A Hypothesized Mechanism for Chronic Pancreatitis Caused by the N34S Mutation of Serine Protease Inhibitor Kazal-Type 1 Based on Conformational Studies

Kulke, Martin; Nagel, Felix; Schulig, Lukas; Geist, Norman; Gabor, Marcel; Mayerle, Julia; Lerch, Markus M.; Link, Andreas; Delcea, Mihaela

doi:10.2147/jir.s304787

Cited by 5 publications

(5 citation statements)

References 52 publications

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“…While we were unable to elucidate the underlying cause of the p.N34S pathogenicity in ARP and CP, we still found minor differences in their complex structures. Previously, structural differences between both SPINK1 variants were hypothesized to be disease causing or modifying [ 15 , 28 ]. However, our crystal structures prove that both SPINK1 variants are mostly similar, and the minor differences we detected are unlikely to translate into functional or clinical effects.…”

Section: Discussionmentioning

confidence: 99%

“…For the past two decades, the structure of the SPINK1 complex with TRY1 has been under debate and was subjected to multiple molecular dynamics simulation studies [ 28 , 29 ], docking simulations [ 30 ], homology modeling [ 15 , 31 ] and spectroscopic studies, using circular dichroism [ 32 , 33 ]. Changes within the SPINK1 binding loop and peptide flipping due to the mutation were proposed.…”

Section: Introductionmentioning

confidence: 99%

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Structural and Biophysical Insights into SPINK1 Bound to Human Cationic Trypsin

Nagel

Palm

Geist

et al. 2022

IJMS

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(1) The serine protease inhibitor Kazal type 1 (SPINK1) inhibits trypsin activity in zymogen granules of pancreatic acinar cells. Several mutations in the SPINK1 gene are associated with acute recurrent pancreatitis (ARP) and chronic pancreatitis (CP). The most common variant is SPINK1 p.N34S. Although this mutation was identified two decades ago, the mechanism of action has remained elusive. (2) SPINK1 and human cationic trypsin (TRY1) were expressed in E. coli, and inhibitory activities were determined. Crystals of SPINK1–TRY1 complexes were grown by using the hanging-drop method, and phases were solved by molecular replacement. (3) Both SPINK1 variants show similar inhibitory behavior toward TRY1. The crystal structures are almost identical, with minor differences in the mutated loop. Both complexes show an unexpected rotamer conformation of the His63 residue in TRY1, which is a member of the catalytic triad. (4) The SPINK1 p.N34S mutation does not affect the inhibitory behavior or the overall structure of the protein. Therefore, the pathophysiological mechanism of action of the p.N34S variant cannot be explained mechanistically or structurally at the protein level. The observed histidine conformation is part of a mechanism for SPINK1 that can explain the exceptional proteolytic stability of this inhibitor.

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Section: Discussionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

Structural and Biophysical Insights into SPINK1 Bound to Human Cationic Trypsin

Nagel

Palm

Geist

et al. 2022

IJMS

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“…Variations in SPINK1, the gene encoding the most prevailing trypsin inhibitor predisposes to idiopathic chronic pancreatitis [19][20][21]. The most common variant, p.N34S, leads to severe CP in homozygous carriers and is regarded as causative [22].…”

Section: Serine Protease Inhibitor Kazal-type 1 (Spink1)mentioning

confidence: 99%

Genetic Testing in Acute and Chronic Pancreatitis

Piseddu

Vielhauer

Mayerle

2022

Curr Treat Options Gastro

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Purpose of review Premature intracellular activation of pancreatic zymogens leads to the initiation of pancreatitis, which in up to 25% leads to chronic tissue destruction, exocrine and endocrine organ failure, and a moderate increased risk of pancreatic cancer development. Whereas in many cases, the trigger of organ damage is identified, diagnostic workup in a significant number of patients does not reveal the underlying etiology of pancreatic inflammation. In these cases, alterations in different pancreatic susceptibility genes have been described to be directly or indirectly involved in disease development. In this review, we want to give an update on the most important pancreatitis risk genes and their impact on clinical diagnostics and risk stratification as well as possible treatment options. Recent findings Genetic testing is not routinely implemented in the diagnostic workup of acute or chronic pancreatitis, as most genetic variations are not considered causative for pancreatitis development but confer increased susceptibility and genetic testing rarely changes disease management. However, in patients with recurrent pancreatitis episodes of unknown etiology after intensive diagnostic work-up, in patients with a family history of pancreatitis, relatives of patients with hereditary pancreatitis, and patients with disease onset at young age, genetic testing and counseling is recommended. Besides well-established susceptibility genes such as PRSS1, SPINK1, CPA1, and CFTR, additional genes such as TRPV6 and rare genetic alterations in established risk genes have been recently identified which significantly contribute to the risk of pancreatitis, involving different molecular mechanisms. Summary When genetic testing is considered, we propose screening at least for PRSS1, SPINK1, CPA1, and CFTR gene variants. The emergence of next-generation sequencing methods could also render larger gene panels possible and clinically meaningful to detect rare variants with high-risk phenotypes. Here we summarize, evaluate, and convey in the form of practical recommendations the current level of knowledge with respect to definition, etiology, and genetic diagnostics of all forms of inherited pancreatitis.

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“…A heavily reduced replica number was sufficient to retain accurate results. Recent studies have successfully proven the application of TIGER2h(s) to enhance sampling of various molecular systems, − but effects of different replica numbers or temperature scales have not yet been investigated in detail. Applied replica counts and temperature ranges to a maximum of 600 K, typically used in protein folding simulations, resulted in only minor deviations that we previously accounted to insufficient convergence. , …”

Section: Introductionmentioning

confidence: 99%

Fundamental Redesign of the TIGER2hs Kernel to Address Severe Parameter Sensitivity

Schulig

Geist

Delcea

et al. 2022

J. Chem. Inf. Model.

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Replica exchange molecular dynamics simulations are one of the most popular approaches to enhance conformational sampling of molecular systems. Applications range from protein folding to protein−protein or other host−guest interactions, as well as binding free energy calculations. While these methods are computationally expensive, highly accurate results can be obtained. We recently developed TIGER2hs, an improved version of the temperature intervals with global exchange of replicas (TIGER2) algorithm. This method combines the replica-based enhanced sampling in an explicit solvent with a hybrid solvent energy evaluation. During the exchange attempts, bulk water is replaced by an implicit solvent model, allowing sampling with significantly less replicas than parallel tempering (REMD). This enables accurate enhanced sampling calculations with only a fraction of computational resources compared to REMD. Our latest results highlight several issues with sampling imbalance and parameter sensitivity within the original TIGER2 exchange algorithms that affect the overall state populations. A high sensitivity on replica number and maximum temperature is eliminated by changing to a pairwise exchange kernel (PE) without additional sorting. Simulations are controlled by adjusting the average temperature change per exchange ⟨ΔT/χ⟩ to below 30 K to mimic a controlled temperature mixing of replicas similar to REMD. Thus, this parameter provides an applicable property for selecting combinations of replica number and maximum temperature to adjust simulations for best accuracy, with flexible resource investment. This increases the robustness of the method and ensures results in excellent agreement with REMD, as demonstrated for three different peptides.

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A Hypothesized Mechanism for Chronic Pancreatitis Caused by the N34S Mutation of Serine Protease Inhibitor Kazal-Type 1 Based on Conformational Studies

Cited by 5 publications

References 52 publications

Structural and Biophysical Insights into SPINK1 Bound to Human Cationic Trypsin

Structural and Biophysical Insights into SPINK1 Bound to Human Cationic Trypsin

Genetic Testing in Acute and Chronic Pancreatitis

Fundamental Redesign of the TIGER2hs Kernel to Address Severe Parameter Sensitivity

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