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Estimating Kinetic Rate Parameters for Enzymatic Degradation of Lyophilized Silk Fibroin Sponges.

ABSTRACT: Sponge-like biomaterials formed from silk fibroin are promising as degradable materials in clinical applications due to their controllable breakdown into simple amino acids or small peptides in vivo. Silk fibroin, isolated from Bombyx mori silkworm cocoons, can be used to form sponge-like materials with a variety of tunable parameters including the elastic modulus, porosity and pore size, and level of nanocrystalline domains. These parameters can be independently tuned during formulation resulting in a wide parameter space and set of final materials. Determining the mechanism and rate constants for biomaterial degradation of these tunable silk materials would allow scientists to evaluate and predict the biomaterial performance for the large array of tissue engineering applications and patient ailments a priori. We first measured in vitro degradation rates of silk sponges using common protein-degrading enzymes such as Proteinase K and Protease XIV. The concentration of the enzyme in solution was varied (1, 0.1, 0.01 U/mL) along with one silk sponge formulation parameter: the level of crystallinity within the sponge. Additionally, two experimental degradation methods were evaluated, termed continuous and discrete degradation methods. Silk concentration, polymer chain length and scaffold pore size were held constant during experimentation and kinetic parameter estimation. Experimentally, we observed that the enzyme itself, enzyme concentration within the bulk solution, and the sponge fabrication water annealing time were the major experimental parameters dictating silk sponge degradation in our experimental design. We fit the experimental data to two models, a Michaelis-Menten kinetic model and a modified first order kinetic model. Weighted, non-linear least squares analysis was used to determine the parameters from the data sets and Monte-Carlo simulations were utilized to obtain estimates of the error. We found that modified first order reaction kinetics fit the time-dependent degradation of lyophilized silk sponges and we obtained first order-like rate constants. These results represent the first investigations into determining kinetic parameters to predict lyophilized silk sponge degradation rates and can be a tool for future mathematical representations of silk biomaterial degradation.

SUBMITTER: Jameson JF

PROVIDER: S-EPMC8290342 | biostudies-literature |

REPOSITORIES: biostudies-literature

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Project description:Three-dimensional porous scaffolds prepared from regenerated silk fibroin using either an all-aqueous process or a process involving an organic solvent, hexafluoroisopropanol (HFIP), have shown promise in cell culture and tissue engineering applications. However, their biocompatibility and in vivo degradation have not been fully established. The present study was conducted to systematically investigate how processing method (aqueous vs. organic solvent) and processing variables (silk fibroin concentration and pore size) affect the short-term (up to 2 months) and long-term (up to 1 year) in vivo behavior of the protein scaffolds in both nude and Lewis rats. The samples were analyzed by histology for scaffold morphological changes and tissue ingrowth, and by real-time RT-PCR and immunohistochemistry for immune responses. Throughout the period of implantation, all scaffolds were well tolerated by the host animals and immune responses to the implants were mild. Most scaffolds prepared from the all-aqueous process degraded to completion between 2 and 6 months, while those prepared from organic solvent (hexafluoroisopropanol (HFIP)) process persisted beyond 1 year. Due to widespread cellular invasion throughout the scaffold, the degradation of aqueous-derived scaffolds appears to be more homogeneous than that of HFIP-derived scaffolds. In general and especially for the HFIP-derived scaffolds, a higher original silk fibroin concentration (e.g. 17%) and smaller pore size (e.g. 100-200microm) resulted in lower levels of tissue ingrowth and slower degradation. These results demonstrate that the in vivo behavior of the three-dimensional silk fibroin scaffolds is related to the morphological and structural features that resulted from different scaffold preparation processes. The insights gained in this study can serve as a guide for processing scenarios to match desired morphological and structural features and degradation time with tissue-specific applications.

Project description:BackgroundThe simulation of metabolic networks in quantitative systems biology requires the assignment of enzymatic kinetic parameters. Experimentally determined values are often not available and therefore computational methods to estimate these parameters are needed. It is possible to use the three-dimensional structure of an enzyme to perform simulations of a reaction and derive kinetic parameters. However, this is computationally demanding and requires detailed knowledge of the enzyme mechanism. We have therefore sought to develop a general, simple and computationally efficient procedure to relate protein structural information to enzymatic kinetic parameters that allows consistency between the kinetic and structural information to be checked and estimation of kinetic constants for structurally and mechanistically similar enzymes.ResultsWe describe qPIPSA: quantitative Protein Interaction Property Similarity Analysis. In this analysis, molecular interaction fields, for example, electrostatic potentials, are computed from the enzyme structures. Differences in molecular interaction fields between enzymes are then related to the ratios of their kinetic parameters. This procedure can be used to estimate unknown kinetic parameters when enzyme structural information is available and kinetic parameters have been measured for related enzymes or were obtained under different conditions. The detailed interaction of the enzyme with substrate or cofactors is not modeled and is assumed to be similar for all the proteins compared. The protein structure modeling protocol employed ensures that differences between models reflect genuine differences between the protein sequences, rather than random fluctuations in protein structure.ConclusionProvided that the experimental conditions and the protein structural models refer to the same protein state or conformation, correlations between interaction fields and kinetic parameters can be established for sets of related enzymes. Outliers may arise due to variation in the importance of different contributions to the kinetic parameters, such as protein stability and conformational changes. The qPIPSA approach can assist in the validation as well as estimation of kinetic parameters, and provide insights into enzyme mechanism.

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Estimating Kinetic Rate Parameters for Enzymatic Degradation of Lyophilized Silk Fibroin Sponges.

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