More Like this

1. An Atomistic Investigation of Adsorption of Bone Morphogenetic Protein-2 on Gold with Nanoscale Topographies

   https://doi.org/10.3390/surfaces5010010  

   Marquetti, Izabele; Desai, Salil (March 2022, Surfaces)

   Nanoscale surface topographies mediated with biochemical cues influence the differentiation of stem cells into different lineages. This research focuses on the adsorption behavior of bone morphogenetic protein (BMP-2) on nanopatterned gold substrates, which can aid in the differentiation of bone and cartilage tissue constructs. The gold substrates were patterned as flat, pillar, linear grating, and linear-grating deep based, and the BMP-2 conformation in end-on configuration was studied over 20 ns. The linear grating deep substrate pattern had the highest adsorption energy of around 125 kJ/mol and maintained its radius of gyration of 18.5 Å, indicating a stable adsorption behavior. Secondary structures including α-helix and β-sheet displayed no denaturation, and thus, the bioavailability of the BMP-2, for the deep linear-grating pattern. Ramachandran plots for the wrist and knuckle epitopes indicated no steric hindrances and provided binding sites to type I and type II receptors. The deep linear-grating substrate had the highest number of contacts (88 atoms) within 5 Å of the gold substrate, indicating its preferred nanoscale pattern choice among the substrates considered. This research provides new insights into the atomistic adsorption of BMP-2 on nanoscale topographies of a gold substrate, with applications in biomedical implants and regenerative medicine. 

   more » « less
2. Orientation effects on the nanoscale adsorption behavior of bone morphogenetic protein-2 on hydrophilic silicon dioxide

   https://doi.org/10.1039/c8ra09165j  

   Marquetti, Izabele; Desai, Salil (January 2019, RSC Advances)

   Bone Morphogenetic Protein-2 (BMP-2) is a growth factor associated with different developmental functions in regenerative medicine and tissue engineering. Because of its favorable properties for the development of bone and cartilage tissue, BMP-2 promotes the biocompatibility of medical implants. In this research, molecular dynamics simulations were implemented to simulate the interaction of BMP-2 with a flat hydrophilic silicon dioxide substrate, an important biomaterial for medical applications. We considered the influence of four orthogonal protein orientations on the adsorption behavior. Results showed that arginine and lysine were the main residues to interact with the silicon dioxide substrate, directly adsorbing onto the surface and overcoming water layers. However, between these charged residues, we observed a preference for arginine to adsorb. Orientations with the α-helix loop closer to the surface at the beginning of the simulations had greater loss of secondary structure as compared to the other configurations. Among all the orientations, the end-on B configuration had favorable adsorption characteristics with a binding energy of 14 000 kJ mol −1 and retention of 21.7% β-sheets as confirmed by the Ramachandran plots. This research provides new insights into the nanoscale interaction of BMP-2 and silicon dioxide substrate with applications in orthopedic implants and regenerative medicine. 

   more » « less
3. SMOC-1 interacts with both BMP and glypican to regulate BMP signaling in C. elegans

   https://doi.org/10.1371/journal.pbio.3002272  

   DeGroot, Melisa S.; Williams, Byron; Chang, Timothy Y.; Maas Gamboa, Maria L.; Larus, Isabel M.; Hong, Garam; Fromme, J. Christopher; Liu, Jun (August 2023, PLOS Biology)

   Mullins, Mary C. (Ed.)

   Secreted modular calcium-binding proteins (SMOCs) are conserved matricellular proteins found in organisms fromCaenorhabditis elegansto humans. SMOC homologs characteristically contain 1 or 2 extracellular calcium-binding (EC) domain(s) and 1 or 2 thyroglobulin type-1 (TY) domain(s). SMOC proteins inDrosophilaandXenopushave been found to interact with cell surface heparan sulfate proteoglycans (HSPGs) to exert both positive and negative influences on the conserved bone morphogenetic protein (BMP) signaling pathway. In this study, we used a combination of biochemical, structural modeling, and molecular genetic approaches to dissect the functions of the sole SMOC protein inC.elegans. We showed that CeSMOC-1 binds to the heparin sulfate proteoglycan GPC3 homolog LON-2/glypican, as well as the mature domain of the BMP2/4 homolog DBL-1. Moreover, CeSMOC-1 can simultaneously bind LON-2/glypican and DBL-1/BMP. The interaction between CeSMOC-1 and LON-2/glypican is mediated specifically by the EC domain of CeSMOC-1, while the full interaction between CeSMOC-1 and DBL-1/BMP requires full-length CeSMOC-1. We provide both in vitro biochemical and in vivo functional evidence demonstrating that CeSMOC-1 functions both negatively in a LON-2/glypican-dependent manner and positively in a DBL-1/BMP-dependent manner to regulate BMP signaling. We further showed that in silico,Drosophilaand vertebrate SMOC proteins can also bind to mature BMP dimers. Our work provides a mechanistic basis for how the evolutionarily conserved SMOC proteins regulate BMP signaling. 

   more » « less
4. The competing influence of surface roughness, hydrophobicity, and electrostatics on protein dynamics on a self-assembled monolayer

   https://doi.org/10.1063/5.0078797  

   Misiura, Anastasiia; Dutta, Chayan; Leung, Wesley; Zepeda O, Jorge; Terlier, Tanguy; Landes, Christy F. (March 2022, The Journal of Chemical Physics)

   Surface morphology, in addition to hydrophobic and electrostatic effects, can alter how proteins interact with solid surfaces. Understanding the heterogeneous dynamics of protein adsorption on surfaces with varying roughness is experimentally challenging. In this work, we use single-molecule fluorescence microscopy to study the adsorption of α-lactalbumin protein on the glass substrate covered with a self-assembled monolayer (SAM) with varying surface concentrations. Two distinct interaction mechanisms are observed: localized adsorption/desorption and continuous-time random walk (CTRW). We investigate the origin of these two populations by simultaneous single-molecule imaging of substrates with both bare glass and SAM-covered regions. SAM-covered areas of substrates are found to promote CTRW, whereas glass surfaces promote localized motion. Contact angle measurements and atomic force microscopy imaging show that increasing SAM concentration results in both increasing hydrophobicity and surface roughness. These properties lead to two opposing effects: increasing hydrophobicity promotes longer protein flights, but increasing surface roughness suppresses protein dynamics resulting in shorter residence times. Our studies suggest that controlling hydrophobicity and roughness, in addition to electrostatics, as independent parameters could provide a means to tune desirable or undesirable protein interactions with surfaces. 

   more » « less
5. Design of Peptides that Fold and Self-Assemble on Graphite

   https://doi.org/10.1021/acs.jcim.2c00419  

   Legleiter, Justin; Thakkar, Ravindra; Velásquez-Silva, Astrid; Miranda-Carvajal, Ingrid; Whitaker, Susan; Tomich, John; Comer, Jeffrey (July 2022, Journal of Chemical Information and Modeling)

   The graphite–water interface provides a unique environment for polypeptides that generally favors ordered structures more than in solution. Therefore, systems consisting of designed peptides and graphitic carbon might serve as a convenient medium for controlled self-assembly of functional materials. Here, we computationally designed cyclic peptides that spontaneously fold into a β-sheet-like conformation at the graphite–water interface and self-assemble, and we subsequently observed evidence of such assembly by atomic force microscopy. Using a novel protocol, we screened nearly 2000 sequences, optimizing for formation of a unique folded conformation while discouraging unfolded or misfolded conformations. A head-to-tail cyclic peptide with the sequence GTGSGTGGPGGGCGTGTGSGPG showed the greatest apparent propensity to fold spontaneously and this optimized sequence was selected for larger scale molecular dynamics simulations, rigorous free-energy calculations, and experimental validation. In simulations ranging from hundreds of nanoseconds to a few microseconds, we observed spontaneous folding of this peptide at the graphite–water interface under many different conditions, including multiple temperatures (295 and 370 K), with different initial orientations relative to the graphite surface, and using different molecular dynamics force fields (CHARMM and Amber). The thermodynamic stability of the folded conformation on graphite over a range of temperatures was verified by replica-exchange simulations and free-energy calculations. On the other hand, in free solution, the folded conformation was found to be unstable, unfolding in tens of picoseconds. Intermolecular hydrogen bonds promoted self-assembly of the folded peptides into linear arrangements where the peptide backbone exhibited a tendency to align along one of the six zigzag directions of the graphite basal plane. For the optimized peptide, atomic force microscopy revealed growth of single-molecule-thick linear patterns of sixfold symmetry, consistent with the simulations, while no such patterns were observed for a control peptide with the same amino acid composition but a scrambled sequence. 

   more » « less