{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,9,3]],"date-time":"2026-09-03T16:21:25Z","timestamp":1788452485908,"version":"build-2803163510"},"reference-count":29,"publisher":"Frontiers Media SA","license":[{"start":{"date-parts":[[2026,4,29]],"date-time":"2026-04-29T00:00:00Z","timestamp":1777420800000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"content-domain":{"domain":["frontiersin.org"],"crossmark-restriction":true},"short-container-title":["Front. Microbiol."],"abstract":"<jats:p>\n                    Some species in the\n                    <jats:italic>Bacillales<\/jats:italic>\n                    and\n                    <jats:italic>Clostridiales<\/jats:italic>\n                    orders form spores under unfavourable environmental conditions. These spores are metabolically dormant and highly resistant to extreme stress. The spore core\u2014analogous to the protoplast of vegetative cells\u2014contains only 25\u201345% water by wet weight, compared to ~80% in vegetative cells. Upon activation by small-molecule nutrients, spores germinate, restoring their core water content, restoring metabolism and becoming easy to kill and then progressing through outgrowth to vegetative growth. GerAB is the B subunit of the prototypical\n                    <jats:italic>Bacillus subtilis<\/jats:italic>\n                    GerA germinant receptor (GR), a membrane protein belonging to the Amino Acid\u2013Polyamine\u2013Organocation (APC) superfamily of transporters. It functions as the L-alanine sensor that initiates germination and was previously predicted, based on molecular dynamics (MD) simulations, to contain a putative water channel. Using MD simulations, we identified low amount of water permeating through GerAB (ranging from 1 to 121 water molecule\/\u03bcs in 10 parallel MD simulations), thus revealing a water pathway in GerAB that diverges from the L-alanine binding pocket, suggesting that water transport may play roles in germination beyond facilitating ligand binding. Analysis of water\u2013residue contact frequencies identified eight hydrophilic residues lining the water\u2019s path. Individual substitution of high-contact residues with similarly sized non-polar residues impaired L-alanine germination and disrupted GerAB structural integrity as assessed by Western Blotting. These mutants also respond to the AGFK germinant mixture (L-asparagine, D-glucose, D-fructose and potassium) in slower, yet individually distinct kinetics compared to that of wild-type (wt) spores. These findings prove that water contact residues in GerAB predicted by MD simulations are crucial for the stability of this protein and thus the germinosome complex with all GRs.\n                  <\/jats:p>","DOI":"10.3389\/fmicb.2026.1800262","type":"journal-article","created":{"date-parts":[[2026,4,29]],"date-time":"2026-04-29T06:07:54Z","timestamp":1777442874000},"update-policy":"https:\/\/doi.org\/10.3389\/crossmark-policy","source":"Crossref","is-referenced-by-count":0,"title":["GerAB residues predicted to interact with water based on MD simulations mediate germinosome stability in Bacillus subtilis spores"],"prefix":"10.3389","volume":"17","author":[{"given":"Longjiao","family":"Chen","sequence":"first","affiliation":[{"name":"Swammerdam Institute for Life Sciences, University of Amsterdam","place":["Amsterdam, Netherlands"]},{"name":"Van\u2019t Hoff Institute for Molecular Sciences, University of Amsterdam","place":["Amsterdam, Netherlands"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Silke","family":"van Buuren","sequence":"additional","affiliation":[{"name":"Swammerdam Institute for Life Sciences, University of Amsterdam","place":["Amsterdam, Netherlands"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"George","family":"Korza","sequence":"additional","affiliation":[{"name":"Department of Molecular Biology and Biophysics, UConn Health","place":["Farmington, CT, United States"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Jocelyne","family":"Vreede","sequence":"additional","affiliation":[{"name":"Van\u2019t Hoff Institute for Molecular Sciences, University of Amsterdam","place":["Amsterdam, Netherlands"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Peter","family":"Setlow","sequence":"additional","affiliation":[{"name":"Department of Molecular Biology and Biophysics, UConn Health","place":["Farmington, CT, United States"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Stanley","family":"Brul","sequence":"additional","affiliation":[{"name":"Swammerdam Institute for Life Sciences, University of Amsterdam","place":["Amsterdam, Netherlands"]}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"1965","published-online":{"date-parts":[[2026,4,29]]},"reference":[{"key":"ref1","doi-asserted-by":"publisher","first-page":"260","DOI":"10.1007\/s00894-023-05670-w","article-title":"Investigation of molecular details of a bacterial cationic amino acid transporter (GkApcT) during arginine transportation using molecular dynamics simulation and umbrella sampling techniques","volume":"29","author":"Afshinpour","year":"2023","journal-title":"J. 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