antibody raised against a pathogenic serpin variant induces mutant-like behaviour in the wild-type protein 
Biochemical Journal  2015;468(Pt 1):99-108.
A monoclonal antibody (mAb) that binds to a transient intermediate may act as a catalyst for the corresponding reaction; here we show this principle can extend on a macro molecular scale to the induction of mutant-like oligomerization in a wild-type protein. Using the common pathogenic E342K (Z) variant of α1-antitrypsin as antigen–whose native state is susceptible to the formation of a proto-oligomeric intermediate–we have produced a mAb (5E3) that increases the rate of oligomerization of the wild-type (M) variant. Employing ELISA, gel shift, thermal stability and FRET time-course experiments, we show that mAb5E3 does not bind to the native state of α1-antitrypsin, but recognizes a cryptic epitope in the vicinity of the post-helix A loop and strand 4C that is revealed upon transition to the polymerization intermediate, and which persists in the ensuing oligomer. This epitope is not shared by loop-inserted monomeric conformations. We show the increased amenity to polymerization by either the pathogenic E342K mutation or the binding of mAb5E3 occurs without affecting the energetic barrier to polymerization. As mAb5E3 also does not alter the relative stability of the monomer to intermediate, it acts in a manner similar to the E342K mutant, by facilitating the conformational interchange between these two states.
We show that a monoclonal antibody can act as a ‘molecular template’ in aberrant protein oligomerization, and the transient intermediate of α1-antitrypsin, a key to the molecular mechanism of disease pathogenesis, expresses a cryptic epitope also present in the oligomer.
PMCID: PMC4422257  PMID: 25738741
aggregation; antibody; α1-antitrypsin; polymerization; protein stability; AF488, Alexa Fluor 488 dye; AF594, Alexa Fluor 594 dye; AT, α1-antitrypsin; ER, endoplasmic reticulum; H/D exchange, hydrogen/deuterium exchange; HRP, horseradish peroxidase; mAb, monoclonal antibody; PBS, phosphate-buffered saline
5.  A single-chain variable fragment intrabody prevents intracellular polymerization of Z α1-antitrypsin while allowing its antiproteinase activity 
The FASEB Journal  2015;29(6):2667-2678.
Mutant Z α1-antitrypsin (E342K) accumulates as polymers within the endoplasmic reticulum (ER) of hepatocytes predisposing to liver disease, whereas low levels of circulating Z α1-antitrypsin lead to emphysema by loss of inhibition of neutrophil elastase. The ideal therapy should prevent polymer formation while preserving inhibitory activity. Here we used mAb technology to identify interactors with Z α1-antitrypsin that comply with both requirements. We report the generation of an mAb (4B12) that blocked α1-antitrypsin polymerization in vitro at a 1:1 molar ratio, causing a small increase of the stoichiometry of inhibition for neutrophil elastase. A single-chain variable fragment (scFv) intrabody was generated based on the sequence of mAb4B12. The expression of scFv4B12 within the ER (scFv4B12KDEL) and along the secretory pathway (scFv4B12) reduced the intracellular polymerization of Z α1-antitrypsin by 60%. The scFv4B12 intrabody also increased the secretion of Z α1-antitrypsin that retained inhibitory activity against neutrophil elastase. MAb4B12 recognized a discontinuous epitope probably located in the region of helices A/C/G/H/I and seems to act by altering protein dynamics rather than binding preferentially to the native state. This novel approach could reveal new target sites for small-molecule intervention that may block the transition to aberrant polymers without compromising the inhibitory activity of Z α1-antitrypsin.—Ordóñez, A., Pérez, J., Tan, L., Dickens, J. A., Motamedi-Shad, N., Irving, J. A., Haq, I., Ekeowa, U., Marciniak, S. J., Miranda, E., Lomas, D. A. A single-chain variable fragment intrabody prevents intracellular polymerization of Z α1-antitrypsin while allowing its antiproteinase activity.
PMCID: PMC4548814  PMID: 25757566
monoclonal antibody; scFv intrabody; serpin polymer; liver disease
6.  Characterising the association of latency with α1-antitrypsin polymerisation using a novel monoclonal antibody 
α1-Antitrypsin is primarily synthesised in the liver, circulates to the lung and protects pulmonary tissues from proteolytic damage. The Z mutant (Glu342Lys) undergoes inactivating conformational change and polymerises. Polymers are retained within the hepatocyte endoplasmic reticulum (ER) in homozygous (PiZZ) individuals, predisposing the individuals to hepatic cirrhosis and emphysema. Latency is an analogous process of inactivating, intra-molecular conformational change and may co-occur with polymerisation. However, the relationship between latency and polymerisation remained unexplored in the absence of a suitable probe. We have developed a novel monoclonal antibody specific for latent α1-antitrypsin and used it in combination with a polymer-specific antibody, to assess the association of both conformers in vitro, in disease and during augmentation therapy. In vitro kinetics analysis showed polymerisation dominated the pathway but latency could be promoted by stabilising monomeric α1-antitrypsin. Polymers were extensively produced in hepatocytes and a cell line expressing Z α1-antitrypsin but the latent protein was not detected despite manipulation of the secretory pathway. However, α1-antitrypsin augmentation therapy contains latent α1-antitrypsin, as did the plasma of 63/274 PiZZ individuals treated with augmentation therapy but 0/264 who were not receiving this medication (p < 10−14). We conclude that latent α1-antitrypsin is a by-product of the polymerisation pathway, that the intracellular folding environment is resistant to formation of the latent conformer but that augmentation therapy introduces latent α1-antitrypsin into the circulation. A suite of monoclonal antibodies and methodologies developed in this study can characterise α1-antitrypsin folding and conformational transitions, and screen methods to improve augmentation therapy.
PMCID: PMC4305080  PMID: 25462157
α1-Antitrypsin; Latency; Polymerisation; Monoclonal antibodies; Augmentation therapy
7.  Altered native stability is the dominant basis for susceptibility of α1-antitrypsin mutants to polymerization 
Biochemical Journal  2014;460(Pt 1):103-115.
Serpins are protease inhibitors whose most stable state is achieved upon transition of a central 5-stranded β-sheet to a 6-stranded form. Mutations, low pH, denaturants and elevated temperatures promote this transition, which can result in a growing polymer chain of inactive molecules. Different types of polymer are possible, but, experimentally only heat has been shown to generate polymers in vitro consistent with ex vivo pathological specimens. Many mutations that alter the rate of heat-induced polymerization have been described, but interpretation is problematic because discrimination is lacking between the effect of global changes in native stability and specific effects on structural mechanism. We show that the temperature midpoint (Tm) of thermal denaturation reflects the transition of α1-antitrypsin to the polymerization intermediate, and determine the relationship with fixed-temperature polymerization half-times (t0.5) in the presence of stabilizing additives [TMAO (trimethylamine N-oxide), sucrose and sodium sulfate], point mutations and disulfide bonds. Combined with a retrospective analysis of 31 mutants characterized in the literature, the results of the present study show that global changes to native state stability are the predominant basis for the effects of mutations and osmolytes on heat-induced polymerization, summarized by the equation: ln(t0.5,mutant/t0.5,wild-type)=0.34×ΔTm. It is deviations from this relationship that hold key information about the polymerization process.
Mutations in α1-antitrypsin increase or decrease its tendency to form pathogenic ordered polymer chains. The present study shows that these effects are primarily exerted through changes in native state stability, and seldom through direct effects on the polymerization mechanism.
PMCID: PMC4080824  PMID: 24552432
cirrhosis; denaturation; disulfide; polymerization; serpin; stability; bis-ANS, 4,4′-dianilino-1,1′-binaphthyl-5,5′-disulfonic acid; HRP, horseradish peroxide; Ni-NTA, Ni2+-nitrilotriacetic acid; RCL, reactive centre loop; TMAO, trimethylamine N-oxide
8.  Increased ERK signalling promotes inflammatory signalling in primary airway epithelial cells expressing Z α1-antitrypsin 
Human Molecular Genetics  2013;23(4):929-941.
Overexpression of Z α1-antitrypsin is known to induce polymer formation, prime the cells for endoplasmic reticulum stress and initiate nuclear factor kappa B (NF-κB) signalling. However, whether endogenous expression in primary bronchial epithelial cells has similar consequences remains unclear. Moreover, the mechanism of NF-κB activation has not yet been elucidated. Here, we report excessive NF-κB signalling in resting primary bronchial epithelial cells from ZZ patients compared with wild-type (MM) controls, and this appears to be mediated by mitogen-activated protein/extracellular signal-regulated kinase, EGF receptor and ADAM17 activity. Moreover, we show that rather than being a response to protein polymers, NF-κB signalling in airway-derived cells represents a loss of anti-inflammatory signalling by M α1-antitrypsin. Treatment of ZZ primary bronchial epithelial cells with purified plasma M α1-antitrypsin attenuates this inflammatory response, opening up new therapeutic options to modulate airway inflammation in the lung.
PMCID: PMC4007119  PMID: 24097797
10.  Sterol metabolism regulates neuroserpin polymer degradation in the absence of the unfolded protein response in the dementia FENIB 
Human Molecular Genetics  2013;22(22):4616-4626.
Mutants of neuroserpin are retained as polymers within the endoplasmic reticulum (ER) of neurones to cause the autosomal dominant dementia familial encephalopathy with neuroserpin inclusion bodies or FENIB. The cellular consequences are unusual in that the ordered polymers activate the ER overload response (EOR) in the absence of the canonical unfolded protein response. We use both cell lines and Drosophila models to show that the G392E mutant of neuroserpin that forms polymers is degraded by UBE2j1 E2 ligase and Hrd1 E3 ligase while truncated neuroserpin, a protein that lacks 132 amino acids, is degraded by UBE2g2 (E2) and gp78 (E3) ligases. The degradation of G392E neuroserpin results from SREBP-dependent activation of the cholesterol biosynthetic pathway in cells that express polymers of neuroserpin (G392E). Inhibition of HMGCoA reductase, the limiting enzyme of the cholesterol biosynthetic pathway, reduced the ubiquitination of G392E neuroserpin in our cell lines and increased the retention of neuroserpin polymers in both HeLa cells and primary neurones. Our data reveal a reciprocal relationship between cholesterol biosynthesis and the clearance of mutant neuroserpin. This represents the first description of a link between sterol metabolism and modulation of the proteotoxicity mediated by the EOR.
PMCID: PMC3889810  PMID: 23814041
11.  Reactive centre loop mutants of α-1-antitrypsin reveal position-specific effects on intermediate formation along the polymerization pathway 
Bioscience Reports  2013;33(3):e00046.
The common severe Z mutation (E342K) of α1-antitrypsin forms intracellular polymers that are associated with liver cirrhosis. The native fold of this protein is well-established and models have been proposed from crystallographic and biophysical data for the stable inter-molecular configuration that terminates the polymerization pathway. Despite these molecular ‘snapshots’, the details of the transition between monomer and polymer remain only partially understood. We surveyed the RCL (reactive centre loop) of α1-antitrypsin to identify sites important for progression, through intermediate states, to polymer. Mutations at P14P12 and P4, but not P10P8 or P2P1′, resulted in a decrease in detectable polymer in a cell model that recapitulates the intracellular polymerization of the Z variant, consistent with polymerization from a near-native conformation. We have developed a FRET (Förster resonance energy transfer)-based assay to monitor polymerization in small sample volumes. An in vitro assessment revealed the position-specific effects on the unimolecular and multimolecular phases of polymerization: the P14P12 region self-inserts early during activation, while the interaction between P6P4 and β-sheet A presents a kinetic barrier late in the polymerization pathway. Correspondingly, mutations at P6P4, but not P14P12, yield an increase in the overall apparent activation energy of association from ~360 to 550 kJ mol−1.
PMCID: PMC3691886  PMID: 23659468
cirrhosis; emphysema; FRET; intermediate; polymerization; serpin; ANS, 8-anilinonaphthalene-1-sulfonic acid; bis-ANS, 4,4′-dianilino-1,1′-binaphthyl-5,5′-disulfonic acid; FRET, Förster resonance energy transfer; NTA, nitrilotriacetic acid; RCL, reactive centre loop; SI, stoichiometry of inhibition; Tm,midpoint of thermal denaturation
12.  A 43-year-old woman on triptorelin presenting with pseudotumor cerebri: a case report 
To the best of our knowledge, this is the first time triptorelin has been reported to cause benign intracranial hypertension.
Case presentation
A 43-year-old Caucasian woman who suffered from chronic menorrhagia was started on triptorelin, a gonadotrophin-releasing hormone analogue. Three days later, she developed gradually worsening headaches accompanied by bilateral visual disturbance. Examination revealed bilateral papilledema and enlarged blind spots on her visual fields. A diagnosis of benign intracranial hypertension was made and confirmed on magnetic resonance imaging.
We recommend that patients at high risk (women who are overweight and of reproductive age) who are using any gonadotrophin-releasing hormone analogue (for example, triptorelin) should be periodically monitored for the possible development of benign intracranial hypertension.
PMCID: PMC3410770  PMID: 22554236
13.  Light through the dark ages: The Arabist contribution to Western ophthalmology 
Oman Journal of Ophthalmology  2012;5(2):75-78.
Europe in the Middle Ages had descended into a dark period, and none more so than in the field of medicine. The rich heritage of the pagan Greeks had largely been ignored or forgotten by medieval Europe, and instead it was the early Arabist world that embraced and developed the Hellenistic medical teachings, emerging not only as guardians of the classical learning still existent, but also as pioneers and innovators, restricted only by the development in the associated fields. The Kahhal (), or Oculist or Eye Specialist, had a privileged place in royal households, especially during the Abbasid period, in contrast to the time of Galen, whose writings referred to ophthalmologists in a rather derogatory manner. This elevated standing in the medical profession allowed Arabist scholars to cultivate remarkably erudite techniques and exceptional texts, which were used until very recently.
PMCID: PMC3441032  PMID: 22993459
Arabist; medicine; ophthalmology; surgery
14.  Fungal Recognition Enhances Mannose Receptor Shedding through Dectin-1 Engagement* 
The Journal of Biological Chemistry  2011;286(10):7822-7829.
The mannose receptor (MR) is an endocytic type I membrane molecule with a broad ligand specificity that is involved in both hemostasis and pathogen recognition. Membrane-anchored MR is cleaved by a metalloproteinase into functional soluble MR (sMR) composed of the extracellular domains of intact MR. Although sMR production was initially considered a constitutive process, enhanced MR shedding has been observed in response to the fungal pathogen Pneumocystis carinii. In this work, we have investigated the mechanism mediating enhanced MR shedding in response to fungi. We show that other fungal species, including Candida albicans and Aspergillus fumigatus, together with zymosan, a preparation of the cell wall of Saccharomyces cerevisiae, mimic the effect of P. carinii on sMR production and that this effect takes place mainly through β-glucan recognition. Additionally, we demonstrate that MR cleavage in response to C. albicans and bioactive particulate β-glucan requires expression of dectin-1. Our data, obtained using specific inhibitors, are consistent with the canonical Syk-mediated pathway triggered by dectin-1 being mainly responsible for inducing MR shedding, with Raf-1 being partially involved. As in the case of steady-state conditions, MR shedding in response to C. albicans and β-glucan particles requires metalloprotease activity. The induction of MR shedding by dectin-1 has clear implications for the role of MR in fungal recognition, as sMR was previously shown to retain the ability to bind fungal pathogens and can interact with numerous host molecules, including lysosomal hydrolases. Thus, MR cleavage could also impact on the magnitude of inflammation during fungal infection.
PMCID: PMC3048669  PMID: 21205820
ADAM; ADAMTS; Fungi; Inflammation; Lectin; Macrophage; Metalloprotease; Mouse; Shedding
15.  Association of MMP - 12 polymorphisms with severe and very severe COPD: A case control study of MMPs - 1, 9 and 12 in a European population 
BMC Medical Genetics  2010;11:7.
Genetic factors play a role in chronic obstructive pulmonary disease (COPD) but are poorly understood. A number of candidate genes have been proposed on the basis of the pathogenesis of COPD. These include the matrix metalloproteinase (MMP) genes which play a role in tissue remodelling and fit in with the protease - antiprotease imbalance theory for the cause of COPD. Previous genetic studies of MMPs in COPD have had inadequate coverage of the genes, and have reported conflicting associations of both single nucleotide polymorphisms (SNPs) and SNP haplotypes, plausibly due to under-powered studies.
To address these issues we genotyped 26 SNPs, providing comprehensive coverage of reported SNP variation, in MMPs- 1, 9 and 12 from 977 COPD patients and 876 non-diseased smokers of European descent and evaluated their association with disease singly and in haplotype combinations. We used logistic regression to adjust for age, gender, centre and smoking history.
Haplotypes of two SNPs in MMP-12 (rs652438 and rs2276109), showed an association with severe/very severe disease, corresponding to GOLD Stages III and IV.
Those with the common A-A haplotype for these two SNPs were at greater risk of developing severe/very severe disease (p = 0.0039) while possession of the minor G variants at either SNP locus had a protective effect (adjusted odds ratio of 0.76; 95% CI 0.61 - 0.94). The A-A haplotype was also associated with significantly lower predicted FEV1 (42.62% versus 44.79%; p = 0.0129). This implicates haplotypes of MMP-12 as modifiers of disease severity.
PMCID: PMC2820470  PMID: 20078883
16.  Blood fibrinogen as a biomarker of chronic obstructive pulmonary disease 
Thorax  2012;68(7):670-676.
Chronic obstructive pulmonary disease (COPD) is a multicomponent condition that is characterised by airflow obstruction that is not fully reversible and is a major global cause of morbidity and mortality. The most widely used marker of disease severity and progression is FEV1. However, FEV1 correlates poorly with both symptoms and other measures of disease progression and thus there is an urgent need for other biological markers to better characterise individuals with COPD. Fibrinogen is an acute phase plasma protein that has emerged as a promising biomarker in COPD. Here we review the current clinical evidence linking fibrinogen with COPD and its associated co-morbidities and discuss its potential utility as a biomarker.
Searches for appropriate studies were undertaken on PubMed using search terms fibrinogen, COPD, emphysema, chronic bronchitis, FEV1, cardiovascular disease, exacerbation and mortality.
There is strong evidence of an association between fibrinogen and the presence of COPD, the presence and frequency of exacerbations and with mortality. Fibrinogen is associated with disease severity but does not predict lung function decline, a measure used as a surrogate for disease activity. The role of fibrinogen in identifying inflammatory co morbidities, particularly cardiovascular disease, remains unclear. Fibrinogen is reduced by p38 mitogen-activated protein kinase inhibitors in individuals with stable disease and by oral corticosteroids during exacerbations.
Fibrinogen is likely to be a useful biomarker to stratify individuals with COPD into those with a high or low risk of future exacerbations and may identify those with a higher risk of mortality.
PMCID: PMC3711372  PMID: 22744884
Fibrinogen; inflammation; COPD; biomarker

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