@article{Davila-Hernandez2023,

title = {Directing polymorph specific calcium carbonate formation with de novo protein templates},

author = {Fatima A Davila-Hernandez and Biao Jin and Harley Pyles and Shuai Zhang and Zheming Wang and Timothy F Huddy and Asim K Bera and Alex Kang and Chun-Long Chen and James J De Yoreo and David Baker},

url = {https://www.nature.com/articles/s41467-023-43608-1, Nature Communications (Open Access)},

doi = {10.1038/s41467-023-43608-1},

issn = {2041-1723},

year  = {2023},

date = {2023-12-01},

urldate = {2023-12-01},

journal = {Nature Communications},

volume = {14},

number = {1},

pages = {8191},

abstract = {Biomolecules modulate inorganic crystallization to generate hierarchically structured biominerals, but the atomic structure of the organic-inorganic interfaces that regulate mineralization remain largely unknown. We hypothesized that heterogeneous nucleation of calcium carbonate could be achieved by a structured flat molecular template that pre-organizes calcium ions on its surface. To test this hypothesis, we design helical repeat proteins (DHRs) displaying regularly spaced carboxylate arrays on their surfaces and find that both protein monomers and protein-Ca supramolecular assemblies directly nucleate nano-calcite with non-natural {110} or {202} faces while vaterite, which forms first in the absence of the proteins, is bypassed. These protein-stabilized nanocrystals then assemble by oriented attachment into calcite mesocrystals. We find further that nanocrystal size and polymorph can be tuned by varying the length and surface chemistry of the designed protein templates. Thus, bio-mineralization can be programmed using de novo protein design, providing a route to next-generation hybrid materials.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{ALGHADEER2023,

title = {Single-cell census of human tooth development enables generation of human enamel},

author = {Ammar Alghadeer and Sesha Hanson-Drury and Anjali P. Patni and Devon D. Ehnes and Yan Ting Zhao and Zicong Li and Ashish Phal and Thomas Vincent and Yen C. Lim and Diana O’Day and Cailyn H. Spurrell and Aishwarya A. Gogate and Hai Zhang and Arikketh Devi and Yuliang Wang and Lea Starita and Dan Doherty and Ian A. Glass and Jay Shendure and Benjamin S. Freedman and David Baker and Mary C. Regier and Julie Mathieu and Hannele Ruohola-Baker},

url = {https://www.cell.com/developmental-cell/fulltext/S1534-5807(23)00360-X, Developmental Cell

https://www.bakerlab.org/wp-content/uploads/2023/08/PIIS153458072300360X.pdf, PDF},

doi = {https://doi.org/10.1016/j.devcel.2023.07.013},

year  = {2023},

date = {2023-08-14},

urldate = {2023-08-14},

journal = {Developmental Cell},

abstract = {Summary 

Tooth enamel secreted by ameloblasts (AMs) is the hardest material in the human body, acting as a shield to protect the teeth. However, the enamel is gradually damaged or partially lost in over 90% of adults and cannot be regenerated due to a lack of ameloblasts in erupted teeth. Here, we use single-cell combinatorial indexing RNA sequencing (sci-RNA-seq) to establish a spatiotemporal single-cell census for the developing human tooth and identify regulatory mechanisms controlling the differentiation process of human ameloblasts. We identify key signaling pathways involved between the support cells and ameloblasts during fetal development and recapitulate those findings in human ameloblast in vitro differentiation from induced pluripotent stem cells (iPSCs). We furthermore develop a disease model of amelogenesis imperfecta in a three-dimensional (3D) organoid system and show AM maturation to mineralized structure in vivo. These studies pave the way for future regenerative dentistry.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{Pyles2019,

title = {Controlling protein assembly on inorganic crystals through designed protein interfaces},

author = {Harley Pyles and Shuai Zhang and James J. De Yoreo and David Baker },

url = {https://www.nature.com/articles/s41586-019-1361-6

https://www.bakerlab.org/wp-content/uploads/2019/07/2019_Pyles_MicaBinder.pdf},

doi = {10.1038/s41586-019-1361-6},

year  = {2019},

date = {2019-07-10},

journal = {Nature},

abstract = {The ability of proteins and other macromolecules to interact with inorganic surfaces is essential to biological function. The proteins involved in these interactions are highly charged and often rich in carboxylic acid side chains, but the structures of most protein–inorganic interfaces are unknown. We explored the possibility of systematically designing structured protein–mineral interfaces, guided by the example of ice-binding proteins, which present arrays of threonine residues (matched to the ice lattice) that order clathrate waters into an ice-like structure6. Here we design proteins displaying arrays of up to 54 carboxylate residues geometrically matched to the potassium ion (K+) sublattice on muscovite mica (001). At low K+ concentration, individual molecules bind independently to mica in the designed orientations, whereas at high K+ concentration, the designs form two-dimensional liquid-crystal phases, which accentuate the inherent structural bias in the muscovite lattice to produce protein arrays ordered over tens of millimetres. Incorporation of designed protein–protein interactions preserving the match between the proteins and the K+ lattice led to extended self-assembled structures on mica: designed end-to-end interactions produced micrometre-long single-protein-diameter wires and a designed trimeric interface yielded extensive honeycomb arrays. The nearest-neighbour distances in these hexagonal arrays could be set digitally between 7.5 and 15.9 nanometres with 2.1-nanometre selectivity by changing the number of repeat units in the monomer. These results demonstrate that protein–inorganic lattice interactions can be systematically programmed and set the stage for designing protein–inorganic hybrid materials.



},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{223,

title = {The structure, dynamics, and energetics of protein adsorption-lessons learned from adsorption of statherin to hydroxyapatite},

author = { Gil Goobes and Rivka Goobes and Wendy J Shaw and James M Gibson and Joanna R Long and Vinodhkumar Raghunathan and Ora Schueler-Furman and Jennifer M Popham and David Baker and Charles T Campbell and Patrick S Stayton and Gary P Drobny},

issn = {1097-458X},

year  = {2008},

date = {2008-01-01},

journal = {Magnetic resonance in chemistry},

volume = {45},

pages = {S32-S47},

abstract = {Proteins are found to be involved in interaction with solid surfaces in numerous natural events. Acidic proteins that adsorb to crystal faces of a biomineral to control the growth and morphology of hard tissue are only one example. Deducing the mechanisms of surface recognition exercised by proteins has implications to osteogenesis, pathological calcification and other proteins functions at their adsorbed state. Statherin is an enamel pellicle protein that inhibits hydroxyapatite nucleation and growth, lubricates the enamel surface, and is recognized by oral bacteria in periodontal diseases. Here, we highlight some of the insights we obtained recently using both thermodynamic and solid state NMR measurements to the adsorption process of statherin to hydroxyapatite. We combine macroscopic energy characterization with microscopic structural findings to present our views of protein adsorption mechanisms and the structural changes accompanying it and discuss the implications of these studies to understanding the functions of the protein adsorbed to the enamel surfaces. Copyright (c) 2007 John Wiley & Sons, Ltd.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{292,

title = {Folding of the C-terminal bacterial binding domain in statherin upon adsorption onto hydroxyapatite crystals},

author = { Gil Goobes and Rivka Goobes and Ora Schueler-Furman and David Baker and Patrick S Stayton and Gary P Drobny},

issn = {0027-8424},

year  = {2006},

date = {2006-10-01},

journal = {Proceedings of the National Academy of Sciences of the United States of America},

volume = {103},

pages = {16083-8},

abstract = {Statherin is an enamel pellicle protein that inhibits hydroxyapatite (HAP) nucleation and growth, lubricates the enamel surface, and is recognized by oral bacteria in periodontal diseases. We report here from solid-state NMR measurements that the proteintextquoterights C-terminal region folds into an alpha-helix upon adsorption to HAP crystals. This region contains the binding sites for bacterial fimbriae that mediate bacterial cell adhesion to the surface of the tooth. The helical segment is shown through long-range distance measurements to fold back onto the intermediate region (residues Y16-P28) defining the global fold of the protein. Statherin, previously shown to be unstructured in solution, undergoes conformation selection on its substrate mineral surface. This surface-induced folding of statherin can be related to its functionality in inhibiting HAP crystal growth and can explain how oral pathogens selectively recognize HAP-bound statherin.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}