Engineering of Kuma030: A Gliadin Peptidase That Rapidly Degrades Immunogenic Gliadin Peptides in Gastric Conditions

Wolf, Clancey; Siegel, Justin B.; Tinberg, Christine E.; Camarca, Alessandra; Gianfrani, Carmen; Paski, Shirley; Guan, R.; Montelione, Gaetano T.; Baker, David; Pultz, Ingrid Swanson

doi:10.1021/jacs.5b08325

Cited by 100 publications

(65 citation statements)

References 42 publications

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“…51 Along the way, these developments have enabled Rosetta to address new biomolecular modeling problems including refinement of low-resolution X-ray structures, 52 development of protein binders, 53 and the design of vaccines, 54 biomineralization peptides, 55 self-assembling materials, 56 and enzymes that perform new functions. 57,58 Instead of arbitrary units, the energy function is now also calibrated to compute energies in kcal/mol. The details of these energy function advances are distributed across code comments, methods development papers, application papers, and individual experts, making it challenging for Rosetta developers and users in both academia and industry to learn the underlying concepts.…”

Section: Introductionmentioning

confidence: 99%

The Rosetta all-atom energy function for macromolecular modeling and design

Alford

Leaver‐Fay

Jeliazkov

et al. 2017

Preprint

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406

631

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Over the past decade, the Rosetta biomolecular modeling suite has informed diverse biological questions and engineering challenges ranging from interpretation of low-resolution structural data to design of nanomaterials, protein therapeutics, and vaccines. Central to Rosetta's success is the energy function: a model parameterized from small molecule and X-ray crystal structure data used to approximate the energy associated with each biomolecule conformation. This paper describes the mathematical models and physical concepts that underlie the latest Rosetta energy function, beta_nov15. Applying these concepts, we explain how to use Rosetta energies to identify and analyze the features of biomolecular models. Finally, we discuss the latest advances in the energy function that extend capabilities from soluble proteins to also include membrane proteins, peptides containing non-canonical amino acids, carbohydrates, nucleic acids, and other macromolecules.

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Section: Introductionmentioning

confidence: 99%

The Rosetta all-atom energy function for macromolecular modeling and design

Alford

Leaver‐Fay

Jeliazkov

et al. 2017

Preprint

Self Cite

406

631

View full text Add to dashboard Cite

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“…Although several experimental therapies for CD have entered clinical trials [4], randomized clinical trials to evaluate drug efficacy have only been conducted on two modes of action – enzyme supplementation therapy [5,6] and modulation of tight junctions in the small intestine [7]. Latiglutenase (formerly ALV003) is a promising example of enzyme supplementation therapy comprised of two recombinant proteins.…”

Section: Introductionmentioning

confidence: 99%

Latiglutenase Improves Symptoms in Seropositive Celiac Disease Patients While on a Gluten-Free Diet

et al. 2017

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Background and Aims Celiac disease (CD) is a widespread condition triggered by dietary gluten and treated with a lifelong gluten-free diet (GFD); however, inadvertent exposure to gluten can result in episodic symptoms. A previous trial of latiglutenase (clinicaltrials.gov; NCT01917630), an orally administered mixture of two recombinant gluten-specific proteases, was undertaken in symptomatic subjects with persistent injury. The primary endpoint for histologic improvement was not met, presumably due to a trial effect. In this post hoc analysis we investigated the efficacy of latiglutenase for reducing symptoms in subgroups of the study participants based on their seropositivity. Methods The study involved symptomatic CD patients following a GFD for at least one year prior to randomization. Patients were treated for 12 weeks with latiglutenase or placebo. Of 398 completed patients 173 (43%) were seropositive at baseline. Symptoms were recorded daily and weekly symptom scores were compiled. P-values were calculated by analysis of covariance (ANCOVA). Results A statistically significant, dose-dependent reduction was detected in the severity and frequency of symptoms in seropositive but not seronegative patients. The severity of abdominal pain and bloating was reduced by 58% and 44%, respectively, in the cohort receiving the highest latiglutenase dose (900 mg, n=14) relative to placebo (n=54). Symptom improvement increased from week 6 to week 12. There was also a trend toward greater symptom improvement with greater baseline symptom severity. Conclusions Seropositive CD patients show symptomatic improvement from latiglutenase taken with meals and would benefit from the availability of this treatment.

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“…Although the degree of prolamin reduction in our current wheat PBF TILLING lines (50-60%) is not sufficient to make them appropriate for celiac patients, additional TILLING approaches are underway that we anticipate will reduce gluten even further. In addition, the wheat PBF TILLING lines may be combined with other approaches, such as gluten-degrading enzyme supplements [73] [74], to benefit individuals with gluten sensitivities. In our previously published work, we provided evidence for this synergistic approach using a non-human primate model of celiac disease [75].…”

Section: Discussionmentioning

confidence: 99%

Development of reduced gluten wheat enabled by determination of the genetic basis of thelys3alow hordein barley mutant

Moehs

Austill

Holm

et al. 2018

Preprint

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Celiac disease is the most common food-induced enteropathy in humans with a prevalence of approximately 1% world-wide [1]. It is induced by digestion-resistant, proline-and glutamine-rich seed storage proteins, collectively referred to as "gluten," found in wheat. Related prolamins are present in barley and rye. Both celiac disease and a related condition called non-celiac gluten sensitivity (NCGS) are increasing in incidence [2] [3]. This has prompted efforts to identify methods of lowering gluten in wheat, one of the most important cereal crops. Here we used BSR-seq (Bulked Segregant RNA-seq) and map-based cloning to identify the genetic lesion underlying a recessive, low prolamin mutation (lys3a) in diploid barley. We confirmed the mutant identity by complementing the lys3a mutant with a transgenic copy of the wild type barley gene and then used TILLING (Targeting Induced Local Lesions in Genomes)[4] to identify induced SNPs (Single Nucleotide Polymorphisms) in the three homoeologs of the corresponding wheat gene. Combining inactivating mutations in the three sub-genomes of hexaploid bread wheat in a single wheat line lowered gliadin and low molecular weight glutenin accumulation by 50-60% and increased free and protein-bound lysine by 33%. This is the first report of the combination of mutations in homoeologs of a single gene that reduces gluten in wheat.Gluten is the common name for a complex mixture of approximately 100 proline-and glutamine-rich seed storage proteins found in wheat endosperm. In hexaploid bread wheat, in particular, gluten is responsible for the unique viscoelastic properties of dough used for making leavened bread. Related prolamins known as hordeins in barley and secalins in rye, but lacking the viscoelastic properties of wheat gluten, are found in the endosperms of these related cereals. Among gluten proteins, the most important for the elasticity and strength of bread dough are the polymeric high molecular weight glutenins [5]; monomeric gluten proteins, primarily gliadins, which are classified based on size, charge and repetitive amino acid sequences into α, β, γ and ω types, contribute to the viscosity of gluten [6] [7].Gluten is the causative factor of celiac disease, the most common food-induced autoimmune enteropathy in humans [1]. Celiac disease is found primarily in individuals expressing human leukocyte antigen (HLA) alleles DQ2 and/or DQ8. Immunodominant peptide epitopes have been found in α gliadins [8] and in ω gliadins of wheat and in C hordeins of barley [9]. Additional epitopes are also found in LMW and HMW-glutenins, gamma-gliadins from wheat and B and gamma hordeins from barley [10] [9]. Celiac disease patients exhibit a range of intestinal and extra-intestinal symptoms of which the most common is flattening of the villi of the small intestine, which can lead to poor absorption of nutrients and other pathological consequences. The only current treatment is a life-long avoidance of all gluten in the diet,which can be challenging given the prevalent use of gluten in diver...

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Engineering of Kuma030: A Gliadin Peptidase That Rapidly Degrades Immunogenic Gliadin Peptides in Gastric Conditions

Cited by 100 publications

References 42 publications

The Rosetta all-atom energy function for macromolecular modeling and design

The Rosetta all-atom energy function for macromolecular modeling and design

Latiglutenase Improves Symptoms in Seropositive Celiac Disease Patients While on a Gluten-Free Diet

Development of reduced gluten wheat enabled by determination of the genetic basis of thelys3alow hordein barley mutant

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