Publications

Publications by Himanshu Khandelia and collaborators

The list below is generated automatically from PubMed whenever this website is built. This removes the need to maintain a separate publication list by hand.

PubMed · ORCID 0000-0001-9913-6394 · SDU Research Portal

Publication list

2026

• On the mechanism of K+ transport through the inter-subunit tunnel of KdpFABC.
  Valia Madapally H, Hussein A, Eriksen MW, Pedersen BP, Stokes DL, Khandelia H. The Journal of general physiology. · DOI
• Corrigendum to “Interaction of N-terminal peptide analogues of the Na+,K+-ATPase with membranes” [BBA Biomembr. 1860 (6) (2018) 1282-1291].
  Nguyen K, Garcia A, Sani MA, Dubey V, Clayton D, Poggetto GD, Cornelius F, Payne RJ, Separovic F, Khandelia H, Clarke RJ. Biochimica et biophysica acta. Biomembranes. · DOI

2025

• A novel model for proton transport mediated by uncoupling protein 1.
  Jacobsen L, Menon S, Gaudry MJ, Hakami Zanjani AA, Reinholdt P, Jastroch M, Khandelia H. Protein science : a publication of the Protein Society. · DOI
• A unique gating mechanism revealed by the cryo-EM structure of monomeric ATP9A flippase.
  Abe K, Marimuthu P, Qian Y, Gopalasingam CC, Gerle C, Shigematsu H, Tanaka K, Khandelia H. The Journal of biological chemistry. · DOI
• Molecular insights into the modulation of the 5HT2A receptor by serotonin, psilocin, and the G protein subunit Gqα.
  Viohl N, Hakami Zanjani AA, Khandelia H. FEBS letters. · DOI

2024

• Molecular Structure of the Na+,K+-ATPase α4β1 Isoform in Its Ouabain-Bound Conformation.
  Abe K, McDermott J, Valia Madapally H, Marimuthu P, Gopalasingam CC, Gerle C, Shigematsu H, Khandelia H, Blanco G. International journal of molecular sciences. · DOI
• Modulation of Annexin-Induced Membrane Curvature by Cholesterol and the Anionic Lipid Headgroup during Plasma Membrane Repair.
  Hakami Zanjani AA, Ebstrup ML, Nylandsted J, Khandelia H. The journal of physical chemistry. B. · DOI
• Phospholamban inhibits the cardiac calcium pump by interrupting an allosteric activation pathway.
  Cleary SR, Seflova J, Cho EE, Bisht K, Khandelia H, Espinoza-Fonseca LM, Robia SL. The Journal of biological chemistry. · DOI
• Bending of a lipid membrane edge by annexin A5 trimers.
  Pandey MP, Telles de Souza PC, Pezeshkian W, Khandelia H. Biophysical journal. · DOI
• Sensing membrane voltage by reorientation of dipolar transmembrane peptides.
  Bisht K, Lomholt MA, Khandelia H. Biophysical journal. · DOI
• Specific protonation of acidic residues confers K+ selectivity to the gastric proton pump.
  Madapally HV, Abe K, Dubey V, Khandelia H. The Journal of biological chemistry. · DOI

2023

• Drastic differences between the release kinetics of two highly related porphyrins in liposomal membranes: mTHPP and pTHPP.
  Kuntsche J, Rajakulendran K, Sabriye HMT, Tawakal N, Khandelia H, Hakami Zanjani AA. Journal of colloid and interface science. · DOI
• ATP-Bound State of the Uncoupling Protein 1 (UCP1) from Molecular Simulations.
  Jacobsen L, Lydersen L, Khandelia H. The journal of physical chemistry. B. · DOI
• Engineering a membrane-binding protein to trimerize and induce high membrane curvature.
  Hakami Zanjani AA, Mularski A, Busk Heitmann AS, Dias C, Møller ME, Maeda K, Nylandsted J, Simonsen AC, Khandelia H. Biophysical journal. · DOI
• The molecular basis of the antidepressant action of the magic mushroom extract, psilocin.
  Hakami Zanjani AA, Nguyen TQT, Jacobsen L, Khandelia H. Biochimica et biophysica acta. Proteins and proteomics. · DOI
• Interaction of psychedelic tryptamine derivatives with a lipid bilayer.
  Zohairi F, Khandelia H, Hakami Zanjani AA. Chemistry and physics of lipids. · DOI

2022

• Interplay of membrane crosslinking and curvature induction by annexins.
  Mularski A, Sønder SL, Heitmann ASB, Pandey MP, Khandelia H, Nylandsted J, Simonsen AC. Scientific reports. · DOI
• Molecular Mechanism of Hydrotropic Properties of GTP and ATP.
  Pandey MP, Sasidharan S, Raghunathan VA, Khandelia H. The journal of physical chemistry. B. · DOI
• Magic mushroom extracts in lipid membranes.
  Nguyen TQT, Lund FW, Zanjani AAH, Khandelia H. Biochimica et biophysica acta. Biomembranes. · DOI
• Structural Basis for Binding of Potassium-Competitive Acid Blockers to the Gastric Proton Pump.
  Tanaka S, Morita M, Yamagishi T, Madapally HV, Hayashida K, Khandelia H, Gerle C, Shigematsu H, Oshima A, Abe K. Journal of medicinal chemistry. · DOI

2021

• Phenothiazines alter plasma membrane properties and sensitize cancer cells to injury by inhibiting annexin-mediated repair.
  Heitmann ASB, Zanjani AAH, Klenow MB, Mularski A, Sønder SL, Lund FW, Boye TL, Dias C, Bendix PM, Simonsen AC, Khandelia H, Nylandsted J. The Journal of biological chemistry. · DOI
• An Intracellular Pathway Controlled by the N-terminus of the Pump Subunit Inhibits the Bacterial KdpFABC Ion Pump in High K+ Conditions.
  Dubey V, Stokes DL, Pedersen BP, Khandelia H. Journal of molecular biology. · DOI
• Long chain sphingomyelin depletes cholesterol from the cytoplasmic leaflet in asymmetric lipid membranes.
  Karlsen ML, Bruhn DS, Pezeshkian W, Khandelia H. RSC advances. · DOI
• EnCurv: Simple Technique of Maintaining Global Membrane Curvature in Molecular Dynamics Simulations.
  Yesylevskyy S, Khandelia H. Journal of chemical theory and computation. · DOI
• Annexin A4 trimers are recruited by high membrane curvatures in giant plasma membrane vesicles.
  Florentsen CD, Kamp-Sonne A, Moreno-Pescador G, Pezeshkian W, Hakami Zanjani AA, Khandelia H, Nylandsted J, Bendix PM. Soft matter. · DOI
• Clearance of activity-evoked K+ transients and associated glia cell swelling occur independently of AQP4: A study with an isoform-selective AQP4 inhibitor.
  Toft-Bertelsen TL, Larsen BR, Christensen SK, Khandelia H, Waagepetersen HS, MacAulay N. Glia. · DOI

2020

• Shuffled lipidation pattern and degree of lipidation determines the membrane interaction behavior of a linear cationic membrane-active peptide.
  Hedegaard SF, Bruhn DS, Khandelia H, Cárdenas M, Nielsen HM. Journal of colloid and interface science. · DOI
• Cholesterol binding to the sterol-sensing region of Niemann Pick C1 protein confines dynamics of its N-terminal domain.
  Dubey V, Bozorg B, Wüstner D, Khandelia H. PLoS computational biology. · DOI
• Serine phosphorylation regulates the P-type potassium pump KdpFABC.
  Sweet ME, Zhang X, Erdjument-Bromage H, Dubey V, Khandelia H, Neubert TA, Pedersen BP, Stokes DL. eLife. · DOI
• Interdisciplinary Synergy to Reveal Mechanisms of Annexin-Mediated Plasma Membrane Shaping and Repair.
  Bendix PM, Simonsen AC, Florentsen CD, Häger SC, Mularski A, Zanjani AAH, Moreno-Pescador G, Klenow MB, Sønder SL, Danielsen HM, Arastoo MR, Heitmann AS, Pandey MP, Lund FW, Dias C, Khandelia H, Nylandsted J. Cells. · DOI
• Thermodynamic Investigation of the Mechanism of Heat Production During Membrane Depolarization.
  Bozorg B, Lomholt MA, Khandelia H. The journal of physical chemistry. B. · DOI

2019

• Interaction of the mononucleotide UMP with a fluid phospholipid bilayer.
  Sasidharan S, Pochinda S, Elgaard-Jørgensen PN, Rajamani S, Khandelia H, Raghunathan VA. Soft matter. · DOI
• A single K+-binding site in the crystal structure of the gastric proton pump.
  Yamamoto K, Dubey V, Irie K, Nakanishi H, Khandelia H, Fujiyoshi Y, Abe K. eLife. · DOI
• Evidence for ATP Interaction with Phosphatidylcholine Bilayers.
  Garcia A, Pochinda S, Elgaard-Jørgensen PN, Khandelia H, Clarke RJ. Langmuir : the ACS journal of surfaces and colloids. · DOI
• On identifying collective displacements in apo-proteins that reveal eventual binding pathways.
  Dube D, Ahalawat N, Khandelia H, Mondal J, Sengupta S. PLoS computational biology. · DOI

2018

• K+ binding and proton redistribution in the E2P state of the H+, K+-ATPase.
  Dubey V, Han M, Kopec W, Solov’yov IA, Abe K, Khandelia H. Scientific reports. · DOI
• Different footprints of the Zika and dengue surface proteins on viral membranes.
  Wewer CR, Khandelia H. Soft matter. · DOI
• Faster Simulations with a 5 fs Time Step for Lipids in the CHARMM Force Field.
  Olesen K, Awasthi N, Bruhn DS, Pezeshkian W, Khandelia H. Journal of chemical theory and computation. · DOI
• Lipid Configurations from Molecular Dynamics Simulations.
  Pezeshkian W, Khandelia H, Marsh D. Biophysical journal. · DOI
• Interaction of N-terminal peptide analogues of the Na+,K+-ATPase with membranes.
  Nguyen K, Garcia A, Sani MA, Diaz D, Dubey V, Clayton D, Dal Poggetto G, Cornelius F, Payne RJ, Separovic F, Khandelia H, Clarke RJ. Biochimica et biophysica acta. Biomembranes. · DOI
• Structural design of intrinsically fluorescent oxysterols.
  Nåbo LJ, Modzel M, Krishnan K, Covey DF, Fujiwara H, Ory DS, Szomek M, Khandelia H, Wüstner D, Kongsted J. Chemistry and physics of lipids. · DOI
• Lipid Configurations from Molecular Dynamics Simulations.
  Pezeshkian W, Khandelia H, Marsh D. Biophysical journal. · DOI
• Correction to: The CAPOS mutation in ATP1A3 alters Na/K-ATPase function and results in auditory neuropathy which has implications for management.
  Tranebjærg L, Strenzke N, Lindholm S, Rendtorff ND, Poulsen H, Khandelia H, Kopec W, Lyngbye TJB, et al.. Human genetics. · DOI
• The role of caveolin-1 in lipid droplets and their biogenesis.
  Pezeshkian W, Chevrot G, Khandelia H. Chemistry and physics of lipids. · DOI
• The CAPOS mutation in ATP1A3 alters Na/K-ATPase function and results in auditory neuropathy which has implications for management.
  Tranebjærg L, Strenzke N, Lindholm S, Rendtorff ND, Poulsen H, Khandelia H, Kopec W, Lyngbye TJB, et al.. Human genetics. · DOI

2017

• Membrane Tubulation in Lipid Vesicles Triggered by the Local Application of Calcium Ions.
  Ali Doosti B, Pezeshkian W, Bruhn DS, Ipsen JH, Khandelia H, Jeffries GDM, Lobovkina T. Langmuir : the ACS journal of surfaces and colloids. · DOI
• A novel role for methyl cysteinate, a cysteine derivative, in cesium accumulation in Arabidopsis thaliana.
  Adams E, Miyazaki T, Hayaishi-Satoh A, Han M, Kusano M, Khandelia H, Saito K, Shin R. Scientific reports. · DOI
• Electrostatic Stabilization Plays a Central Role in Autoinhibitory Regulation of the Na+,K+-ATPase.
  Jiang Q, Garcia A, Han M, Cornelius F, Apell HJ, Khandelia H, Clarke RJ. Biophysical journal. · DOI
• Glutamate Water Gates in the Ion Binding Pocket of Na+ Bound Na+, K+-ATPase.
  Han M, Kopec W, Solov’yov IA, Khandelia H. Scientific reports. · DOI

2016

• Quantifying the Relationship between Curvature and Electric Potential in Lipid Bilayers.
  Bruhn DS, Lomholt MA, Khandelia H. The journal of physical chemistry. B. · DOI
• Tuning of the Na,K-ATPase by the beta subunit.
  Hilbers F, Kopec W, Isaksen TJ, Holm TH, Lykke-Hartmann K, Nissen P, Khandelia H, Poulsen H. Scientific reports. · DOI
• Perillyl alcohol: Dynamic interactions with the lipid bilayer and implications for long-term inhalational chemotherapy for gliomas.
  da Fonseca CO, Khandelia H, Salazar MD, Schönthal AH, Meireles OC, Quirico-Santos T. Surgical neurology international. · DOI

2015

• Membrane accessibility of glutathione.
  Garcia A, Eljack ND, Sani MA, Separovic F, Rasmussen HH, Kopec W, Khandelia H, Cornelius F, Clarke RJ. Biochimica et biophysica acta. · DOI
• Design of new fluorescent cholesterol and ergosterol analogs: Insights from theory.
  Nåbo LJ, List NH, Witzke S, Wüstner D, Khandelia H, Kongsted J. Biochimica et biophysica acta. · DOI
• The N Terminus of Sarcolipin Plays an Important Role in Uncoupling Sarco-endoplasmic Reticulum Ca2+-ATPase (SERCA) ATP Hydrolysis from Ca2+ Transport.
  Sahoo SK, Shaikh SA, Sopariwala DH, Bal NC, Bruhn DS, Kopec W, Khandelia H, Periasamy M. The Journal of biological chemistry. · DOI
• Selective chemical binding enhances cesium tolerance in plants through inhibition of cesium uptake.
  Adams E, Chaban V, Khandelia H, Shin R. Scientific reports. · DOI
• K+ congeners that do not compromise Na+ activation of the Na+,K+-ATPase: hydration of the ion binding cavity likely controls ion selectivity.
  Mahmmoud YA, Kopec W, Khandelia H. The Journal of biological chemistry. · DOI
• The effects of globotriaosylceramide tail saturation level on bilayer phases.
  Pezeshkian W, Chaban VV, Johannes L, Shillcock J, Ipsen JH, Khandelia H. Soft matter. · DOI

2014

• Accelerating All-Atom MD Simulations of Lipids Using a Modified Virtual-Sites Technique.
  Loubet B, Kopec W, Khandelia H. Journal of chemical theory and computation. · DOI
• Distribution of neutral lipids in the lipid droplet core.
  Chaban VV, Khandelia H. The journal of physical chemistry. B. · DOI
• Lipid structure in triolein lipid droplets.
  Chaban VV, Khandelia H. The journal of physical chemistry. B. · DOI
• Insights into the role of cyclic ladderane lipids in bacteria from computer simulations.
  Chaban VV, Nielsen MB, Kopec W, Khandelia H. Chemistry and physics of lipids. · DOI
• Molecular mechanism of Na(+),K(+)-ATPase malfunction in mutations characteristic of adrenal hypertension.
  Kopec W, Loubet B, Poulsen H, Khandelia H. Biochemistry. · DOI
• Reinforcing the membrane-mediated mechanism of action of the anti-tuberculosis candidate drug thioridazine with molecular simulations.
  Kopec W, Khandelia H. Journal of computer-aided molecular design. · DOI
• Pairing of cholesterol with oxidized phospholipid species in lipid bilayers.
  Khandelia H, Loubet B, Olzyńska A, Jurkiewicz P, Hof M. Soft matter. · DOI

2013

• Tension moderation and fluctuation spectrum in simulated lipid membranes under an applied electric potential.
  Loubet B, Lomholt MA, Khandelia H. The Journal of chemical physics. · DOI
• Propofol modulates the lipid phase transition and localizes near the headgroup of membranes.
  Hansen AH, Sørensen KT, Mathieu R, Serer A, Duelund L, Khandelia H, Hansen PL, Simonsen AC. Chemistry and physics of lipids. · DOI
• Conformations of double-headed, triple-tailed phospholipid oxidation lipid products in model membranes.
  Hermetter A, Kopec W, Khandelia H. Biochimica et biophysica acta. · DOI
• Molecular dynamics simulations of the interactions of medicinal plant extracts and drugs with lipid bilayer membranes.
  Kopeć W, Telenius J, Khandelia H. The FEBS journal. · DOI
• Novel Ultrathin Membranes Composed of Organic Ions.
  Chaban VV, Verspeek B, Khandelia H. The journal of physical chemistry letters. · DOI
• Lipid peroxidation and water penetration in lipid bilayers: a W-band EPR study.
  Conte E, Megli FM, Khandelia H, Jeschke G, Bordignon E. Biochimica et biophysica acta. · DOI

2012

• Molecular mechanism of the allosteric enhancement of the umami taste sensation.
  Mouritsen OG, Khandelia H. The FEBS journal. · DOI
• Protein kinase A (PKA) phosphorylation of Na+/K+-ATPase opens intracellular C-terminal water pathway leading to third Na+-binding site in molecular dynamics simulations.
  Poulsen H, Nissen P, Mouritsen OG, Khandelia H. The Journal of biological chemistry. · DOI

2010

• Interaction of salicylate and a terpenoid plant extract with model membranes: reconciling experiments and simulations.
  Khandelia H, Witzke S, Mouritsen OG. Biophysical journal. · DOI
• Inclusion of terpenoid plant extracts in lipid bilayers investigated by molecular dynamics simulations.
  Witzke S, Duelund L, Kongsted J, Petersen M, Mouritsen OG, Khandelia H. The journal of physical chemistry. B. · DOI
• Triglyceride blisters in lipid bilayers: implications for lipid droplet biogenesis and the mobile lipid signal in cancer cell membranes.
  Khandelia H, Duelund L, Pakkanen KI, Ipsen JH. PloS one. · DOI
• Neurological disease mutations compromise a C-terminal ion pathway in the Na(+)/K(+)-ATPase.
  Poulsen H, Khandelia H, Morth JP, Bublitz M, Mouritsen OG, Egebjerg J, Nissen P. Nature. · DOI

2009

• Relative free energy of binding between antimicrobial peptides and SDS or DPC micelles.
  Sayyed-Ahmad A, Khandelia H, Kaznessis YN. Molecular simulation. · DOI
• To gate or not to gate: using molecular dynamics simulations to morph gated plant aquaporins into constitutively open conformations.
  Khandelia H, Jensen MØ, Mouritsen OG. The journal of physical chemistry. B. · DOI
• Lipid gymnastics: evidence of complete acyl chain reversal in oxidized phospholipids from molecular simulations.
  Khandelia H, Mouritsen OG. Biophysical journal. · DOI

2008

• High-affinity small molecule-phospholipid complex formation: binding of siramesine to phosphatidic acid.
  Parry MJ, Alakoskela JM, Khandelia H, Kumar SA, Jäättelä M, Mahalka AK, Kinnunen PK. Journal of the American Chemical Society. · DOI
• Correlation between simulated physicochemical properties and hemolycity of protegrin-like antimicrobial peptides: predicting experimental toxicity.
  Langham AA, Khandelia H, Schuster B, Waring AJ, Lehrer RI, Kaznessis YN. Peptides. · DOI
• The impact of peptides on lipid membranes.
  Khandelia H, Ipsen JH, Mouritsen OG. Biochimica et biophysica acta. · DOI

2007

• Structure of the antimicrobial beta-hairpin peptide protegrin-1 in a DLPC lipid bilayer investigated by molecular dynamics simulation.
  Khandelia H, Kaznessis YN. Biochimica et biophysica acta. · DOI
• Cation-pi interactions stabilize the structure of the antimicrobial peptide indolicidin near membranes: molecular dynamics simulations.
  Khandelia H, Kaznessis YN. The journal of physical chemistry. B. · DOI

2006

• Driving engineering of novel antimicrobial peptides from simulations of peptide-micelle interactions.
  Khandelia H, Langham AA, Kaznessis YN. Biochimica et biophysica acta. · DOI
• Molecular dynamics investigation of the influence of anionic and zwitterionic interfaces on antimicrobial peptides’ structure: implications for peptide toxicity and activity.
  Khandelia H, Kaznessis YN. Peptides. · DOI
• How can a beta-sheet peptide be both a potent antimicrobial and harmfully toxic? Molecular dynamics simulations of protegrin-1 in micelles.
  Langham AA, Khandelia H, Kaznessis YN. Biopolymers. · DOI

2005

• Molecular dynamics simulations of helical antimicrobial peptides in SDS micelles: what do point mutations achieve?
  Khandelia H, Kaznessis YN. Peptides. · DOI
• Molecular dynamics simulations of the helical antimicrobial peptide ovispirin-1 in a zwitterionic dodecylphosphocholine micelle: insights into host-cell toxicity.
  Khandelia H, Kaznessis YN. The journal of physical chemistry. B. · DOI