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  1. George, A, Patil, AG, and Mahalakshmi, R*. ATP-independent assembly machinery of bacterial outer membranes: BAM complex structure and function set the stage for next-generation therapeutics. Protein Science. 2024, 33: e4896 (DOI: 10.1002/pro.4896).

  2. Bora, JR, and Mahalakshmi, R*. Empowering canonical biochemicals with cross-linked novelty: Recursions in applications of protein cross-links. Proteins. 2023, In press (DOI: 10.1002/prot.26571).

  3. Bora, JR, and Mahalakshmi, R*. Photoradical-mediated catalyst-independent protein cross-link with unusual fluorescence properties. ChemBioChem. 2023, 24(17): e202300380 (DOI: 10.1002/cbic.202300380).

  4. Rosencrans, WM, Queralt-Martin, M, Lessen, HJ, Larimi, MG, Rajendran, M, Chou, T-F, Mahalakshmi, R, Sodt, AJ, Yu, T-Y, Bezrukov, SM*, and Rostovtseva, TM*. Defining the roles and regulation of the mitochondrial VDAC isoforms one molecule at a time. Biophys. J. 2023, 122(3; Suppl. 1): 93a (DOI: 10.1016/j.bpj.2022.11.700).

  5. De Pinto, V, Mahalakshmi, R, and Messina, A. VDAC Structure and Function: An Up-to-Date View. Front. Physiol. 2022, 13: 871586 (DOI: 10.1002/cbic.202300380).

  6. Sayyed, UMH, and Mahalakshmi, R*. Mitochondrial Protein Translocation Machinery: From TOM Structural Biogenesis to Functional Regulation. J. Biol. Chem. 2022, 298(5): 101870 (DOI: 10.1016/j.jbc.2022.101870).

  7. George, A, Ravi, R, Tiwari, PB, Srivastava, SR, Jain, V, and Mahalakshmi, R*. Engineering a Hyperstable Yersinia pestis Outer Membrane Protein Ail Using Thermodynamic Design. J. Am. Chem. Soc. 2022, 144(4): 1545-1555 (DOI: 10.1021/jacs.1c05964).

  8. Khan, A, Kuriachan, G, and Mahalakshmi, R*. Cellular interactome of mitochondrial VDACs: Oligomerization and channel (mis)regulation. ACS Chem. Neurosci. 2021, 12(19):3497-3515 (DOI: 10.1021/acschemneuro.1c00429).

  9. Lella, M and Mahalakshmi, R*. De novo Design of Metal Binding Cleft in a Trp-Trp Stapled Thermostable β-Hairpin Peptide. Peptide Sci. 2021,113(6):e24240 (DOI: 10.1002/pep2.24240).

  10. Tiwari, PB and Mahalakshmi, R*. Molecular Assembly Pathway of Mitochondrial Sam50 in Native Membranes. Biophys. J. 2021, 120(3; Suppl. 1): 285a (DOI: 10.1016/j.bpj.2020.11.1826).

  11. Tiwari, PB and Mahalakshmi, R*. Interplay of protein primary sequence, lipid membrane, and chaperone in β-barrel assembly. Protein Sci. 2021, 30(3):624-637(DOI: 10.1002/pro.4022).

  12. Srivastava, SR and Mahalakshmi, R*. Evolutionary selection of a 19-stranded mitochondrial β-barrel scaffold bears structural and functional significance. J. Biol. Chem. 2020, 295(43):14653-14665 (DOI: 10.1074/jbc.RA120.014366).

  13. Mahalakshmi, R*. Do folding elements trade-off with function in the human mitochondrial metabolite transporter? FASEB J. 2020, 34 (S1): 1-1 (DOI: 10.1096/fasebj.2020.34.s1.00070).

  14. Srivastava, SR and Mahalakshmi, R*. Linking Folding Landscape with Function in the Human Mitochondrial VDAC2. Biophys. J. 2020, 118(3; Suppl. 1): 367a (DOI: 10.1016/j.bpj.2019.11.2104).

  15. Rosencrans, WM, Queralt-Martin, M, Hoogerheide, DP, Gurnev, PA, Yu, T-Y, Mahalakshmi, R*, Bezrukov, SM*, and Rostovtseva, TM*. Dynamic Plasticity of Mitochondrial VDAC2 Revealed by Single-Molecule Electrophysiology. Biophys. J. 2020, 118(3; Suppl. 1): 273a (DOI: 10.1016/j.bpj.2019.11.1569).

  16. Mahalakshmi, R*. Oxidative Thiol Modifications as Molecular Redox Sensors in Human Mitochondria. Biophys. J. 2020, 118(3; Suppl. 1): 449a (DOI: 10.1016/j.bpj.2019.11.2506).

  17. Gupta, A and Mahalakshmi, R*. Single residue physico-chemical characteristics kinetically partition membrane protein self-assembly and aggregation. J. Biol. Chem. 2020, 295(5):1181-1194 (DOI: 10.1074/jbc.RA119.011342).

  18. Iyer, BR, Gupta, S, Noordeen, H, Ravi, R, Pawar, MD, George, A and Mahalakshmi, R*. Molecular Switch between Structural Compaction and Thermodynamic Stability by the Xxx-Pro Interface in Transmembrane beta-Barrels. Biochemistry 2020, 59(3):303-314 (DOI: 10.1021/acs.biochem.9b00731).

  19. Gupta, A and Mahalakshmi, R*. Reversible folding energetics of Yersinia Ail barrel reveals a hyperfluorescent intermediate. Biochim. Biophys. Acta Biomembr. 2020, 1862(2):183097 (DOI: 10.1016/j.bbamem.2019.183097).

  20. Iyer, BR and Mahalakshmi, R*. Hydrophobic characteristic is energetically preferred for cysteine in a model membrane protein. Biophys. J. 2019, 117:25-35(DOI: 10.1016/j.bpj.2019.05.024).

  21. Gupta, A and Mahalakshmi, R*. Helix-strand interaction regulates stability and aggregation of the human mitochondrial membrane protein channel VDAC3. J. Gen. Physiol. 2019, jgp.201812272 (DOI: 10.1085/jgp.201812272).

  22. Mahalakshmi, R*. Aromatic Interactions in β-Hairpin Scaffold Stability: A Historical Perspective. Arch. Biochem. Biophys. 2019, 661:39-49 (DOI: 10.1016/j.abb.2018.11.001).

  23. Srivastava, SR, Zadafiya, P and Mahalakshmi, R*. Hydrophobic mismatch modulates stability and plasticity of human mitochondrial VDAC2. Biophys. J. 2018, 115:2386-2394 (DOI: 10.1016/j.bpj.2018.11.001).

  24. Iyer, BR, Vetal, PV #, Noordeen, H #, Zadafiya, P# and Mahalakshmi, R*. Salvaging the thermodynamic destabilization of interface histidine in transmembrane β-barrels. Biochemistry 2018, 57:6669-6678 (DOI: 10.1021/acs.biochem.8b00805).

  25. Lella, M and Mahalakshmi, R*. Direct Structural Annotation of Membrane Protein Aggregation Loci using Peptide-Based Reverse-Mapping. J. Phys. Chem. Lett. 2018, 9:2967-2971 (DOI: 10.1021/acs.jpclett.8b00953).

  26. Chaturvedi, D and Mahalakshmi, R*. Folding determinants of transmembrane β-barrels using engineered OMP chimeras. Biochemistry 2018, 57(13):1987-1996 (DOI: 10.1021/acs.biochem.8b00012).

  27. Mahalakshmi, R*. Human Mitochondrial VDAC Functionality Governs Scaffold Stability. Biophys. J. 2018, 114(3): 243a (DOI: 10.1016/j.bpj.2017.11.1353).

  28. Chaturvedi, D and Mahalakshmi, R*. Position–specific contribution of interface tryptophans on membrane protein energetics. Biochim. Biophys. Acta Biomembr. 2018, 1860(2): 451-457 (DOI: 10.1016/j.bbamem.2017.11.003).

  29. Chaturvedi, D* and Mahalakshmi, R*. Transmembrane β-barrels: Evolution, folding and energetics. Biochim. Biophys. Acta Biomembr. 2017, 1859(12): 2467-2482 (DOI: 10.1016/j.bbamem.2017.09.020).

  30. Mahalakshmi, R*, Maurya, SR#, Burdak, B#, Surti, P#, Patel, M and Jain, V*. Structural plasticity of T4 transcription co-activator gp33 revealed by a protease-resistant unfolded state. Biochem. Biophys. Res. Commun. 2017, 492(1): 61-66 (DOI: 10.1016/j.bbrc.2017.08.038).

  31. Iyer, BR#, Zadafiya, P#, Vetal, PV and Mahalakshmi, R*. Energetics of side chain partitioning of β-signal residues in unassisted folding of a transmembrane β-barrel protein. J. Biol. Chem. 2017, 292: 12351-12365 (DOI: 10.1074/jbc.M117.789446).

  32. Lella, M* and Mahalakshmi, R*. Metamorphic Proteins: Emergence of dual protein folds from one primary sequence. Biochemistry 2017, 56: 2971-2984 (DOI: 10.1021/acs.biochem.7b00375).

  33. Mahalakshmi, R*. Thermodynamic partitioning forces at the membrane protein interface. FASEB J. 2017, 31(1): S761.15 (Conference abstract).

  34. Maurya, SR and Mahalakshmi, R*. Mitochondrial VDAC2 and cell homeostasis: highlighting hidden structural features and unique functionalities. Biol. Rev. Camb. Phil. Soc. 2017, 92(4): 1843-1858 (DOI: 10.1111/brv.12311).

  35. Iyer, BR#, Gupta, A# and Mahalakshmi, R*. Approaches for preparation and biophysical characterization of transmembrane β-barrels. In Chemical and Synthetic Approaches in Membrane Biology, Ed: Shukla AK, Springer Protocols Handbooks, Humana Press; 2017, 49-116 (DOI: 10.1007/8623_2016_4) (Invited Review).

  36. Lella, M and Mahalakshmi, R*. Solvation Driven Conformational Transitions in the Second Transmembrane Domain of Mycobacteriophage Holin. Biopolymers 2017, 108: 1-10 (DOI: 10.1002/bip.22894).

  37. Maurya, SR and Mahalakshmi, R*. Control of human VDAC-2 scaffold dynamics by interfacial tryptophans is position specific. Biochim. Biophys. Acta Biomembr. 2016, 1858(12): 2993-3004 (DOI: 10.1016/j.bbamem.2016.09.011).

  38. Iyer, BR and Mahalakshmi, R*. Distinct structural elements govern folding, stability and catalysis in the outer membrane enzyme PagP. Biochemistry 2016, 55(35): 4960-4970 (DOI: 10.1021/acs.biochem.6b00678).

  39. de Pinto, V*, Reina, S, Gupta, A, Messina, AA, Mahalakshmi, R. Role of cysteines in mammalian VDAC isoforms’ function. Biochim. Biophys. Acta Bioenerg. 2016, 1857: 1219-1227 (DOI: 10.1016/j.bbabio.2016.02.020) (Invited Review).

  40. Lella, M and Mahalakshmi, R*. Engineering a Transmembrane Nanopore Ion Channel from a Membrane Breaker Peptide. J. Phys. Chem. Lett. 2016, 7(13): 2298-2303 (DOI: 10.1021/acs.jpclett.6b00987).

  41. Makwana, KM and Mahalakshmi, R*. Capping β-Hairpin with N-terminal D-Amino Acid Stabilizes Peptide Scaffold. Biopolymers 2016, 106: 260-266 (DOI: 10.1002/bip.22837).

  42. Maurya, SR and Mahalakshmi, R*. VDAC-2: Mitochondrial outer membrane regulator masquerading as a channel? FEBS J. 2016, 283: 1831-1836 (DOI: 10.1111/febs.13637) (Invited Review).

  43. Reina, S, Checchetto, V, Saletti, R, Gupta, A, Chaturvedi, D, Guardiani, C, Guarino, F, Scorciapino, MA, Magri, A, Foti, S, Ceccarelli, M, Messina, AA, Mahalakshmi, R, Szabo, I and de Pinto, V. Unexpected Modifications of Cysteines in VDAC3: Indication that VDAC3 may Signal the Mitochondrial Intermembrane Redox State. Biophys. J. 2016, 110(3, S1): 19a (DOI: 10.1016/j.bpj.2015.11.162).

  44. Lella, M, Kamilla, S, Jain, V* and Mahalakshmi, R*. Molecular Mechanism of Holin Transmembrane Domain I in Pore Formation and Bacterial Cell Death. ACS Chem. Biol. 2016, 11: 910-920 (DOI: 10.1021/acschembio.5b00875).

  45. Makwana, KM and Mahalakshmi, R*. Stereopositional Outcome in the Packing of Dissimilar Aromatics in Designed β-Hairpins. Chem. Eur. J. 2016, 22(12): 4147-4156 (DOI: 10.1002/chem.201504428).

  46. Reina, S‡, Checchetto, V‡, Saletti, R, Gupta, A§, Chaturvedi, D§, Guardiani, C, Guarino, F, Scorciapino, MA, Magri, A, Foti, S, Ceccarelli, M*, Messina, AA*, Mahalakshmi, R*, Szabo, I* and de Pinto, V*. Can modification of VDAC(s) cysteine residues act as a sensor of oxidative state of the intermembrane space of mitochondria? Biochim. Biophys. Acta Bioenerg. 2016, 1857: e10 (DOI: 10.1016/j.bbabio.2016.04.035). ‡,§Equal contribution.

  47. Reina, S‡, Checchetto, V‡, Saletti, R, Gupta, A§, Chaturvedi, D§, Guardiani, C, Guarino, F, Scorciapino, MA, Magri, A, Foti, S, Ceccarelli, M*, Messina, AA*, Mahalakshmi, R*, Szabo, I* and de Pinto, V*. VDAC3 as a sensor of oxidative state of the intermembrane space of mitochondria: the putative role of cysteine residue modifications. Oncotarget 2016, 7(3): 2249-2268 (DOI: 10.18632/oncotarget.6850). ‡,§Equal contribution.

  48. Maurya, SR and Mahalakshmi, R*. N-helix and cysteines inter-regulate human mitochondrial VDAC-2 function and biochemistry. J. Biol. Chem. 2015, 290(51): 30240-30252 (DOI: 10.1074/jbc.M115.693978).

  49. Makwana, KM* and Mahalakshmi, R*. Implications of Aromatic-Aromatic Interactions: From Protein Structures to Peptide Models. Protein Sci. 2015, 24: 1920-1933 (DOI: 10.1002/pro.2814) (Invited Review).

  50. Iyer, BR and Mahalakshmi, R*. Residue–dependent thermodynamic cost and barrel plasticity balances activity in the PhoPQ–activated enzyme PagP of Salmonella typhimurium. Biochemistry 2015, 54: 5712-5722 (DOI: 10.1021/acs.biochem.5b00543).

  51. Makwana, KM and Mahalakshmi, R*. Structure Stabilizing Role of Aromatic Interactions is Decided by Spatial Arrangement of Aromatic Pairs: A Case Study With Designed Peptide β-Hairpins. Peptides 2015, Proceedings of the 24th American Peptide Symposium, Eds: Srivastava V, Yudin A, Lebl M. 2015, American Peptide Society, San Diego, CA, pp 220-222 (DOI: 10.17952/24APS.2015.220).

  52. Makwana, KM and Mahalakshmi, R*. Trp-Trp Cross-Linking: A Structure-Reactivity Relationship in the Formation and Design of Hyperstable Peptide β-Hairpin and α-Helix Scaffolds. Org. Lett. 2015, 17: 2498-2501 (DOI: 10.1021/acs.orglett.5b01017).

  53. Makwana, KM and Mahalakshmi, R*. NMR Analysis of Tuning Cross-Strand Phe/Tyr/Trp – Trp Interactions in Designed β-Hairpin Peptides: Terminal Switch from L- to D-Amino Acid as a Strategy for β- Hairpin Capping. J. Phys. Chem. B 2015, 119: 5376-5385 (DOI: 10.1021/acs.jpcb.5b00554).

  54. Mahalakshmi, R*. Folding and stability of transmembrane β-barrels of bacterial and human origin: Probing underlying similarities and principal differences using in vitro systems. Proc. Indian Natn. Sci. Acad. 2015, 81(2): 463-478 (DOI: 10.16943/ptinsa/2015/v81i2/48099) (Invited Review).

  55. Makwana, KM and Mahalakshmi, R*. Nature of aryl-tyrosine interactions contribute to β-hairpin scaffold stability: NMR evidence for alternate ring geometry. Phys. Chem. Chem. Phys. 2015, 17: 4220-4230 (DOI: 10.1039/C4CP04991H).

  56. Gupta, A, Iyer, BR, Chaturvedi, D#, Maurya, SR# and Mahalakshmi, R*. Thermodynamic, structural and functional properties of membrane protein inclusion bodies are analogous to purified counterparts: Case study from bacteria and humans. RSC Adv. 2015, 5(2): 1227-1234 (DOI: 10.1039/C4RA11207E). #Equal contribution.

  57. Chaturvedi, D and Mahalakshmi, R*. Juxtamembrane tryptophans possess distinct roles in defining the OmpX barrel-micelle boundary and packing-facilitated protein-micelle association. FEBS Lett. 2014, 588: 4464-4471 (DOI: 10.1016/j.febslet.2014.10.017).

  58. Makwana, KM and Mahalakshmi, R*. Asymmetric contribution of aromatic interactions stems from spatial positioning of the interacting aryl pairs in β-hairpins. ChemBioChem 2014, 15: 2357- 2360 (DOI: 10.1002/cbic.201402340).

  59. Gupta, A#, Zadafiya, P# and Mahalakshmi, R*. Differential Contribution of Tryptophans to the Folding and Stability of the Attachment Invasion Locus Transmembrane β-Barrel from Yersinia pestis. Sci. Rep. 2014, 4: 6508 (DOI: 10.1038/srep06508). #Equal contribution.

  60. Ravikiran, B and Mahalakshmi, R*. Unusual post-translational protein modifications : The benefits of sophistication. RSC Adv. 2014, 4(64): 33958-33974 (DOI: 10.1039/C4RA04694C) (Invited Review).

  61. Makwana, KM and Mahalakshmi, R*. Comparative analysis of cross strand aromatic-Phe interactions in designed peptide β-hairpins. Org. Biomol. Chem. 2014, 12(13): 2053-2061 (DOI: 10.1039/C3OB42247J). Selected for front cover illustration of issue.

  62. Maurya, SR and Mahalakshmi, R*. Cysteine Residues Impact the Stability and Micelle Interaction Dynamics of the Human Mitochondrial β-barrel Anion Channel hVDAC-2. PLoS One 2014, 9(3): e92183 (DOI: 10.1371/journal.pone.0092183).

  63. Maurya, SR and Mahalakshmi, R*. Influence of Protein - Micelle Ratios and Cysteine Residues on the Kinetic Stability and Unfolding Rates of Human Mitochondrial VDAC-2. PLoS One 2014, 9(1): e87701 (DOI: 10.1371/journal.pone.0087701).

  64. Chaturvedi, D and Mahalakshmi, R*. Methionine Mutations of Outer Membrane Protein X Influence Structural Stability and beta-Barrel Unfolding. PLoS One 2013, 8(11): e79351 (DOI: 10.1371/journal.pone.0079351).

  65. Lella, M and Mahalakshmi, R*. Pro-Gly mediated conformational switch of Mycobacteriophage D29 holin transmembrane domain I is lipid concentration driven. Chem. Commun. 2013, 49(83): 9594-9596 (DOI: 10.1039/C3CC45058A).

  66. Makwana, KM, Raghothama, SR* and Mahalakshmi, R*. Stabilizing effect of electrostatic vs aromatic interactions in diproline nucleated peptide β-hairpins. Phys. Chem. Chem. Phys. 2013, 15 (37): 15321-15324 (DOI: 10.1039/C3CP52770K). Selected as “Hot Article”.

  67. Maurya, SR and Mahalakshmi, R*. Modulation of human mitochondrial voltage-dependent anion channel 2 (hVDAC-2) structural stability by cysteine-assisted barrel-lipid interactions. J. Biol. Chem. 2013, 288(35): 25584-25592 (DOI: 10.1074/jbc.M113.493692).

  68. Maurya, SR#, Chaturvedi, D#, Mahalakshmi, R*. Modulating lipid dynamics and membrane fluidity to drive rapid folding of a transmembrane barrel. Sci. Rep. 2013, 3: 1989 (DOI: 10.1038/srep01989). #Equal contribution.

  69. Gupta, A, Chaturvedi, D, Mahalakshmi, R*. Modified CNBr cleavage protocol for efficient separation of Met-Ser containing OmpX-Om14 membrane protein fusion. International Review of Biophysical Chemistry 2012, 3(5): 147-156.

  70. Plesniak, LA, Mahalakshmi, R, Rypien, C, Yang, Y, Racic, J and Marassi, FM. Expression, refolding, and initial structural characterization of the Y. pestis Ail outer membrane protein in lipids. Biochim. Biophys. Acta Biomembr. 2011, 1808: 482-489.

  71. Petrovic, AG, Polavarapu, PL, Mahalakshmi, R and Balaram, P. Characterization of folded conformations in a tetrapeptide containing two tryptophan residues by vibrational circular dichroism (p S76-S85). Chirality 2009, 21: E76-E85.

  72. Mahalakshmi, R and Marassi, FM. Orientation of the E. coli outer membrane protein OmpX in phospholipid bilayer membranes determined by solid-state NMR. Biochemistry 2008, 47: 6531- 6538. Selected as “Hot Article”.

  73. Mahalakshmi, R, Franzin, CM, Choi, J and Marassi, FM. NMR structural studies of the bacterial outer membrane protein OmpX in oriented lipid bilayer membranes. Biochim. Biophys. Acta Biomembr. 2007, 1768:3216-3224.

  74. Mahalakshmi, R, Sengupta, A, Raghothama, S, Shamala, N and Balaram, P. Tryptophan rich peptides: influence of indole rings on backbone conformation. Biopolymers 2007, 88: 36- 54.

  75. Mahalakshmi, R and Balaram, P. The use of D-amino acids in peptide design (book chapter). In D-amino acids: A new frontier in amino acid and protein research, Eds: Konno R, Brüeckner H, d' Aniello A, Fisher GH, Fujii N, Homma H. Nova Science Pub.; 2006, Chap. 5.9: 415-430.

  76. Mahalakshmi, R, Raghothama, S and Balaram, P. NMR analysis of aromatic interactions in designed peptide beta-hairpins. J. Am. Chem. Soc. 2006, 128: 1125-1138.

  77. Mahalakshmi, R and Balaram, P. Non-protein amino acids in the design of secondary structure scaffolds. In Protein Design: Methods and Applications, Eds: Guerois R, de la Paz ML, Methods Mol. Biol., Humana Press; 2006, 340: 71-94.

  78. Mahalakshmi, R, Shanmugam, G, Polavarapu, PL and Balaram, P. Circular dichroism of designed peptide helices and beta-hairpins: Analysis of Trp- and Tyr-rich peptides. ChemBioChem 2005, 6: 2152-2157.

  79. Mahalakshmi, R, Sengupta, A, Raghothama, S, Shamala, N and Balaram, P. Tryptophan containing peptide helices: interactions involving the indole side chain. J. Peptide Res. 2005, 66:277-296.

  80. Sengupta, A, Mahalakshmi, R, Shamala, N and Balaram, P. Aromatic interactions in tryptophan-containing peptides: Crystal structures of model tryptophan peptides and phenylalanine analogs. J. Peptide Res. 2005, 65:113-129.

  81. Padmashri, R, Chakrabarti, KS, Sahal, D, Mahalakshmi, R, Sarma, SP and Sikdar, SK. Functional characterization of the pentapeptide QYNAD on rNav1.2 channels and its NMR structure. Pflugers. Arch. - Eur. J. Physiol. 2004, 447: 895-907.

 
 
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