Our Publications

Preprints

• Aleksandrova AA, Sarti E, *Forrest LR, EncoMPASS: an Encyclopedia of Membrane Proteins Analyzed by Structure and Symmetry. https://doi.org/10.1101/391961
• Heinz V, Güler G, Leone V, Madej MG, Maksimov S, Gärtner RM, Rudi O, Hamdi F, Kastritis PL, Mäntele W, Krämer R, Forrest LR, Perez C, Ziegler C. Osmotic stress response in BetP: How lipids and K⁺ team up to overcome downregulation. https://doi.org/10.1101/2022.06.02.493408 

Peer-reviewed articles

Complete list of Lucy's published articles on PubMed 
or on ORCID: orcid.org/0000-0003-1855-7985

2022

• Leone V, Bradshaw RT, Koshy C, Lee PS, Fenollar-Ferrer C, Heinz V, Ziegler C, *Forrest LR. Autoregulation of a trimeric transporter involves the cytoplasmic domains of both adjacent subunits. Biophys J 122(3):577-594
• Staritzbichler R, Yaklich E, Sarti E, Ristic N, Hildebrand PW, *Forrest LR. AlignMe: an update of the web server for alignment of membrane protein sequences. Nucl Acids Res 50(W1):W29-W35
• Lee PS, Bradshaw RT, Marinelli F, Kihn K, Smith A, Wintrode PL, Deredge DJ, Faraldo-Goméz JD, *Forrest LR. Interpreting hydrogen-deuterium exchange experiments with molecular simulations: Tutorials and applications of the HDXer ensemble reweighting software. Living Journal of Computational Molecular Science 3(1):1521

2021

• Kihn KC, Wilson T, Smith AK, Bradshaw RT, Wintrode PL, Forrest LR, Wilks A, Deredge DJ. Modeling the native ensemble of PhuS using enhanced sampling MD and HDX-ensemble reweighting. Biophys J 10.1016/j.bpj.2021.11.010
• Staritzbichler R, Sarti E, Yaklich E, Aleksandrova A, Stamm M, Khafizov K, *Forrest LR. Refining pairwise sequence alignments of membrane proteins by the incorporation of anchors. PLoS One 16(4):e0239881.
• Zhang YW, Uchendu S, Leone V, Bradshaw RT, Sangwa N, Forrest LR, Rudnick G. Chloride-dependent conformational changes in the GlyT1 glycine transporter. Proc Natl Acad Sci USA 118:e2017431118
• Zhou W, Trinco G, Slotboom DJ, *Forrest LR, Faraldo-Gómez JD. On the role of a conserved methionine in the Na+-coupling mechanism of a neurotransmitter transporter homolog. Neurochem Res 1–13

2020

• Bradshaw RT, Marinelli F, *Faraldo-Gómez JD, *Forrest LR. Structural interpretation of hydrogen-deuterium exchange with maximum-entropy simulation reweighting. Biophys J 118(7):1649-1664
• Huffer KE, Aleksandrova AA, Jara-Oseguera A, Forrest LR, Swartz KJ. Global alignment and assessment of TRP channel transmembrane domain structures to explore functional mechanisms. eLife 9:e58660
• Aleksandrova AA, Sarti E, *Forrest LR. MemSTATS: A Benchmark Set of Membrane Protein Symmetries and Pseudo-Symmetries. J Mol Biol 432(2):597-604

2019

• Zhou W, Fiorin G, Anselmi C, Karimi-Varzaneh HA, Poblete H, *Forrest LR, Faraldo-Gómez JD. Large-scale state-dependent membrane remodeling by a transporter protein. eLife 8:e50576 (2019)
• Fung TC, Vuong HE, Luna CDG, Pronovost GN, Aleksandrova AA, Riley NG, Vavilina A, McGinn J, Rendon T, Forrest LR, Hsiao EY. Intestinal serotonin and fluoxetine exposure modulate bacterial colonization in the gut. Nature Microbiol 4(12):2064-2073 (2019)
• Liao Y-C, Fernandopulle M, Wang G, Choi H, Hao L, Drerup CM, Qamar S, Nixon-Abel J, Shen Y, Meadows W, Vendruscolo M, Knowles T, Nelson M, Czekalska M, Musteikyte G, Gachechiladze M, Patel R, Stephens C, Pasolli A, Forrest LR, St George-Hyslop P, Lippincott-Schwartz J, Ward ME. RNA granules hitchhike on lysosomes for long-distance transport, using annexin A11 as a molecular tether. Cell 178(7):147-164 (2019)
• Hellsberg E, Ecker GF, Stary-Weinzinger A, *Forrest LR. A structural model of the human serotonin transporter in an outward-occluded state. PLoS One 14(6):e0217377 (2019)
• Leone V, Waclawska I, Koshy C, Kossman K, Sharma M, Prisner TF, Ziegler C, Endeward B, *Forrest LR. Interpretation of spectroscopic data using molecular simulations for the secondary active transporter BetP. J Gen Physiol 151: 381-394 (2019)
• Sarti E, Aleksandrova AA, Ganta SK, Yavatkar AS, Forrest LR. EncoMPASS: an online database for analyzing structure and symmetry in membrane proteins. Nucl Acids Res 47: D315–D321 (2019)
• Fenollar-Ferrer C, Forrest LR. Structural models of the NaPi-II sodium-phosphate transporters. Pflügers Arch 471:43-51 (2019)

2018

• Zhang Y-W, Tavoulari S, Sinning S, Aleksandrova AA, Forrest LR, Rudnick G. Structural elements required for coupling ion and substrate transport in the neurotransmitter transporter homolog LeuT. Proc Natl Acad Sci 115:E8854-E8862 (2018)
• Yaffe D, Forrest LR, Schuldiner S. The ins and outs of vesicular monoamine transporters. J Gen Physiol 150:671-682 (2018)
• Giovanola M, Vollero A, Cinquetti R, Bossi E, Forrest LR, Di Cairano ES, Castagna M. Threonine 67 is a key component in the coupling of the NSS amino acid transporter KAAT1. Biochim Biophys Acta 1860:1179-1186 (2018)

2017

• Ficici E, Faraldo-Gómez JD, Jennings ML, *Forrest LR. Asymmetry of inverted-topology repeats in the AE1 anion exchanger suggests an elevator-like mechanism. J Gen Physiol 419:1149-1164 (2017)
• Dayan O, Nagarajan A, Shah R, Ben-Yona A, *Forrest LR, Kanner BI. An extra amino acid residue in transmembrane domain 10 of the GABA transporter GAT-1 is required for efficient ion-coupled transport. J Biol Chem 292:5418-5428 (2017)
• Adhikary S, Deredge D, Nagarajan N, Forrest LR, Wintrode P, Singh SK. Conformational dynamics of a neurotransmitter sodium symporter in a lipid bilayer. Proc Natl Acad Sci 114:E1786–E1795 (2017)

2016

• Yaffe D, Vergara-Jaque A, Forrest LR, Schuldiner S. Emulating proton induced conformational changes in vesicular monoamine transporter VMAT2 by mutagenesis. Proc Natl Acad Sci 113:E7390-E7398 (2016)
• Davis BA, Nagarajan A, Forrest LR, Singh SK. Mechanism of paroxetine inhibition of the serotonin transporter. Scientific Reports 6: 23789 (2016)
• Patti M, Fenollar-Ferrer C, Werner A, Forrest LR, Forster IC. Cation interactions and membrane potential induce conformational changes in NaPi-IIb. Biophys J 111: 973-988 (2016)
• Mulligan C, Fenollar-Ferrer C, Fitzgerald GA, Vergara-Jaque A, Li Y, *Forrest LR, Mindell J. The bacterial dicarboxylate transporter, VcINDY, has a two-domain elevator-type mechanism. Nat Struct Mol Biol, 23: 256-263 (2016)

2015

• Tavoulari S, Margheritis E, Nagarajan A, Dewitt DC, Zhang Y-W, Rosado E, Ravera S, Rhoades E, Forrest LR, Rudnick G. Two sites control conformational change in a neurotransmitter transporter homolog. J Biol Chem, 291: 1456-1471 (2015)
• Silverstein N, Ewers D, Forrest LR, Fahlke C, Kanner B. Molecular determinants of substrate specificity in sodium-coupled glutamate transporters. J Biol Chem, 290: 28988-28996 (2015)
• Vergara-Jaque A, Fenollar-Ferrer C, Mulligan C, Mindell JA, *Forrest LR. Family resemblances: A common fold for some dimeric ion-coupled secondary transporters. J Gen Physiol 146:423-434 (2015)
• *Forrest LR. Structural symmetry in membrane proteins. Annual Reviews Biophys 44:311-337 (2015)
• Vergara-Jaque A, Fenollar-Ferrer C, Kaufmann D, *Forrest LR. Repeat-swap homology modeling of secondary active transporters: updated protocol and prediction of elevator-type mechanisms. Frontiers in Pharmacology - Neuropharmacology 6:183 (2015)
• Stamm M, *Forrest LR. Structure alignment of membrane proteins: Comparison of available tools and a consensus strategy. Proteins 83:1720-1723 (2015)
• Schweikhard ES, Burckhardt BC, Joos F, Fenollar-Ferrer C, Forrest LR, Kempson SA, Ziegler C. Role of N-glycosylation in renal betaine transport. Biochemical J 470:169-179 (2015)
• Fenollar-Ferrer C, Forster IC, Patti M, Knoepfel T, Werner A, *Forrest LR. Functional identification of the first sodium binding site of the phosphate cotransporter NaPi-IIa (SLC34A1). Biophys J 108:2465-2480 (2015)
• Fowler PW, Orwick-Rydmark M, Radestock S, Solcan N, Dijkman PM, Lyons JA, Kwok J, Caffrey M, Watts A, *Forrest LR, Newstead S. Gating topology of the proton-coupled oligopeptide symporters. Structure 23:290-301 (2015)

2014

• Yaffe D, Vergara-Jaque A, Shuster Y, Listov D, Meena S, Singh SK, *Forrest LR, Schuldiner S. Functionally important carboxyls in a bacterial homologue of the vesicular monoamine transporter (VMAT). J Biol Chem 389:34229-34240 (2014)
• Fenollar-Ferrer C, Stockner T, Schwarz TC, Pal A, Gotovina J, Hofmaier T, Jayaraman K, Adhikary S, Mehdipour AR, Oliver K, Rudnick G, Tavoulari S, Singh SK, Konrat R, Sitte HH, *Forrest LR. Structure and regulatory interactions of the cytoplasmic terminal domains of serotonin transporter. Biochemistry 53:5444-5460  (2014)
• Perez C, Faust B, Mehdipour AR, Francesconi KA, *Forrest LR, Ziegler C. Substrate-bound outward-open state of the betaine transporter BetP provides insights into Na(+) coupling. Nat Commun 5:4231 (2014)
• Fenollar-Ferrer C, Patti M, Knoepfel T, Werner A, Forster IC, *Forrest LR. Structural fold and binding sites of the human Na⁺-phosphate cotransporter NaPi-II. Biophys J 106:1268-1279 (2014)
• Stamm M, Staritzbichler R, Khafizov K, *Forrest LR. AlignMe - A membrane protein sequence alignment web server. Nucleic Acids Res 42(Web Server issue):W246-51 (2014)
• Yaffe D, Radestock S, Shuster Y, *Forrest LR, Schuldiner S. Identification of molecular hinge points mediating alternating access in the vesicular monoamine transporter VMAT2. Proc Natl Acad Sci  110: E1332-41 (2014)

2013

• Stamm M, Staritzbichler R, Khafizov K, *Forrest LR. Alignment of helical membrane protein sequences using AlignMe. PLoS ONE 8(3):e57731 (2013)
• Forrest LR, (Pseudo-)Symmetrical Transport. Science 339:399-401 (2013)
• Silverstein N, Crisman TJ, *Forrest LR, Kanner BI. Cysteine scanning mutagenesis of transmembrane helix 3 of a brain glutamate transporter reveals two conformationally sensitive positions. J Biol Chem 288:964-73 (2013)

2012

• Khafizov K, Perez C, Koshy C, Quick M, Fendler K, Ziegler C, *Forrest LR. Investigation of the sodium binding sites in the betaine transporter BetP. Proc Natl Acad Sci  109:E3035-44 (2012)
• Gradogna A, Fenollar-Ferrer C, *Forrest LR, Pusch M. Dissecting a regulatory calcium-binding site of CLC-K kidney chloride channels. J Gen Physiol 140:681-96 (2012)
• Schushan M, Rimon A, Haliloglu T, Forrest LR, Padan E, Ben-Tal N. A model-structure of a periplasm-facing state of the NhaA antiporter suggests the molecular underpinnings of pH-induced conformational changes. J Biol Chem 287:18249-61 (2012)

2011

• Perez C, Khafizov K, Kraemer R, *Forrest LR, Ziegler C. Role of trimerization in the osmoregulated betaine transporter BetP. EMBO Rep 12:804-10 (2011)
• Radestock S, *Forrest LR. The alternating-access mechanism of MFS transporters arises from inverted-topology repeats. J Mol Biol 407:698-715 (2011)
• Staritzbichler R, Anselmi C, *Forrest LR, Faraldo-Gomez JD. GRIFFIN: A versatile methodology for optimization of protein-lipid interfaces for membrane protein simulations. J Chem Theor Comput 7:1167-1176 (2011), doi: 10.1021/ct100576m
• Tsai C-J, Khafizov K, Hakulinen J, *Forrest LR, Kraemer R, Kuehlbrandt W, and Ziegler C. Structural asymmetry in the betaine transporter BetP trimer indicates three different conformational states. J Mol Biol 407:368-381 (2011) 
• Tavoulari S, Rizwan AN, *Forrest LR, Rudnick G. Reconstructing a chloride binding site in a bacterial neurotransmitter transporter homologue Biol Chem 286:2834-2842 (2011)
• Faraldo-Gomez JD, *Forrest LR. Modeling and simulation of ion- and ATP-driven membrane proteins.Curr Opin Struct Biol   21:1-7 (2011)
• Forrest LR, Kraemer R, Ziegler C. The structural basis of secondary active transport mechanisms. Biochim Biophys Acta 1807:167-188 (2011)

2010

• Khafizov K, Staritzbichler R, Stamm M, *Forrest LR. A study of the evolution of inverted-topology repeats from LeuT-fold transporters using AlignMe.  Biochemistry 49:10702-10713 (2010)

2009

• Crisman TJ, Qu S, Kanner BI, & *Forrest LR. Inward-facing conformation of glutamate transporters as revealed by their inverted-topology structural repeats. Proc Natl Acad Sci 106: 20752-20757 (2009)
• Tavoulari, S, *Forrest LR,Rudnick G. Fluoxetine (prozac) binding to serotonin transporter is modulated by chloride and conformational changes. J Neurosci 29:9635-9643 (2009)
• Forrest LR, Rudnick G. The rocking bundle: A mechanism for ion-coupled solute flux by symmetrical transporters. Physiology 24:377-386 (2009)

2008

• Forrest LR, Zhang YW, Jacobs MT, Gesmonde J, Xie L, Honig B, Rudnick G. A mechanism for alternating access in neurotransmitter transporters.  Proc Natl Acad Sci USA 105:10338-10343 (2008)
• Troetschel C, Follmann M, Nettekoven JA, Mohrbach T, Forrest LR, Burkovski A, Marin K, Kraemer, R. Methionine uptake in Corynebacterium glutamicum by MetQNI and by MetPS, a novel methionine and alanine importer of the NSS neurotransmitter transporter family. Biochemistry 47:12698-12709 (2008)
• Hildebrand PW, Guenther S, Goede A, Forrest LR, Froemmel C, Preissner R. Hydrogen-bonding and packing features of membrane proteins: functional implications. Biophys J 94:1945-1953 (2008)

2007

• Forrest LR, Tavoulari S, Zhang Y-W, Rudnick G, Honig B. Identification of a chloride ion binding site in Na⁺/Cl^--dependent transporters.Proc Natl Acad Sci 104:12761-12766 (2007)
• Soto CS, Fasnacht M, Zhu J, Forrest LR, Honig B. Loop modeling: sampling, filtering, and scoring. Proteins 70:834-843 (2007)

2006

• Forrest LR, Tang CL, Honig B. On the accuracy of homology modeling and sequence alignment methods applied to membrane proteins. Biophysical Journal 91:508-517 (2006)
• Punta M, Forrest LR, Bigelow H, Kernytsky A, Liu J, Rost B. Membrane protein prediction methods. Methods 41:460-474 (2006)

2005

• Forrest LR, Honig B. An assessment of the accuracy of methods for predicting hydrogen positions in protein structures. Proteins 61:296-309 (2005)

2004

• Gimpelev M, Forrest LR, Murray D, Honig B. Helix packing patterns in membrane and soluble proteins. Biophysical Journal 87:4075-4086 (2004)
• Faraldo-Gomez JD, Forrest LR, Baaden M, Bond PJ, Domene C, Patargias G, Cuthbertson J, Sansom MSP. Conformational sampling and dynamics of membrane proteins from 10-nanosecond computer simulations. Proteins 57:783-791 (2004)

2003

• Crozier PS, Stevens MJ, Forrest LR, Woolf TB. Molecular dynamics simulation of dark-adapted rhodopsin in an explicit membrane bilayer: Coupling between local retinal and larger scale conformational change. J Mol Biol 333:493-514 (2003)
• Forrest LR, Woolf TB. Discrimination of native loop conformations in membrane proteins: Decoy library design and evaluation of effective energy scoring functions. Proteins 52:492-509 (2003)

2000

• Forrest LR, Kukol A, Arkin IT, Tieleman DP, Sansom MSP. Exploring models of the influenza A M2 channel: MD simulations in a phospholipid bilayer. Biophysical Journal 78:79-92 (2000)
• Schnick C, Forrest LR, Groth G, Sansom MSP. Molecular contacts in the transmembrane c-subunit oligomer of F-ATPases identified by tryptophan substitution mutagenesis. Biochimica & Biophysica Acta 1459:49-60 (2000)
• Law RJ, Forrest LR, Ranatunga KM, La Rocca P, Tieleman DP, Sansom MSP. Structure and dynamics of the pore-lining helix of the nicotinic receptor: MD simulations in water, lipid bilayers and transbilayer bundles. Proteins. 39:47-55 (2000)
• Capener CE, Shrivastava IH, Ranatunga KM, Forrest LR, Smith GR, Sansom MSP. Homology modelling and molecular dynamics simulation studies of an inward rectifier potassium channel. Biophysical Journal 78:2929-2942 (2000)
• Shrivastava IH, Capener CE, Forrest LR, Sansom MSP. Structure and dynamics of K channel pore-lining helices: A comparative simulation study. Biophysical Journal 78:55-69 (2000)
• Cordes F, Kukol A, Forrest LR, Arkin IT, Sansom MSP, Fischer WB. The structure of the HIV-1 Vpu ion channel: Modelling and simulation studies.  Biochimica et Biophysica Acta 1512:291-298 (2000)
• Forrest LR, Sansom MSP. Membrane simulations: Bigger and better? Current Opinions in Structural Biology 10:174-181 (2000)
• Fischer WB, Pitkeathly M, Wallace BA, Forrest LR, Smith GR, Sansom MSP. Transmembrane peptide NB of influenza B: a simulation, structure, and conductance study. Biochemistry 39:12708-16 (2000)

1999

• Fischer WB, Forrest LR, Smith GR, Sansom MSP. Transmembrane domains of viral ion channel proteins: A molecular dynamics simulation study. Biopolymers 53:529-538 (1999)
• Randa HS, Forrest LR, Voth GA, Sansom MSP. Molecular dynamics of synthetic leucine-serine ion channels in a phospholipid membrane.  Biophysical Journal 77:2400-2410 (1999)
• Forrest LR, Tieleman DP, Sansom MSP. Defining the transmembrane helix of M2 protein from influenza A by molecular dynamics simulations in a lipid bilayer. Biophysical Journal 76:1886-1896 (1999)

1998

• Tieleman DP, Forrest LR, Berendsen HJC, Sansom MSP. Lipid properties and the orientation of aromatic residues in OmpF, influenza M2 and alamethicin systems: Molecular dynamics simulations. Biochemistry 37:17544-17561 (1998)
• Forrest LR, DeGrado WF, Dieckmann GR, Sansom MSP. Two models of the influenza A M2 channel domain: Verification by comparison. Folding & Design 3:443-448 (1998)
• Sansom MSP, Forrest LR, Bull R. Viral ion channels: Molecular modeling and simulation. Bioessays 20:992-1000 (1998)

(*corresponding authorship)