Review
Chemistry, Multidisciplinary
Jie Zhu, Nicole Avakyan, Albert Kakkis, Alexander M. Hoffnagle, Kenneth Han, Yiying Li, Zhiyin Zhang, Tae Su Choi, Youjeong Na, Chung-Jui Yu, F. Akif Tezcan
Summary: Proteins, as nature's primary building blocks for sophisticated molecular machines and materials, have inspired extensive efforts in the rational design of artificial protein assemblies in the last two decades. Scientists have devised creative strategies by combining tools and principles of various disciplines to control the self-assembly of complex proteins, leading to artificial protein assemblies with unprecedented structures and functions, as well as protein-based materials with unusual properties.
Review
Biotechnology & Applied Microbiology
Ruiqi Zeng, Chenyan Lv, Chengtao Wang, Guanghua Zhao
Summary: Protein assembly for biomaterial generation is rapidly developing and has diverse applications in biotechnology, including encapsulation, bioimaging, photosynthetic apparatus, and magnetogenetic applications. This review focuses on the construction of protein-based nanomaterials through self-assembly and discusses the design and construction of 0D, 1D, 2D, 3D protein assembled nanomaterials, as well as their potential applications.
BIOTECHNOLOGY ADVANCES
(2021)
Review
Chemistry, Multidisciplinary
Nairiti J. Sinha, Matthew G. Langenstein, Darrin J. Pochan, Christopher J. Kloxin, Jeffery G. Saven
Summary: Peptides have been extensively used to construct nanomaterials with targeted structures through hierarchical assembly. Both rationally designed peptides derived from natural protein domains and intuitively or computationally designed peptides that form beta-sheets and helical structures have been successful in creating nanoscale morphologies with defined 1-d, 2-d, and 3-d architectures.
Article
Biochemistry & Molecular Biology
Rosalie Lipsh-Sokolik, Dina Listov, Sarel J. Fleishman
Summary: The AbDesign approach allows for the computational assembly of a large number of new protein backbones by combining naturally occurring modular fragments, resulting in highly efficient proteins with dozens of mutations. This method provides sub-angstrom level control over the positioning of active-site groups, which is necessary for obtaining highly active proteins.
Article
Chemistry, Multidisciplinary
Mingming Du, Kun Zhou, Runze Yu, Yufeng Zhai, Gang Chen, Qiangbin Wang
Summary: This study utilized an anisotropic building block RhuA and introduced histidine residues to achieve the construction of highly ordered protein superstructures through pi-pi stacking interactions, shedding light on the structural and dynamic aspects of protein assembly.
Article
Multidisciplinary Sciences
Diogo E. P. Pinto, Petr Sulc, Francesco Sciortino, John Russo
Summary: The control over self-assembly of complex structures, particularly at the colloidal scale, has been a significant challenge in material science. The formation of amorphous aggregates often disrupts the desired assembly pathway. In this study, we investigate the self-assembly problem of three Archimedean shells using patchy particles as model building blocks. By recasting the assembly problem as a Boolean satisfiability problem, we find effective designs and selectively suppress unwanted structures.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2023)
Article
Engineering, Environmental
Jing Yang, Di Zhao, Decui Yao, Yige Wang, Huanrong Li
Summary: Supramolecular self-assembly induced by lanthanide ions (Ln(3+)) was used to create functional luminescent materials with fast self-healing and good mechanical performance, showing promising applications in smart sensors. The materials exhibit reversibly responsive fluorochromic properties and high stretchability, providing new insights for the development of e-skin and smart optical devices.
CHEMICAL ENGINEERING JOURNAL
(2021)
Article
Chemistry, Multidisciplinary
Filip Hasecke, Chamani Niyangoda, Gustavo Borjas, Jianjun Pan, Garrett Matthews, Martin Muschol, Wolfgang Hoyer
Summary: The study found that in the assembly of A beta and lysozyme, protofibrils bind to the lateral surfaces of amyloid fibrils, inhibiting the self-proliferation of amyloid fibrils. This suggests that metastable oligomers counteract the replacement by amyloid fibrils through competing for monomers and blocking secondary nucleation sites.
ANGEWANDTE CHEMIE-INTERNATIONAL EDITION
(2021)
Article
Chemistry, Multidisciplinary
Farzaneh Mohajerani, Botond Tyukodi, Christopher J. Schlicksup, Jodi A. Hadden-Perilla, Adam Zlotnick, Michael F. Hagan
Summary: In this study, computer simulations and analysis were used to reveal the assembly process of hepatitis B virus (HBV) and the mechanism of capsid polymorphism. The findings are important for understanding the HBV lifecycle and developing new antiviral drugs.
Review
Pharmacology & Pharmacy
Corey. A. Stevens, Kuljeet Kaur, Harm-Anton Klok
Summary: Protein-polymer conjugates combine the stability of polymers with the diversity, specificity, and functionality of biomolecules, resulting in hybrid materials with unique properties for drug delivery applications. Engineering amphiphilicity into these bioconjugate materials can lead to phase separation and assembly of high-order structures, with multiple levels of organization and emergence of new properties at each level influenced by lower levels.
ADVANCED DRUG DELIVERY REVIEWS
(2021)
Review
Chemistry, Multidisciplinary
Hong-Bo Cheng, Shuchun Zhang, Enying Bai, Xiaoqiao Cao, Jiaqi Wang, Ji Qi, Jun Liu, Jing Zhao, Liqun Zhang, Juyoung Yoon
Summary: Diarylethene (DAE) photoswitch, as a smart trigger, has shown superior performance in stimulus-responsive materials. The introduction of DAE into an assembly system has been an attractive strategy, enabling the manifestation of photochromic behavior at the system level, promoting the design and manufacture of advanced materials.
ADVANCED MATERIALS
(2022)
Article
Engineering, Biomedical
Ni-Yuan Zhang, Xing-Jie Hu, Hong-Wei An, Jian-Xiao Liang, Hao Wang
Summary: AIEgens in highly aggregated states exhibit enhanced fluorescence, making them promising modules for highly emissive fluorescence biomaterials. Peptide-AIEgens hybrid biomaterials combine the biocompatibility and biofunction-editing properties of peptides, offering functions such as targeting ability, specificity, and stimuli-responsiveness. The programmable design of peptide-AIEgens enables the construction of intelligent entities with defined biological functions.
Review
Chemistry, Inorganic & Nuclear
Basudev Maity, Mohd Taher, Shyamalava Mazumdar, Takafumi Ueno
Summary: Metalloenzymes play vital roles in biology, and artificial metalloenzymes use synthetic metal cofactors to promote non-natural reactions. Significant progress has been made in manipulating artificial metalloenzymes for various organic transformation reactions, such as C-H activation and C-C coupling. Advanced methods like Directed evolution, high throughput screening, and rational design have driven the research of artificial metalloenzymes. The applications of artificial metalloenzymes have expanded to control cellular functions such as prodrug activation. However, the study of artificial metalloenzymes in more complex processes and reaction environments is relatively limited.
COORDINATION CHEMISTRY REVIEWS
(2022)
Article
Multidisciplinary Sciences
Adam J. Wargacki, Tobias P. Worner, Michiel van de Waterbeemd, Daniel Ellis, Albert J. R. Heck, Neil P. King
Summary: Recent advances in computational methods have enabled the predictive design of self-assembling protein nanomaterials with atomic-level accuracy. Investigation shows that the assembly of these materials is highly cooperative, providing a controllable route for the manufacture of designed protein nanomaterials.
NATURE COMMUNICATIONS
(2021)
Article
Multidisciplinary Sciences
Zander Harteveld, Jaume Bonet, Stephene Rosset, Che Yang, Fabian Sesterhenn, Bruno E. Correia
Summary: De novo protein design is a powerful tool to explore new sequences and structures not found in nature. By using the TopoBuilder method, we were able to design sequences that adopt predicted folds and demonstrated their stability through experimental characterization.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2022)
Article
Chemistry, Multidisciplinary
Ryan C. Oliver, Wojciech Potrzebowski, Seyed Morteza Najibi, Martin Nors Pedersen, Lise Arleth, Najet Mahmoudi, Ingemar Andre
Article
Multidisciplinary Sciences
Benjamin Basanta, Matthew J. Bick, Asim K. Bera, Christoffer Norn, Cameron M. Chow, Lauren P. Carter, Inna Goreshnik, Frank Dimaio, David Baker
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2020)
Article
Multidisciplinary Sciences
Christoffer Norn, Basile I. M. Wicky, David Juergens, Sirui Liu, David Kim, Doug Tischer, Brian Koepnick, Ivan Anishchenko, Foldit Players, David Baker, Sergey Ovchinnikov
Summary: The protein design problem aims to find an appropriate amino acid sequence for a desired protein structure, with optimization over all possible sequences and structures using protein structure prediction and backpropagation. The trRosetta model is more effective than Rosetta single-point energy estimations, and combining trRosetta and Rosetta models can result in more funneled energy landscapes.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2021)
Article
Biochemical Research Methods
Filip Ljung, Ingemar Andre
Summary: The study introduces ZEAL, an interactive tool for superimposing global and local protein structures based on their shape resemblance. ZEAL outperforms other methods for shape-based superposition and is particularly effective for comparing proteins with limited sequence and backbone-fold similarity. The tool can be used to study relationships between shape and protein function, with particularly common global surface shape similarity found among DNA binding proteins.
Article
Biochemistry & Molecular Biology
Diego A. Leonardo, Italo A. Cavini, Fernanda A. Sala, Deborah C. Mendonca, Higor V. D. Rosa, Patricia S. Kumagai, Edson Crusca Jr, Napoleao F. Valadares, Ivo A. Marques, Jose Brandao-Neto, Claudia E. Munte, Hans R. Kalbitzer, Nicolas Soler, Isabel Uson, Ingemar Andre, Ana P. U. Araujo, Humberto D'Muniz Pereira, Richard C. Garratt
Summary: Septins are composed of different paralogues that must be correctly assembled into functional filaments important for essential cellular events. Most septins possess C-terminal domains capable of forming coils, and the study reveals dimeric structures with both parallel and antiparallel arrangements. Both arrangements are energetically accessible, with antiparallel structures presenting a mixed coiled-coil interface.
JOURNAL OF MOLECULAR BIOLOGY
(2021)
Article
Biochemistry & Molecular Biology
Marie Sofie Moller, Sita Vaag Olesen, Ingemar Andre
Summary: This study investigates the stability of ultra-high affinity in the LD-LDI complex, demonstrating that high affinity of LD-LDI requires interactions of several residues at the rim of the protein interface. The mutational analysis reveals that ultra-high binding affinity can be conferred without hotspot residues.
Article
Biochemistry & Molecular Biology
Christoffer Norn, Ingemar Andre, Douglas L. Theobald
Summary: Evolutionary pressures and thermodynamic stability constraints play key roles in shaping the global amino acid substitution patterns observed in proteins, as evidenced by a new hybrid biophysical and evolutionary model. This model accurately recapitulates the complex yet universal patterns seen in common amino acid substitution matrices, suggesting that selection for thermodynamically stable proteins and nucleotide mutation bias filtered by genetic code structure are primary drivers behind these patterns.
Article
Multidisciplinary Sciences
Veronica Lattanzi, Ingemar Andre, Urs Gasser, Marija Dubackic, Ulf Olsson, Sara Linse
Summary: Amyloid fibrils, specifically A beta 42 fibrils, in neurodegenerative diseases like Alzheimer's, are toxic to neuronal cells. Small-angle scattering is used to study the dimension and shape of these fibrils, revealing an elliptical cross-section with a peptide arrangement of two filaments containing four monomers per plane. Additionally, fitting the data with a continuum model provides an atomistic model of the fibril structure.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2021)
Article
Biology
Signe Christensen, Sebastian Raemisch, Ingemar Andre
Summary: Chaperones play a crucial role in cellular quality control by removing misfolded and aggregated proteins. The chaperone DnaK responds to molecular stress by recognizing hydrophobic regions of misfolded proteins. This study found that the level of DnaK response is correlated to protein stability when overexpressing recombinant proteins. Additionally, stable proteins showed variability in protein abundance and DnaK response among cells.
COMMUNICATIONS BIOLOGY
(2022)
Article
Biochemistry & Molecular Biology
Daniel Varela, Vera Karlin, Ingemar Andre
Summary: In this study, a protein-protein docking algorithm called EvoDOCK was developed, which enables accurate and fast local and global protein-protein docking at the atomic level, improving accuracy and computational speed.
Article
Multidisciplinary Sciences
Andy Hsien-Wei Yeh, Christoffer Norn, Yakov Kipnis, Doug Tischer, Samuel J. Pellock, Declan Evans, Pengchen Ma, Gyu Rie Lee, Jason Z. Zhang, Ivan Anishchenko, Brian Coventry, Longxing Cao, Justas Dauparas, Samer Halabiya, Michelle DeWitt, Lauren Carter, K. N. Houk, David Baker
Summary: We have successfully designed an artificial luciferase with high selectivity and catalytic efficiency using a deep-learning-based approach. This achievement is a major milestone in computational enzyme design and has broad applications in biomedical research.
Article
Multidisciplinary Sciences
Isaac D. Lutz, Shunzhi Wang, Christoffer Norn, Alexis Courbet, Andrew J. Borst, Yan Ting Zhao, Annie Dosey, Longxing Cao, Jinwei Xu, Elizabeth M. Leaf, Catherine Treichel, Patrisia Litvicov, Zhe Li, Alexander D. Goodson, Paula Rivera-Sanchez, Ana -Maria Bratovianu, Minkyung Baek, Neil P. King, Hannele Ruohola-Baker, David Baker
Summary: Due to evolutionary selection, naturally occurring protein assemblies have subunits that fit together with substantial shape complementarity to create optimal architectures for function. We present a top-down reinforcement learning-based design approach that utilizes Monte Carlo tree search to sample protein conformers while considering overall architecture and specific functional constraints. Cryo-electron microscopy structures of designed disk-shaped nanopores and ultracompact icosahedra closely resemble computational models. The icosahedra facilitate high-density display of immunogens and signaling molecules, enhancing vaccine response and angiogenesis induction. Our approach allows for top-down design of complex protein nanomaterials with desired properties and exemplifies the power of reinforcement learning in protein design.
Article
Biochemical Research Methods
Christoffer Norn, Ingemar Andre
Summary: Thermodynamic stability plays a crucial role in protein evolution, affecting mutation rates and residue-residue covariation. By simulating protein evolution and calculating protein stability, researchers have found that stability is related to mutation rates and the spectrum of accepted mutations. These findings provide mechanistic insights into the evolutionary consequences of protein stability variation.
PLOS COMPUTATIONAL BIOLOGY
(2023)
Article
Biology
Meliha Mehmeti, Caroline Bergenfelz, Eva Kallberg, Camilla Rydberg Millrud, Per Bjork, Fredrik Ivars, Bengt Johansson-Lindbom, Sven Kjellstrom, Ingemar Andre, Karin Leandersson
COMMUNICATIONS BIOLOGY
(2019)
