Searching for the Green Man: Researching Pilgrimage in Israel/Palestine and Egypt

This article examines contemporary pilgrimage in Israel / Palestine and Egypt, based upon field work conducted December 2017-February 2018 and personal narrative. My argument is twofold: first, I contend that Pilgrimage Studies allows scholars to move beyond reductive labels and consider the implicit ‘messiness’ of religious faith and ritual praxis. I introduce the Islamic al-Khidr and Moses story from Qur’an 18.60-82, as an interpretative model, suggesting that rigid categorization—especially concerning religious identity and sectarian division—promotes a false narrative of monolithic faith traditions that, upon closer examination, does not fully exist. Second, by referencing my ethnographic experiences, I consider pilgrimage as fundamentally located in the body, often fraught with moral ambiguity and physical trauma

Factors determining the pKa values of the ionizable groups in proteins: their intrinsic pKas and the effects of hydrogen bonding on buried carboxyl groups

A goal of the modern protein chemist is the design of novel proteins with specific activities or functions. One hurdle to overcome is the ability to accurately predict the pKas of ionizable groups upon their burial in the interior of a protein, where they are typically perturbed from their intrinsic pKas. Most discussion of intrinsic pKas is based on model compound data collected prior to the 1960's. We present here a new set of intrinsic pKas based on model peptides, which we think are more applicable than the model compound values. We observe some differences with the model compound values, and discuss these by critically examining the compounds originally used for the dataset. One interaction affecting the pKas of ionizable groups in proteins that is not well understood is the effect of hydrogen bonds. The side chain carboxyl of Asp33 in RNase Sa is buried, forms 3 intramolecular hydrogen bonds, and has a pKa of 2.4 in the folded protein. One of these hydrogen bonds is to the side chain hydroxyl of Thr56. We mutated Thr56 to alanine and valine and observed that the mutations relieves the perturbation on the carboxyl group and elevates its pKa by 1.5 and 2 units, respectively. The side chain carboxyl of Asp76 in RNase T1 is completely buried, forms 3 intramolecular hydrogen bonds to other side chain groups, and has a pKa of 0.5 in the folded protein. Mutating any of the hydrogen bonding groups to the carboxyl affects its pKa differently, depending on the group mutated. Mutating all of the hydrogen bonding groups, creating a triple mutant of RNase T1, reverses the perturbation on the pKa and elevates it to about 6.4, very near the observed pKa of other carboxyl groups buried in hydrophobic environments. We compared these experimental results with predicted results from theoretical models based on the Solvent Accessibility Corrected Tanford- Kirkwood Equation and the finite difference solution to the linearized Poisson- Boltzmann Equation. The comparisons revealed that these models, most often used by theoreticians, are flawed when typically applied, and some possible improvements are proposed

Charge-charge interactions are key determinants of the pK values of ionizable groups in ribonuclease Sa (pI=3.5) and a basic variant (pI=10.2)

The pK values of the titratable groups in ribonuclease Sa (RNase Sa) (pI=3.5), and a charge-reversed variant with five carboxyl to lysine substitutions, 5K RNase Sa (pI=10.2), have been determined by NMR at 20 °C in 0.1 M NaCl. In RNase Sa, 18 pK values and in 5K, 11 pK values were measured. The carboxyl group of Asp33, which is buried and forms three intramolecular hydrogen bonds in RNase Sa, has the lowest pK (2.4), whereas Asp79, which is also buried but does not form hydrogen bonds, has the most elevated pK (7.4). These results highlight the importance of desolvation and charge–dipole interactions in perturbing pK values of buried groups. Alkaline titration revealed that the terminal amine of RNase Sa and all eight tyrosine residues have significantly increased pK values relative to model compounds. A primary objective in this study was to investigate the influence of charge–charge interactions on the pK values by comparing results from RNase Sa with those from the 5K variant. The solution structures of the two proteins are very similar as revealed by NMR and other spectroscopic data, with only small changes at the N terminus and in the α-helix. Consequently, the ionizable groups will have similar environments in the two variants and desolvation and charge–dipole interactions will have comparable effects on the pK values of both. Their pK differences, therefore, are expected to be chiefly due to the different charge–charge interactions. As anticipated from its higher net charge, all measured pK values in 5K RNase are lowered relative to wild-type RNase Sa, with the largest decrease being 2.2 pH units for Glu14. The pK differences (pKSa−pK5K) calculated using a simple model based on Coulomb's Law and a dielectric constant of 45 agree well with the experimental values. This demonstrates that the pK differences between wild-type and 5K RNase Sa are mainly due to changes in the electrostatic interactions between the ionizable groups. pK values calculated using Coulomb's Law also showed a good correlation (R=0.83) with experimental values. The more complex model based on a finite-difference solution to the Poisson–Boltzmann equation, which considers desolvation and charge–dipole interactions in addition to charge–charge interactions, was also used to calculate pK values. Surprisingly, these values are more poorly correlated (R=0.65) with the values from experiment. Taken together, the results are evidence that charge–charge interactions are the chief perturbant of the pK values of ionizable groups on the protein surface, which is where the majority of the ionizable groups are positioned in proteins.This work was supported by grants GM-37039 and GM-52483 from the National Institutes of Health (USA), grants BE-1060 and BE-1281 from the Robert A. Welch Foundation, and a grant PB-93-06777 to M.R. from the Dirección General de Investigación Cientı́fica y Técnica (Spain

Self-assembly of a model amphiphilic oligopeptide incorporating an arginine headgroup

The self-assembly in aqueous solution of the alanine-rich peptide A12R2 containing twelve alanine residues and two arginine residues has been investigated. This oligomeric peptide was synthesized via NCA-polymerization methods. The surfactant-like peptide is found via FTIR to form antiparallel dimers which aggregate into twisted fibrils, as revealed by cryogenic-transmission electron microscopy. The fibril substructure is probed via detailed X-ray scattering experiments, and are uniquely comprised of twisted tapes only 5 nm wide, set by the width of the antiparallel A12R2 dimers. The packing of the alanine residues leads to distinct “b-sheet” spacings compared to those for amyloid-forming peptides. For this peptide, b-sheet structure coexists with some a-helical content. These ultrafine amyloid fibrils present arginine at high density on their surfaces, and this may lead to applications in nanobiotechnology

Common and Distant Structural Characteristics of Feruloyl Esterase Families from Aspergillus oryzae

Background: Feruloyl esterases (FAEs) are important biomass degrading accessory enzymes due to their capability of cleaving the ester links between hemicellulose and pectin to aromatic compounds of lignin, thus enhancing the accessibility of plant tissues to cellulolytic and hemicellulolytic enzymes. FAEs have gained increased attention in the area of biocatalytic transformations for the synthesis of value added compounds with medicinal and nutritional applications. Following the increasing attention on these enzymes, a novel descriptor based classification system has been proposed for FAEs resulting into 12 distinct families and pharmacophore models for three FAE sub-families have been developed. Methodology/Principal Findings: The feruloylome of Aspergillus oryzae contains 13 predicted FAEs belonging to six sub-families based on our recently developed descriptor-based classification system. The three-dimensional structures of the 13 FAEs were modeled for structural analysis of the feruloylome. The three genes coding for three enzymes, viz., A.O.2, A.O.8 and A.O.10 from the feruloylome of A. oryzae, representing sub-families with unknown functional features, were heterologously expressed in Pichia pastoris, characterized for substrate specificity and structural characterization through CD spectroscopy. Common feature-based pharamacophore models were developed according to substrate specificity characteristics of the three enzymes. The active site residues were identified for the three expressed FAEs by determining the titration curves of amino acid residues as a function of the pH by applying molecular simulations. Conclusions/Significance: Our findings on the structure-function relationships and substrate specificity of the FAEs of A. oryzae will be instrumental for further understanding of the FAE families in the novel classification system. The developed pharmacophore models could be applied for virtual screening of compound databases for short listing the putative substrates prior to docking studies or for post-processing docking results to remove false positives. Our study exemplifies how computational predictions can complement to the information obtained through experimental methods. © 2012 Udatha et al.published_or_final_versio

Determination of the pK(a) of the N-terminal amino group of ubiquitin by NMR

This work was supported by the Medical Research Council (grants U117533887 and grant U117565398 until March 2015) and by the Francis Crick Institute which receives its core funding from Cancer Research UK (FC001142, FC10029), the UK Medical Research Council (FC001142, FC10029), and the Wellcome Trust (FC001142, FC10029)

Re-membering the Holy Family in Islamic Cairo

This paper examines the veneration of the Prophet Muhammad’s Holy Family, both historically and today. The paper draws upon affect theory and trauma studies to move beyond questions of historical/textual criticism to consider what ‘visiting’ the Holy Family means to their audiences. Affect theory compels us to imagine what bodies (both individual and social) experience, feel, and emote in story-telling and ritual performance within sacred space. Trauma studies likewise accentuates what bodies experience and feel, especially in deeply distressing physical or psychic struggles. Trauma studies, particularly, encourages us to focus on the power of ‘story’ in shaping individual (and social) identities, recognizing that, in many ways, we are a product of the stories we tell ourselves (and those society tells us). When approaching the Holy Family with these questions in mind, I consider (more specifically): what attracts practitioners and pilgrims to sacred spaces dedicated to broken bodies, and what do they experience therein? To answer such questions, I begin by surveying early medieval hadith and hagiographies that describe the Family’s lives and legacies, paying particular attention to al-Sayyida Zaynab and al-Husayn (the Prophet Muhammad’s grandchildren). I consider a variety of pilgrimage (or ‘visitation’) rituals, including story-telling and emotional elegies that ‘re-member’ the Family’s traumas, recognizable by most human beings as lived by mothers, fathers, sons, sisters, and kin groups. I also consider embodied ritual performances that link practitioners with the Family’s own bodies/relics through full sensory engagement (smelling, tasting, and feeling). Finally, the paper complements historical investigation (primarily hagiographies and pilgrimage journals) with recent fieldwork conducted at al-Sayyida Zaynab and al-Husayn mosques in 2019 and 2021. Through interviews and observation, I consider the embodied ritual performances within the shrine rooms that often disrupt traditional gender expectations

Brown Bag Book Club: G. Willow Wilson\u27s \u3cem\u3eMs. Marvel\u3c/em\u3e

A discussion of G. Willow Wilson’s Ms. Marvel [ISBN 978-0785190219], led by Dr. Mary Thurlkill, UM Department of Philosophy and Religion

Sacred Scents in Early Christianity and Islam

Medieval scholars and cultural historians have recently turned their attention to the question of “smells” and what olfactory sensations reveal about society in general and holiness in particular. Sacred Scents in Early Christianity and Islam contributes to that conversation, explaining how early Christians and Muslims linked the “sweet smell of sanctity” with ideals of the body and sexuality; created boundaries and sacred space; and imagined their emerging communal identity. Most importantly, scent—itself transgressive and difficult to control—signaled transition and transformation between categories of meaning. Christian and Islamic authors distinguished their own fragrant ethical and theological ideals against the stench of oppositional heresy and moral depravity. Orthodox Christians ridiculed their ‘stinking’ Arian neighbors, and Muslims denounced the ‘reeking’ corruption of Umayyad and Abbasid decadence. Through the mouths of saints and prophets, patriarchal authors labeled perfumed women as existential threats to vulnerable men and consigned them to enclosed, private space for their protection as well as society’s. At the same time, theologians praised both men and women who purified and transformed their bodies into aromatic offerings to God. Both Christian and Muslim pilgrims venerated sainted men and women with perfumed offerings at tombstones; indeed, Christians and Muslims often worshipped together, honoring common heroes such as Abraham, Moses, and Jonah. Sacred Scents begins by surveying aroma’s quotidian functions in Roman and pre-Islamic cultural milieus within homes, temples, poetry, kitchens, and medicines. Existing scholarship tends to frame ‘scent’ as something available only to the wealthy or elite; however, perfumes, spices, and incense wafted through the lives of most early Christians and Muslims. It ends by examining both traditions’ views of Paradise, identified as the archetypal Garden and source of all perfumes and sweet smells. Both Christian and Islamic texts explain Adam and Eve’s profound grief at losing access to these heavenly aromas and celebrate God’s mercy in allowing earthly remembrances. Sacred scent thus prompts humanity’s grief for what was lost and the yearning for paradisiacal transformation still to come.https://egrove.olemiss.edu/libarts_book/1060/thumbnail.jp