pysimm: A python package for simulation of molecular systems

Fortunato, Michael W-P; Colina, Coray M.

doi:10.1016/j.softx.2016.12.002

Cited by 70 publications

(67 citation statements)

References 14 publications

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“…The PEGDA macromer chains with molecular weights of 10 ( n = 224) and 5 kDa ( n = 110) for ideal networks of pure PEGDA and PEG–peptide conjugates, respectively, were generated using the open‐source Python package pysimm . pysimm uses a linear force field assisted pseudo‐self‐avoiding random‐walk algorithm where molecular units are added stepwise to the growing polymer chain end . Structural relaxation and short MD runs are performed immediately following each molecular insertion.…”

Section: Computational Methodologymentioning

confidence: 99%

An Insight into Structural and Mechanical Properties of Ideal‐Networked Poly(Ethylene Glycol)–Peptide Hydrogels from Molecular Dynamics Simulations

Rukmani

Anstine

Munasinghe

et al. 2020

Macro Chemistry & Physics

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Simulations of local structure and interactions in stimuli‐responsive hydrogel networks at atomistic resolution has the capability to compliment experimental efforts by providing insight into current soft materials design challenges. This work simulates ideal hexafunctional networks of poly(ethylene glycol) (PEG)‐diacrylate (PEGDA) and PEG–peptide hydrogels with two enzyme‐responsive peptide sequences, Gly‐Leu‐Lys (GLK) and Gly‐Pro‐Gln‐Gly‐Ile‐Phe‐Gly‐Gln‐Lys (GPQGIFGQK), using molecular dynamics (MD) simulations at water contents from 84% to 90%. This presents the first atomistic MD study of a PEG–peptide hydrogel. The mesh sizes obtained are compared to common swelling theories and the available micropore space for diffusion is compared to the sizes of a family of matrix metalloproteinases (MMPs) to predict size‐based exclusion. The effects of interactions between PEG, peptide, and water on the chemical environment surrounding the cleaving site of peptides are investigated by examining partial radial distribution functions and solvent accessible surface areas. The chemical environment around the peptide sequence is found to be more hydrophobic in PEG‐9‐peptide hydrogels, thereby favoring cleavage by the hydrophobic binding pocket of MMPs. Furthermore, the mechanical moduli of the hydrogels is also examined, and an increase with the incorporation of peptide sequences and a general decrease with increasing water concentration is observed.

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Section: Computational Methodologymentioning

confidence: 99%

An Insight into Structural and Mechanical Properties of Ideal‐Networked Poly(Ethylene Glycol)–Peptide Hydrogels from Molecular Dynamics Simulations

Rukmani

Anstine

Munasinghe

et al. 2020

Macro Chemistry & Physics

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“…This manner is analogous to the algorithm in the Polymatic code embedded in pysimm package. 31 Furthermore, additional NVT MD steps (i.e., md2 type MD simulation in Fig. 3) are inserted into the linking cycles to further relax and equilibrate the system.…”

Section: Simulation Methodsmentioning

confidence: 99%

Atomistic structure generation of covalent triazine-based polymers by molecular simulation

Song

Meng

et al. 2020

RSC Adv.

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“…The reduce code in Ambertools 64 was used to determine amino acid protonation states. The structures of free pCBMA (DP 18) and free pOEGMA (DP 25) were generated using the PySimm 65 software package’s forcefield assisted linear self- avoiding random walk. The initiator structure was the positively charged ATRP initiator used experimentally in this study.…”

Section: Methodsmentioning

confidence: 99%

Transforming protein-polymer conjugate purification by tuning protein solubility

et al. 2019

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Almost all commercial proteins are purified using ammonium sulfate precipitation. Protein-polymer conjugates are synthesized from pure starting materials, and the struggle to separate conjugates from polymer, native protein, and from isomers has vexed scientists for decades. We have discovered that covalent polymer attachment has a transformational effect on protein solubility in salt solutions. Here, protein-polymer conjugates with a variety of polymers, grafting densities, and polymer lengths are generated using atom transfer radical polymerization. Charged polymers increase conjugate solubility in ammonium sulfate and completely prevent precipitation even at 100% saturation. Atomistic molecular dynamic simulations show the impact is driven by an anti-polyelectrolyte effect from zwitterionic polymers. Uncharged polymers exhibit polymer length-dependent decreased solubility. The differences in salting-out are then used to simply purify mixtures of conjugates and native proteins into single species. Increasing protein solubility in salt solutions through polymer conjugation could lead to many new applications of protein-polymer conjugates.

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pysimm: A python package for simulation of molecular systems

Cited by 70 publications

References 14 publications

An Insight into Structural and Mechanical Properties of Ideal‐Networked Poly(Ethylene Glycol)–Peptide Hydrogels from Molecular Dynamics Simulations

An Insight into Structural and Mechanical Properties of Ideal‐Networked Poly(Ethylene Glycol)–Peptide Hydrogels from Molecular Dynamics Simulations

Atomistic structure generation of covalent triazine-based polymers by molecular simulation

Transforming protein-polymer conjugate purification by tuning protein solubility

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