☆ 4.6 Review

Modeling of supramolecular biopolymers: Leading the in silico revolution of tissue engineering and nanomedicine

NANOTECHNOLOGY REVIEWS (2022)

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Article Cell & Tissue Engineering

Stem Cell-Seeded 3D-Printed Scaffolds Combined with Self-Assembling Peptides for Bone Defect Repair

Haixia Xu et al.

Summary: The study successfully treated calvarial defects by combining BMSC-seeded 3D-printed PCL with SAPs, promoting bone regeneration and neovascularization. Results showed that PCL/BMSC/SAP implants significantly enhanced bone and blood vessel formation, offering an effective approach for treating bone defects.

TISSUE ENGINEERING PART A (2022)

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Article Biochemistry & Molecular Biology

NMR studies of lipid regulation of the K+ channel KcsA

Dongyu Zhang et al.

Summary: The membrane environment, including specific lipid characteristics, plays important roles in the folding, stability, and gating of the prokaryotic potassium channel KcsA. The findings suggest that anionic lipids may promote channel inactivation.

BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES (2021)

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Article Chemistry, Multidisciplinary

Rapid Computational Analysis of DNA Origami Assemblies at Near-Atomic Resolution

Jae Young Lee et al.

Summary: The computational method presented in this study allows for rapid analysis of structured DNA assemblies at near-atomic resolution, accurately predicting their shape, dynamic properties, and mechanical rigidities. The method achieves high computational efficiency and molecular-level accuracy through a multiscale analysis framework, making it a valuable tool for iterative design-analysis-revision processes in DNA nanotechnology.

ACS NANO (2021)

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Review Engineering, Chemical

Supramolecular Biopolymers for Tissue Engineering

Rosario Perez-Pedroza et al.

Summary: SBPs are polymeric units derived from macromolecules that can assemble with each other through noncovalent interactions. They possess advantages in tissue engineering, such as easy functionalization, self-healing, biodegradability, stimuli-responsiveness, and nonimmunogenicity.

ADVANCES IN POLYMER TECHNOLOGY (2021)

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Article Nanoscience & Nanotechnology

Interfacial Photo-Cross-Linking: Simple but Powerful Approach for Fabricating Capsule Polymer Particles with Tunable pH-Responsive Controlled Release Capability

Yukiya Kitayama et al.

Summary: Spherical poly(2-diethylaminoethyl methacrylate-co-2-cinnamoylethyl methacrylate) (P(DEAEMA-CEMA)) particles were directly encapsulated with controlled pH-responsive release properties via interfacial photo-cross-linking. The encapsulated materials were stably retained under neutral pH conditions and released under acidic pH conditions, with release kinetics controlled by pH. The pH-responsive release properties were regulated by changing the polymer composition in P(DEAEMA-CEMA), demonstrating potential for broad applications in advanced research fields.

ACS APPLIED MATERIALS & INTERFACES (2021)

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Review Pharmacology & Pharmacy

Understanding molecular mechanisms of biologics drug delivery and stability from NMR spectroscopy

Pyae Phyo et al.

Summary: Protein therapeutics play a predominant role in the modern pharmaceutical market, but face limitations of membrane impermeability and structural instability. Effective formulations are crucial for improving bioavailability and stability. Understanding membrane affinity, cellular internalization, and release of drug-loaded carrier vehicles can enhance delivery efficiency and therapeutic efficacy.

ADVANCED DRUG DELIVERY REVIEWS (2021)

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Article Chemistry, Multidisciplinary

Halogen Bonding: An Underestimated Player in Membrane-Ligand Interactions

Rafael Santana Nunes et al.

Summary: Halogen bonds (XBs) are noncovalent interactions in which halogen atoms act as electrophilic species interacting with Lewis bases. This type of interaction is relevant in biological membrane systems, influencing the pharmacological or toxicological activity of halogenated compounds. Molecular dynamics simulations provide evidence of the effects of XBs on ligands' membrane insertion profile and orientational preferences.

JOURNAL OF THE AMERICAN CHEMICAL SOCIETY (2021)

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Article Biochemical Research Methods

OpenAWSEM with Open3SPN2: A fast, flexible, and accessible framework for large-scale coarse-grained biomolecular simulations

Wei Lu et al.

Summary: This paper presents two new implementations of efficient and accurate coarse-grained protein and DNA simulation forcefields, OpenAWSEM and Open3SPN2, which can now run hundreds of times faster than before, facilitating studies of large biomolecular machines. These implementations are showcased to achieve around a 30-fold speedup in protein and protein-DNA simulations over existing implementations, allowing for more accurate modeling of protein folding, structure prediction, and protein-DNA binding. The simulation tool provided in this paper aims to bridge the gap between molecular simulations and cellular studies by offering a user-friendly and efficient platform for simulating large cellular processes.

PLOS COMPUTATIONAL BIOLOGY (2021)

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Article Biochemistry & Molecular Biology

Scaffolds from Self-Assembling Tetrapeptides Support 3D Spreading, Osteogenic Differentiation, and Angiogenesis of Mesenchymal Stem Cells

Salwa Alshehri et al.

Summary: Using self-assembling tetrapeptide scaffolds can promote the growth and osteogenic differentiation of human mesenchymal stem cells, with the ability to adjust stiffness by changing concentration; the scaffold can also enhance angiogenesis of human umbilical vein endothelial cells in vitro, indicating great potential for bone tissue engineering applications.

BIOMACROMOLECULES (2021)

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Article Biophysics

A multiscale coarse-grained model of the SARS-CoV-2 virion

Alvin Yu et al.

Summary: This article presents the current status and ongoing development of a largely bottom-up coarse-grained (CG) model of the SARS-CoV-2 virion. The CG model was constructed using data from cryo-electron microscopy, x-ray crystallography, and computational predictions to build molecular models of structural SARS-CoV-2 proteins, which were then assembled into the complete virion model. The CG model allows for capturing viral behavior that is difficult to observe in atomistic simulations and can be iteratively improved with new data.

BIOPHYSICAL JOURNAL (2021)

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Article Chemistry, Multidisciplinary

Amine-Derivatized L-Phenylalanine and L-Tyrosine as Versatile Self-Assembled Platforms of Diverse Supramolecular Architectures: From Mesocrystals to Organogels

Federico Movilla et al.

Summary: This study demonstrates the remarkable ability of molecules based on L-tyrosine and L-phenylalanine to self-assemble into different structures in varying environmental conditions, from crystalline materials to organogels. The self-assembly process is influenced by reaction conditions, environmental factors, and functional groups, and was studied using a combination of techniques including X-ray diffraction and small-angle X-ray scattering. The results suggest potential applications in diverse environments such as oil spill recovery.

CRYSTAL GROWTH & DESIGN (2021)

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Article Chemistry, Physical

Machine Learning in QM/MM Molecular Dynamics Simulations of Condensed-Phase Systems

Lennard Boeselt et al.

Summary: QM/MM molecular dynamics simulations are computationally expensive due to the need to explicitly treat all valence electrons and perform a self-consistent field procedure. Machine-learned models show promise in reducing the computational cost and improving accuracy.

JOURNAL OF CHEMICAL THEORY AND COMPUTATION (2021)

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Article Biotechnology & Applied Microbiology

Multiscale Structural Elucidation of Peptide Nanotubes by X-Ray Scattering Methods

Theyencheri Narayanan et al.

Summary: This review explores the structural investigations of self-assembled peptide nanotubes using X-ray scattering techniques. Compared to electron microscopy, scattering methods allow for studies of nanotubes in solution under the right physicochemical conditions and probe their formation mechanisms. Additionally, a combination of X-ray scattering methods enables the elucidation of structural organization from the molecular scale to the nanotube dimension.

FRONTIERS IN BIOENGINEERING AND BIOTECHNOLOGY (2021)

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Article Chemistry, Physical

In Situ-Cross-linked Supramolecular Eco-Binders for Improved Capacity and Stability of Lithium-Sulfur Batteries

Limin Man et al.

Summary: A novel eco-binder WPUP was developed to improve the charge-discharge cycle performance of rechargeable lithium-sulfur batteries, resulting in enhanced capacity and cycling stability. The design strategy of this binder shows great potential in developing high-capacity and long cycle stable LSBs.

ACS APPLIED ENERGY MATERIALS (2021)

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Article Chemistry, Multidisciplinary

Unexpected Role of Achiral Glycine in Determining the Suprastructural Handedness of Peptide Nanofibrils

Muhan Wang et al.

Summary: The study investigates the impact of introducing achiral glycine into amphiphilic peptides on supramolecular chiral structures, revealing a significant alteration in handedness. Glycine was found to unexpectedly regulate the conformational preference of single beta-strands, leading to diverse beta-strand conformations.

ACS NANO (2021)

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Review Engineering, Biomedical

Machine learning and big data provide crucial insight for future biomaterials discovery and research

Jacob Kerner et al.

Summary: Machine learning has been widely utilized in various fields, including biomaterials, optimizing data collection and analysis. Recent advances in biomaterials have focused on quantitative structure properties relationships, introducing four basic models for rapid development and addressing the lack of machine learning implementation in the field. This article aims to spark greater interest and awareness in utilizing computational methods for biomaterials research.

ACTA BIOMATERIALIA (2021)

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Review Pharmacology & Pharmacy

Self-assembling peptides as vectors for local drug delivery and tissue engineering applications

Christina Karavasili et al.

Summary: Molecular self-assembly has opened up a new era in the development of advanced biomaterials for local drug delivery and tissue engineering. Self-assembling peptides (SAPs) are highlighted for their biocompatibility and biodegradability, showing potential in enhancing pharmacokinetic and pharmacodynamic responses, as well as regenerative potential. By utilizing peptide engineering to create short, water-soluble SAP biomaterials, their multifunctionality is enhanced, making them potent bio-materials for various biomedical applications.

ADVANCED DRUG DELIVERY REVIEWS (2021)

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Article Chemistry, Analytical

Antibody-Responsive Ratiometric Fluorescence Biosensing of Biemissive Silver Nanoclusters Wrapped in Switchable DNA Tweezers

Jia-Yang He et al.

Summary: The study successfully demonstrated a ratiometric fluorescence biosensing method using tweezerlike DNA architecture and dual-emitting AgNCs for specific detection of anti-Dig, providing reliable quantization at the picomolar level.

ANALYTICAL CHEMISTRY (2021)

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Article Biochemistry & Molecular Biology

Anisotropically Functionalized Aptamer-DNA Nanostructures for Enhanced Cell Proliferation and Target-Specific Adhesion in 3D Cell Cultures

Keonwook Nam et al.

Summary: The study investigates the efficiency of anisotropically functionalized DNA nanostructures as biological signal inducers in 3D cell cultivation, with a focus on controlling cell adhesion capability. The results demonstrate significantly enhanced cell proliferation and homogeneous distribution of encapsulated cells within hydrogel matrices, showing promise for advancing conventional 3D culture platforms.

BIOMACROMOLECULES (2021)

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Review Cell Biology

Simulating realistic membrane shapes

Weria Pezeshkian et al.

Summary: Biological membranes exhibit diversity in their shapes and complexity in chemical compositions that are linked to many cellular functions. Simulation studies using a diverse range of computational techniques are able to capture this complexity at increasing levels of realism and connect the microscopic view on protein-lipid interactions to cellular morphologies at the level of entire organelles. Recent advances highlight the understanding of this complexity, identify current bottlenecks, and sketch possible ways ahead.

CURRENT OPINION IN CELL BIOLOGY (2021)

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Article Polymer Science

Tissue engineering needs new biomaterials: Poly(xylitol-dodecanedioic acid)-co-polylactic acid (PXDDA-co-PLA) and its nanocomposites

Amir Sotoudeh et al.

Summary: The research introduced new biopolymers through chemical reactions between Xylitol, Dodecanedioic acid (DDA) and Lactic acid (LA), and analyzed their properties using various techniques. The presence of LA was found to have significant effects on the morphology and hydrophilic properties of the polymeric samples. Additionally, the inclusion of LA monomers and bio glass nanoparticles influenced the viscoelastic properties and degradation rate of the nanocomposite samples.

EUROPEAN POLYMER JOURNAL (2021)

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Article Polymer Science

Thermal and dynamic mechanical behavior of poly(lactic acid) (PLA)-based electrospun scaffolds for tissue engineering

Nicola Ciarfaglia et al.

Summary: The aim of the study is to modulate the characteristics of electrospun scaffolds by selecting appropriate polymers, leading to better performance in terms of hydrophilicity and thermomechanical properties, with samples containing 3% cellulose nanocrystals and elastin peptide showing the best results.

JOURNAL OF APPLIED POLYMER SCIENCE (2021)

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Article Chemistry, Multidisciplinary

Constraints on the Structure of Fibrils Formed by a Racemic Mixture of Amyloid-β Peptides from Solid-State NMR, Electron Microscopy, and Theory

Jevgenij A. Raskatov et al.

Summary: The study investigated the structural characteristics of D,L-A beta 40 fibrils using electron microscopy, solid-state nuclear magnetic resonance (NMR), and density functional theory (DFT) calculations. While resembling known L-A beta 40 fibril structures, D,L-A beta 40 fibrils were found to exhibit an antiparallel rippled sheet structure with different intermolecular hydrogen bond registries. Solid-state NMR data and DFT calculations support the presence of antiparallel alignments in the beta-strand segments of D,L-A beta 40 fibrils, providing insight into the self-assembly of amyloidogenic peptides.

JOURNAL OF THE AMERICAN CHEMICAL SOCIETY (2021)

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Article Biochemistry & Molecular Biology

Protein glycosylation in extracellular vesicles: Structural characterization and biological functions

Janaina Macedo-da-Silva et al.

Summary: Extracellular vesicles (EVs) are lipid-bilayer enclosed particles that play crucial roles in intercellular communication, biomolecule delivery, cellular disposal, homeostasis maintenance, potential biomarkers, and drug carriers. The content of EVs, which includes DNA, lipids, metabolites, proteins, and microRNA, has been studied in various diseases, showcasing their significance in disease pathology and treatment.

MOLECULAR IMMUNOLOGY (2021)

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Article Multidisciplinary Sciences

Highly accurate protein structure prediction with AlphaFold

John Jumper et al.

Summary: Proteins are essential for life, and accurate prediction of their structures is a crucial research problem. Current experimental methods are time-consuming, highlighting the need for accurate computational approaches to address the gap in structural coverage. Despite recent progress, existing methods fall short of atomic accuracy in protein structure prediction.

NATURE (2021)

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Article Multidisciplinary Sciences

Accurate prediction of protein structures and interactions using a three-track neural network

Minkyung Baek et al.

Summary: Through the three-track network, we achieved accuracies approaching those of DeepMind in CASP14, enabling rapid solution of challenging x-ray crystallography and cryo-electron microscopy structure modeling problems, and providing insights into the functions of proteins with currently unknown structure.

SCIENCE (2021)

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Review Biochemistry & Molecular Biology

A Primer on the oxDNA Model of DNA: When to Use it, How to Simulate it and How to Interpret the Results

A. Sengar et al.

Summary: The oxDNA model is widely used in various fields and can be accessed through two open source packages. This article presents a set of example simulations with clear documentation, introducing how to simulate the model and reviewing its fundamental properties. It also outlines how simulation results can be interpreted and provides guidance on whether using oxDNA for simulating a system is worthwhile.

FRONTIERS IN MOLECULAR BIOSCIENCES (2021)

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Article Biochemistry & Molecular Biology

OxDNA.org: a public webserver for coarse-grained simulations of DNA and RNA nanostructures

Erik Poppleton et al.

Summary: OxDNA and oxRNA are popular coarse-grained models used in DNA/RNA nanotechnology. OxDNA.org is a web interface for running, visualizing and analyzing molecular dynamics simulations, making it easier for users to integrate simulations into nanostructure design pipelines.

NUCLEIC ACIDS RESEARCH (2021)

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Mechanical properties of DNA and DNA nanostructures: comparison of atomistic, Martini and oxDNA models

Supriyo Naskar et al.

Summary: This study estimates the mechanical properties of short dsDNA and DNA nanotubes using Martini and oxDNA models, showing good agreement with previous studies and experiments. Martini models fail to capture the salt concentration effects on mechanical properties, while oxDNA captures the effects on small dsDNA but not on DNTs. Time evolved structures from oxDNA models are comparable to all-atom MD simulated structures, providing a route to study DNA mechanics on a larger scale.

JOURNAL OF MATERIALS CHEMISTRY B (2021)

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Review Chemistry, Multidisciplinary

Electrospun and co-electrospun biopolymer nanofibers for skin wounds on diabetic patients: an overview

Paola Campa-Siqueiros et al.

Summary: Research indicates that wound healing treatment in diabetic patients globally requires a substantial amount of funding, and explores the potential use of co-electrospun nanofibers as wound dressings, containing healing agents in the core with a protective shell, to accelerate the wound healing process.

RSC ADVANCES (2021)

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Engineering bioactive synthetic polymers for biomedical applications: a review with emphasis on tissue engineering and controlled release

Edna Johana Bolivar-Monsalve et al.

Summary: Synthetic polymers (SyPs) have various applications in biomedical engineering, with advantages in mechanical properties, chemical structure, and consistency. Functionalization of SyPs is necessary for applications such as tissue engineering.

MATERIALS ADVANCES (2021)

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Multiscale QM/MM molecular dynamics simulations of the trimeric major light-harvesting complex II

Sayan Maity et al.

Summary: Photosynthetic processes are influenced by sunlight, with the right amount driving anabolic pathways and excessive or insufficient sunlight causing damage. Studying the dynamics and exciton transfer in the Light-Harvesting Complex helps understand energy absorption and dissipation in plants. Molecular dynamics simulations and spectral density analysis provide insights into the complex system's accuracy and reliability, contributing to the understanding of energy transfer processes in plants.

PHYSICAL CHEMISTRY CHEMICAL PHYSICS (2021)

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The interaction of supramolecular anticancer drug amphiphiles with phospholipid membranes

Phu K. Tang et al.

Summary: The shape of drug delivery vehicles, such as nanostructures like nanofilaments and nanotubes, plays a crucial role in their interaction with cellular membranes, impacting their effectiveness. Peptide-based drug amphiphiles (DAs) are potential candidates for drug delivery, with their interaction with membranes dependent on the number of conjugated drugs. Computational simulations suggest that the hydrogen bond density between the nanostructure and membrane may modulate their interaction, offering insights for rational design of peptide-based drug delivery vehicles.

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Regulated Surface Morphology of Polyaniline/Polylactic Acid Composite Nanofibers via Various Inorganic Acids Doping for Enhancing Biocompatibility in Tissue Engineering

Rongtao Liu et al.

Summary: The addition of different acidic dopants in PANI/PLA composite nanofibers can regulate surface morphology, improve biocompatibility, and have a positive impact on tissue engineering.

NANOSCALE RESEARCH LETTERS (2021)

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Farid Alisafaei et al.

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Extending the Martini Coarse-Grained Force Field to N-Glycans

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Theoretical elucidation of the amino acid interaction with graphene and functionalized graphene nanosheets: insights from DFT calculation and MD simulation

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Density functional theory studies on cytosine analogues for inducing double-proton transfer with guanine

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Double-Well Ultra-Coarse-Grained Model to Describe Protein Conformational Transitions

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The Answer Lies in the Energy: How Simple Atomistic Molecular Dynamics Simulations May Hold the Key to Epitope Prediction on the Fully Glycosylated SARS-CoV-2 Spike Protein

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Review Biotechnology & Applied Microbiology

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FRONTIERS IN BIOENGINEERING AND BIOTECHNOLOGY (2019)

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Elucidating the Ordering in Self-Assembled Glycocalyx Mimicking Supramolecular Copolymers in Water

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Revealing the Sequence-Structure-Electronic Property Relation of Self-Assembling π-Conjugated Oligopeptides by Molecular and Quantum Mechanical Modeling

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Molecular dynamics simulation of reversible electroporation with Martini force field

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Biomolecular Simulations of Halogen Bonds with a GROMOS Force Field

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CURRENT OPINION IN STRUCTURAL BIOLOGY (2018)

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Molecular Simulations of Ion Effects on the Thermodynamics of RNA Folding

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Reversible self-assembly of superstructured networks

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Sequence-Dependent Persistence Lengths of DNA

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Combining the MARTINI and Structure-Based Coarse-Grained Approaches for the Molecular Dynamics Studies of Conformational Transitions in Proteins

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The Theory of Ultra-Coarse-Graining. 3. Coarse-Grained Sites with Rapid Local Equilibrium of Internal States

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NANOSCALE RESEARCH LETTERS (2017)

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Injectable bioactive akermanite/alginate composite hydrogels for in situ skin tissue engineering

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Improved Peptide and Protein Torsional Energetics with the OPLS-AA Force Field

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Protein Simulations in Fluids: Coupling the OPEP Coarse-Grained Force Field with Hydrodynamics

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Refinement of the Sugar-Phosphate Backbone Torsion Beta for AMBER Force Fields Improves the Description of Z- and B-DNA

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The Supramolecular Organization of a Peptide-Based Nanocarrier at High Molecular Detail

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Supramolecular Glycosylation Accelerates Proteolytic Degradation of Peptide Nanofibrils

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Complementary Co-assembling Peptides: From In Silico Studies to In Vivo Application

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ANNALS OF BIOMEDICAL ENGINEERING (2014)

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CHARMM All-Atom Additive Force Field for Sphingomyelin: Elucidation of Hydrogen Bonding and of Positive Curvature

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BIOPOLYMERS (2014)

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The OPEP protein model: from single molecules, amyloid formation, crowding and hydrodynamics to DNA/RNA systems

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CHEMICAL SOCIETY REVIEWS (2014)

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Modelling and analysis of early aggregation events of BMHP1-derived self-assembling peptides

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Mechanism of Folding and Binding of an Intrinsically Disordered Protein As Revealed by ab Initio Simulations

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Going Backward: A Flexible Geometric Approach to Reverse Transformation from Coarse Grained to Atomistic Models

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Lipid14: The Amber Lipid Force Field

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A unified coarse-grained model of biological macromolecules based on mean-field multipole-multipole interactions

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JOURNAL OF MOLECULAR MODELING (2014)

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Refined OPLS All-Atom Force Field for Saturated Phosphatidylcholine Bilayers at Full Hydration

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Lipid Organization of the Plasma Membrane

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Double-stranded RNA under force and torque: Similarities to and striking differences from double-stranded DNA

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PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2014)

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Synthetic biodegradable functional polymers for tissue engineering: a brief review

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SCIENCE CHINA-CHEMISTRY (2014)

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DFT optimization and DFT-MD studies of glucose, ten explicit water molecules enclosed by an implicit solvent, COSMO

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Molecular dynamics study of DNA oligomers under angled pulling

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RSC ADVANCES (2014)

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Hyaluronan and cardiac regeneration

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Tuning supramolecular mechanics to guide neuron development

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Perspective on the Martini model

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CHEMICAL SOCIETY REVIEWS (2013)

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Nanomaterials design and tests for neural tissue engineering

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CHEMICAL SOCIETY REVIEWS (2013)

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Modeling Protein-Protein Recognition in Solution Using the Coarse-Grained Force Field SCORPION

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JOURNAL OF CHEMICAL THEORY AND COMPUTATION (2013)

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PaLaCe: A Coarse-Grain Protein Model for Studying Mechanical Properties

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PRIMO: A Transferable Coarse-Grained Force Field for Proteins

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Polarizable Atomic Multipole-Based AMOEBA Force Field for Proteins

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Steered Molecular Dynamics Studies of the Potential of Mean Force for Peptide Amphiphile Self-Assembly into Cylindrical Nanofibers

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On the Foldability of Tryptophan-Containing Tetra- and Pentapeptides: An Exhaustive Molecular Dynamics Study

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Mixing MARTINI: Electrostatic Coupling in Hybrid Atomistic-Coarse-Grained Biomolecular Simulations

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JOURNAL OF PHYSICAL CHEMISTRY B (2013)

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Coarse-Grained Model for Predicting RNA Folding Thermodynamics

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JOURNAL OF PHYSICAL CHEMISTRY B (2013)

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Mechanical Identities of RNA and DNA Double Helices Unveiled at the Single-Molecule Level

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Assessing the Utility of Infrared Spectroscopy as a Structural Diagnostic Tool for β-Sheets in Self-Assembling Aromatic Peptide Amphiphiles

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Self-Assembling Peptides Improve the Stability of Glucagon-like Peptide-1 by Forming a Stable and Sustained Complex

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Synthesis and characterization of designed BMHP1-derived self-assembling peptides for tissue engineering applications

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ACTA BIOMATERIALIA (2012)

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Self-Assembling Nanotubes Consisting of Rigid Cyclic γ-Peptides

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First-principles study of the adsorption of lysine on hydroxyapatite (100) surface

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Sustained delivery of VEGF from designer self-assembling peptides improves cardiac function after myocardial infarction

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Controlled release of urea from chitosan microspheres prepared by emulsification and cross-linking method

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Improving Internal Peptide Dynamics in the Coarse-Grained MARTINI Model: Toward Large-Scale Simulations of Amyloid- and Elastin-like Peptides

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GROMOS 53A6GLYC, an Improved GROMOS Force Field for Hexopyranose-Based Carbohydrates

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Reference Simulations of Noncanonical Nucleic Acids with Different χ Variants of the AMBER Force Field: Quadruplex DNA, Quadruplex RNA, and Z-DNA

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Toward Quantitative Coarse-Grained Models of Lipids with Fluids Density Functional Theory

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Membrane Protein Simulations Using AMBER Force Field and Berger Lipid Parameters

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JOURNAL OF CHEMICAL THEORY AND COMPUTATION (2012)

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A New Multiscale Algorithm and Its Application to Coarse-Grained Peptide Models for Self-Assembly

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LIPID11: A Modular Framework for Lipid Simulations Using Amber

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AWSEM-MD: Protein Structure Prediction Using Coarse-Grained Physical Potentials and Bioinformatically Based Local Structure Biasing

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Insights into Intrastrand Cross-Link Lesions of DNA from QM/MM Molecular Dynamics Simulations

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Modeling the Self-Assembly of Peptide Amphiphiles into Fibers Using Coarse-Grained Molecular Dynamics

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TISSUE ENGINEERING PART A (2012)

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Review Biology

Hyaluronic acid-based scaffold for central neural tissue engineering

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Assembly of MreB Filaments on Liposome Membranes: A Synthetic Biology Approach

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RNA Folding Pathways and the Self-Assembly of Ribosomes

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ACCOUNTS OF CHEMICAL RESEARCH (2011)

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Physical Properties of Polymorphic Yeast Prion Amyloid Fibers

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Definition and testing of the GROMOS force-field versions 54A7 and 54B7

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EUROPEAN BIOPHYSICS JOURNAL WITH BIOPHYSICS LETTERS (2011)

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Validation of the GROMOS 54A7 Force Field with Respect to β-Peptide Folding

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Electrospun Collagen: A Tissue Engineering Scaffold with Unique Functional Properties in a Wide Variety of Applications

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Biomaterial-Biomolecule Interaction: DFT-D Study of Glycine Adsorption on Cr2O3

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Simulation of Chaperonin Effect on Protein Folding: A Shift from Nucleation-Condensation to Framework Mechanism

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Morphology and Persistence Length of Amyloid Fibrils Are Correlated to Peptide Molecular Structure

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Molecular simulations predict novel collagen conformations during cross-link loading

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Evaluation of Early and Late Effects into the Acute Spinal Cord Injury of an Injectable Functionalized Self-Assembling Scaffold

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Steered Molecular Dynamics Study of Mechanical Response of Full Length and Short Collagen Molecules

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Density functional theory calculations and molecular dynamics simulations of the adsorption of biomolecules on graphene surfaces

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Review Biochemistry & Molecular Biology

Self-Assembly of Peptide Amphiphiles: From Molecules to Nanostructures to Biomaterials

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Molecular simulations of carbohydrates and protein-carbohydrate interactions: motivation, issues and prospects

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DRUG DISCOVERY TODAY (2010)

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Coarse-Grained Model of Collagen Molecules Using an Extended MARTINI Force Field

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CHARMM General Force Field: A Force Field for Drug-Like Molecules Compatible with the CHARMM All-Atom Additive Biological Force Fields

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DFT molecular dynamics (DFTMD) simulations of carbohydrates: COSMO solvated α-maltose

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Current Status of the AMOEBA Polarizable Force Field

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Lipid microdomains and the regulation of ion channel function

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Interplay between Secondary and Tertiary Structure Formation in Protein Folding Cooperativity

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Application of collagen-chitosan/fibrin glue asymmetric scaffolds in skin tissue engineering

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Nanoconfinement controls stiffness, strength and mechanical toughness of β-sheet crystals in silk

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Hydroxyapatite as a key biomaterial: quantum-mechanical simulation of its surfaces in interaction with biomolecules

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PRIMO/PRIMONA: A coarse-grained model for proteins and nucleic acids that preserves near-atomistic accuracy

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QM/MM Methods for Biomolecular Systems

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Self-Assembly of Multidomain Peptides: Sequence Variation Allows Control over Cross-Linking and Viscoelasticity

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REACH Coarse-Grained Normal Mode Analysis of Protein Dimer Interaction Dynamics

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Synthetic biology of minimal systems

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CRITICAL REVIEWS IN BIOCHEMISTRY AND MOLECULAR BIOLOGY (2009)

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Generic coarse-grained model for protein folding and aggregation

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Martini Coarse-Grained Force Field: Extension to Carbohydrates

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Production of self-assembling biomaterials for tissue engineering

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Folding pathway of the B1 domain of protein G explored by multiscale modeling

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Systematic Multiscale Parameterization of Heterogeneous Elastic Network Models of Proteins

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BIOPHYSICAL JOURNAL (2008)

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Mechanical properties of physiological and pathological models of collagen peptides investigated via steered molecular dynamics simulations

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The MARTINI coarse-grained force field: Extension to proteins

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Dynamic charge interactions create surprising rigidity in the ER/K α-helical protein motif

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PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2008)

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GLYCAM06: A generalizable Biomolecular force field. Carbohydrates

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JOURNAL OF COMPUTATIONAL CHEMISTRY (2008)

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Beyond the code: the mechanical properties of DNA as they relate to mitosis

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CHROMOSOMA (2008)

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The MARTINI force field: Coarse grained model for biomolecular simulations

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Improved residue contact prediction using support vector machines and a large feature set

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Multiscale modeling of biomolecular systems: in serial and in parallel

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CURRENT OPINION IN STRUCTURAL BIOLOGY (2007)

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Biological Designer Self-Assembling Peptide Nanofiber Scaffolds Significantly Enhance Osteoblast Proliferation, Differentiation and 3-D Migration

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Designer Self-Assembling Peptide Nanofiber Scaffolds for Adult Mouse Neural Stem Cell 3-Dimensional Cultures

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Review Chemistry, Physical

Self-assembly and applications of biomimetic and bioactive peptide-amphiphiles

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SOFT MATTER (2006)

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Benchmark database of accurate (MP2 and CCSD(T) complete basis set limit) interaction energies of small model complexes, DNA base pairs, and amino acid pairs

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Measurement of the elastic modulus of single bacterial cellulose fibers using atomic force microscopy

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LANGMUIR (2005)

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Validation of the 53A6 GROMOS force field

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EUROPEAN BIOPHYSICS JOURNAL WITH BIOPHYSICS LETTERS (2005)

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A coarse-grained molecular model for glycosaminoglycans: Application to chondroitin, chondroitin sulfate, and hyaluronic acid

M Bathe et al.

BIOPHYSICAL JOURNAL (2005)

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Mechanical unfolding of RNA hairpins

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PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2005)

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Single-molecule measurements of the persistence length of double- stranded RNA

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BIOPHYSICAL JOURNAL (2005)

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NMR solution structure of a peptide from the mdm-2 binding domain of the p53 protein that is selectively cytotoxic to cancer cells

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M3B: A coarse grain force field for molecular simulations of malto-oligosaccharides and their water mixtures

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A biomolecular force field based on the free enthalpy of hydration and solvation: The GROMOS force-field parameter sets 53A5 and 53A6

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Review Biotechnology & Applied Microbiology

Fabrication of novel biomaterials through molecular self-assembly

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NATURE BIOTECHNOLOGY (2003)

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A reactive molecular dynamics model of thermal decomposition in polymers: 1. Poly(methyl methacrylate)

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POLYMER (2003)

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Characterization of polylactic acid polyglycolic acid composites for cartilage tissue engineering

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TISSUE ENGINEERING (2003)

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An improved OPLS-AA force field for carbohydrates

D Kony et al.

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Self-assembly at all scales

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Anisotropy of fluctuation dynamics of proteins with an elastic network model

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BIOPHYSICAL JOURNAL (2001)

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