Reviewability and supportability: New complementary principles to empower research software practices DOI Creative Commons
Haoling Zhang, Alberto Maillo,

Sumeer Ahmad Khan

et al.

Computational and Structural Biotechnology Journal, Journal Year: 2024, Volume and Issue: 23, P. 3989 - 3998

Published: Nov. 7, 2024

In today's scientific landscape, research software has evolved from being a supportive tool to becoming fundamental driver of discovery, particularly in life sciences. Beyond its roots engineering, now plays crucial role facilitating efficient data analysis and enabling the exploration complex natural phenomena. The advancements simulations modeling through have significantly accelerated pace while reducing associated costs. This growing reliance underscores importance ensuring reproducibility - cornerstone rigor trustworthiness. Although verifying presents challenges, well-developed openly accessible enhances transparency aids early detection errors. can be challenging, improves facilitates error detection. mini-review examines characteristics summarizes key events that shaped development, alongside changes requirements guidelines. Moreover, we propose two additional principles

Language: Английский

Local structural flexibility drives oligomorphism in computationally designed protein assemblies DOI Creative Commons
Alena Khmelinskaia, Neville P. Bethel, Farzad Fatehi

et al.

Nature Structural & Molecular Biology, Journal Year: 2025, Volume and Issue: unknown

Published: Feb. 26, 2025

Many naturally occurring protein assemblies have dynamic structures that allow them to perform specialized functions. Although computational methods for designing novel self-assembling proteins advanced substantially over the past decade, they primarily focus on static structures. Here we characterize three distinct computationally designed exhibit unanticipated structural diversity arising from flexibility in their subunits. Cryo-EM single-particle reconstructions and native mass spectrometry reveal two architectures assemblies, while six cryo-EM third likely represent a subset of its solution-phase Structural modeling molecular dynamics simulations indicate constrained within subunits each assembly promotes defined range rather than nonspecific aggregation. Redesigning flexible region one building block rescues intended monomorphic assembly. These findings highlight as powerful design principle, enabling exploration new functional spaces design. This study reports unexpected due subunit flexibility. Fixing restores architecture, suggesting strategy assemblies.

Language: Английский

Citations

4

Programmability and biomedical utility of intrinsically-disordered protein polymers DOI

Maria Camila Giraldo-Castaño,

Kai A Littlejohn,

Alexa Regina Chua Avecilla

et al.

Advanced Drug Delivery Reviews, Journal Year: 2024, Volume and Issue: 212, P. 115418 - 115418

Published: July 31, 2024

Language: Английский

Citations

4

Exploration of the hierarchical assembly space of collagen-like peptides beyond the triple helix DOI Creative Commons
Le Yu, Mark A. B. Kreutzberger, Thi H. Bui

et al.

Nature Communications, Journal Year: 2024, Volume and Issue: 15(1)

Published: Nov. 29, 2024

The de novo design of self-assembling peptides has garnered significant attention in scientific research. While alpha-helical assemblies have been extensively studied, exploration polyproline type II helices, such as those found collagen, remains relatively limited. In this study, we focus on understanding the sequence-structure relationship hierarchical collagen-like peptides, using defense collagen Surfactant Protein A a model. By dissecting sequence derived from and synthesizing short successfully construct discrete bundle hollow triple helices. Amino acid substitution studies pinpoint hydrophobic charged residues that are critical for oligomer formation. These insights guide resulting formation diverse quaternary structures, including heterogenous bundled oligomers, two-dimensional nanosheets, pH-responsive nanoribbons. Our study represents advancement harnessing higher-order beyond helix. Despite advances machine learning approaches, collagen-based materials difficult. based natural structure family proteins, designed helical peptide to form ribbons variety bundled, porous architectures.

Language: Английский

Citations

4

Computational protein design DOI Creative Commons
Katherine I. Albanese, Sophie Barbe, Derek N. Woolfson

et al.

Nature Reviews Methods Primers, Journal Year: 2025, Volume and Issue: 5(1)

Published: Feb. 27, 2025

Citations

0

Advances in designed bionanomolecular assemblies for biotechnological and biomedical applications DOI Creative Commons
Jaka Snoj, Weijun Zhou, Ajasja Ljubetič

et al.

Current Opinion in Biotechnology, Journal Year: 2025, Volume and Issue: 92, P. 103256 - 103256

Published: Jan. 18, 2025

Recent advances in protein engineering have revolutionized the design of bionanomolecular assemblies for functional therapeutic and biotechnological applications. This review highlights progress creating complex architectures, encompassing both finite extended assemblies. AI tools, including AlphaFold, RFDiffusion, ProteinMPNN, significantly enhanced scalability success de novo designs. Finite assemblies, like nanocages coiled-coil-based structures, enable precise molecular encapsulation or domain presentation. Extended filaments 2D/3D lattices, offer unparalleled structural versatility applications such as vaccine development, responsive biomaterials, engineered cellular scaffolds. The convergence artificial intelligence-driven experimental validation promises strong acceleration development tailored offering new opportunities synthetic biology, materials science, biotechnology, biomedicine.

Language: Английский

Citations

0

Dual-Ligand Assisted Anisotropic Assembly for the Construction of NIR-II Light-Propelled Mesoporous Nanomotors DOI
Jia Jia, Runfeng Lin, Minchao Liu

et al.

Journal of the American Chemical Society, Journal Year: 2025, Volume and Issue: unknown

Published: Jan. 27, 2025

The advent of autonomous nanomotors presents exciting opportunities for nanodrug delivery. However, significant potential remains enhancing the asymmetry and advancing development second near-infrared (NIR-II) light-propelled capable operating within deep tissues. Herein, we developed a dual-ligand assisted anisotropic assembly strategy that enables precise regulation interfacial energy between selenium (Se) nanoparticle periodic mesoporous organosilica (PMO). This facilitates controllable growth PMO on Se nanoparticle, leading to formation Se&PMO Janus nanohybrids. exposure ratio subunit nanohybrids can be finely tuned from 0% 75%. Leveraging transformability subunit, variety functional MxSe&PMO nanocomposites (MxSe denotes metal selenide) were further derived. As proof concept, CuSe&PMO nanohybrids, with NIR-II photothermal properties, employed as light-driven nanomotors. By precisely controlling CuSe nanostructure, these achieved optimal self-propulsion, thus cellular uptake promoting tumor penetration. Furthermore, high loading capacity hydrophobic framework enabled incorporation disulfiram, thereby significantly boosting efficacy synergistic active-motion therapy.

Language: Английский

Citations

0

Improvement in positional accuracy of neural-network predicted hydration sites of proteins by incorporating atomic details of water-protein interactions and site-searching algorithm DOI Creative Commons

Kochi Sato,

Masayoshi Nakasako

Biophysics and Physicobiology, Journal Year: 2025, Volume and Issue: 22(1), P. n/a - n/a

Published: Jan. 1, 2025

Visualization of hydration structures over the entire protein surface is necessary to understand why aqueous environment essential for folding and functions. However, it still difficult experiments. Recently, we developed a convolutional neural network (CNN) predict probability distribution water molecules surfaces in cavities. The deep was optimized using solely patterns atoms surrounding each molecule high-resolution X-ray crystal successfully provided distributions molecules. Despite effectiveness distribution, positional differences predicted positions obtained from local maxima as sites remained inadequate reproducing structure models. In this work, modified by subdividing atomic classes based on electronic properties composing amino acids. addition, exclusion volumes atom were taken distribution. These information chemical leads an improvement prediction accuracy. We selected best CNN 47 CNNs constructed systematically varying number channels layers networks. Here, report improvements accuracy reorganized together with details architecture, training data, peak search algorithm.

Language: Английский

Citations

0

Computer‐Aided Technology for Bioactive Protein Design and Clinical Application DOI

Chufan Wang,

Yeyun Chen, Lei Ren

et al.

Macromolecular Bioscience, Journal Year: 2025, Volume and Issue: unknown

Published: April 22, 2025

Abstract Computer‐aided protein design (CAPD) has become a transformative field, harnessing advances in computational power and deep learning to deepen the understanding of structure, function, design. This review provides comprehensive overview CAPD techniques, with focus on their application protein‐based therapeutics such as monoclonal antibodies, drugs, antigens, polymers. starts key methods, particularly those integrating learning‐based predictions generative models. These approaches have significantly enhanced drug properties, including binding affinity, specificity, reduction immunogenicity. also covers CAPD's role optimizing vaccine antigen design, improving stability, customizing polymers for delivery applications. Despite considerable progress, faces challenges model overfitting, limited data rare families, need efficient experimental validation. Nevertheless, ongoing advancements coupled interdisciplinary collaborations, are poised overcome these obstacles, advancing engineering therapeutic development. In conclusion, this highlights future potential transform development, personalized medicine, biotechnology.

Language: Английский

Citations

0

Protein design and optimization for synthetic cells DOI
Béla P. Frohn, Shunshi Kohyama, Petra Schwille

et al.

Nature Reviews Bioengineering, Journal Year: 2025, Volume and Issue: unknown

Published: May 19, 2025

Language: Английский

Citations

0

Self-assembly of anisotropic nano-building-blocks DOI Creative Commons

Cuiling Hou,

Zhenhua Chen, Z. Chang

et al.

Next Nanotechnology, Journal Year: 2025, Volume and Issue: 8, P. 100185 - 100185

Published: Jan. 1, 2025

Language: Английский

Citations

0