Publications from the Grotjahn Lab

Medina M†, Chang Y†, Rahmani H, Fuentes D, Barad BA§, Grotjahn DA§. Surface Morphometrics reveals local membrane thickness variation in organellar subcompartments . bioRxiv 2025.†Equal contribution §Corresponding author

Chang Y, Barad BA, Hamid J, Rahmani H, Zid BM, Grotjahn DA§. Cytoplasmic ribosomes on mitochondria alter the local membrane environment for protein import. Journal of Cell Biology 2025.§Corresponding author

Chawla R†, Tom JKA†, Boyd T, Tu NH, Bai T Grotjahn DA, Park D, Deniz AA, Racki LR. Reentrant DNA shellts tune polyphosphate condensate size. Nature Communications 2024 †Equal contribution

Dahmane S, Schexnaydre E, Zhang J, Rosendal E, Chotiwan N, Singh BK, Yau W, Lundmark R, Barad BA, Grotjahn DA, Liese S, Carlson A, Overby A, Carlson L. Cryo-electron tomography reveals coupled flavivirus replication, budding and maturation. bioRxiv 2024.

Liang Y, Zhang R, Li Y, Huo M, Ma Z, Singh D, Gao C, Rahmani H, Bandi S, Zhang L, Weinreb R, Malhotra A, Grotjahn DA, Awdishu L, Ideker T, Gilson M, Xie P. Multi-Modal Large Language Model Enables All-Purpose Prediction of Drug Mechanisms and Properties. bioRxiv 2024.

Zhang L, Guo H, Schaffer L, Ko YS, Singh D, Rahmani H, Grotjahn DA, Villa E, Gilson M, Wang W, Ideker T, Xing E , Xie P. ProteinAligner: A Multi-modal Pretraining Framework for Protein Foundation Models. bioRxiv 2024.

Huo M, Guo H, Cheng X, Singh D, Rahmani H, Li Shen, Gerlof P, Ideker T, Grotjahn DA, Villa E, Song L, Xie P. Multi-Modal Large Language Model Enables Protein Function Prediction. bioRxiv 2024.

Baron KR†, Oviedo S† Krasny S, Zaman M, Aldakhlallah R, Mathur P, Pfeffer G, Bollong MJ, Shutt T, Grotjahn DA§ and Wiseman RL§. Pharmacologic activation of integrated stress response kinases inhibits pathologic mitochondrial fragmentation. eLife 2024 †Equal contribution §Corresponding author

Mahalingan KK, Grotjahn DA, Li Y, Lander GC, Zehr EA, and Roll-Mecak A. Structural basis for alpha-tubulin-specific and modification history dependent glutamate chain elongation by tubulin tyrosine ligase-like family enzymes. Nature Chemical Biology 2024

Boneš E, Khan D, Bohak C, Barad BA, Grotjahn DA, Viola I, Theußl T. MidSurfer: A parameter-free approach for mid-surface extraction from segmented volumetric data. arXiv 2024

Newman LE, Tadepalle N, Weiser Novak S, Rojas GR, Tadepalle N, Schiavon CR, Grotjahn DA, Towers CG, Tremblay M, Donnelly MP, Ghosh S, Medina M, Rocha S, Rodriguez-Enriquez R, Chevez JA, Lemersal I, Manor U, Shadel GS. Mitochondrial DNA replication stress triggers a pro-inflammatory endosomal pathway of nucleoid disposal. Nature Cell Biology 2024

Klupt S, Fam KT, Zhang X, Chodisetti PK, Mehmood A, Boyd T, Grotjahn D, Park D, Hang HC. Secreted antigen A peptidoglycan hydrolase is essential for Enterococcus faecium cell separation and priming of immune checkpoint inhibitor cancer therapy. eLife 2024

Aiyer A, Baldwin PR, Tan SM, Shan Z, Oh J, Mehrani A, Bowman ME, Louie ME, Passos DO, Đorđević-Marquardt S, Mietzsch M, Hull JA, Hoshika S, Barad BA, Grotjahn DA, McKenna R, Agbandje-McKenna M, Benner SA, Noel JAP, Wang D, Tan YZ, Lyumkis D.Overcoming resolution attenuation during tilted cryo-EM data collection. Nat Commun 2024

Mageswaran SK†, Grotjahn DA†§, Zeng X, Barad BA, Medina M, Hoang MH, Dobro MJ, Chang YW, Xu M, Yang WY, Jensen, GJ§ . Nanoscale details of mitochondrial constriction revealed by cryo-electron tomography. Biophys J 2023 †Equal contribution §Corresponding authors

Perea V, Cole C, Lebeau J, Dolina V, Baron KR, Madhavan A, Kelly JW, Grotjahn DG, Wiseman RL. PERK signaling promotes mitochondrial elongation by remodeling membrane phosphatidic acid. EMBO J 2023

Barad BA†, Medina M†, Fuentes D, Wiseman, RL, Grotjahn DA§. Quantifying organellar ultrastructure in cryo-electron tomography using a surface morphometrics pipeline. Journal of Cell Biology 2023 †Equal contribution §Corresponding author

Basanta B, Hirschi MM, Grotjahn DA, Lander, GC. A case for glycerol as an acceptable additive for single particle cryoEM samples. Acta Crystallogr D Struct Biol 2022

Gardner A, Ludovic A, Fuentes D, Maritan M, Barad BA, Medina, M, Olson AJ, Grotjahn DA, Goodsell DS. CellPAINT: Turnkey illustration of molecular cell biology. Front. Bioinform 2021

Basanta B, Chowdhury S, Lander GC§, Grotjahn DA§. A guided approach for subtomogram averaging of challenging macromolecular assemblies. JSBx 2020 §Corresponding authors

Grotjahn DA and Lander GC. Setting the dynein motor in motion: New insights from electron tomography. JBC 2019.

Grotjahn DA, Chowdhury S, Xu Y, McKenney RJ, Schroer TA, Lander GC. Cryo-electron tomography reveals that dynactin recruits a team of dyneins for processive motility. NSMB 2018.

Ge X, Grotjahn DA, Welch E, Lyman-Gingerich J, Holguin C, Dimitrova E, Abrams EW, Gupta T, Marlow FL, Yabe T, Adler A, Mullins MC, Pelegri F. PLOS Genetics 2014.