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Themis Lazaridis

InstitutionCity College, CUNY
DepartmentDepartment of Chemistry
AddressCity College, CUNY, Marshak Science Building
Covenant Avenue at 138th Street
New York NY 10031
Phone(212) 650-8364
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    Collapse Overview 
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    Biophysical Chemistry and Molecular Biophysics aim to understand how biological systems work in terms of the fundamental laws of Physics and Chemistry. Biomolecules, such as proteins and nucleic acids, usually have well defined conformations which often change in the course of their function. Our goal is to understand the forces that operate within and between biomolecules and develop quantitative mathematical models for their energy as a function of conformation. Such models are useful in many ways, such as predicting the three-dimensional structure from sequence, characterizing conformational changes involved in biological function, or predicting the binding affinity between two biomolecules.

    One of the most difficult interactions to model is that between biomolecules and solvent. A simple analytical function that gives the solvation free energy for an arbitrary conformation would be highly desirable. Several years ago we developed a model (EEF1) based on the idea that solute atoms exclude solvent from the region they occupy. More recently we extended this model to biological membranes, which are essentially a heterogeneous solvent. This has allowed a much more efficient study of the interaction of peptides and soluble proteins with membranes, a process that is implicated in many biological processes such as membrane fusion, innate immunity, or signal transduction.

    Collapse Bibliographic 
    Collapse selected publications
    Publications listed below are automatically derived from MEDLINE/PubMed and other sources, which might result in incorrect or missing publications. Faculty can login to make corrections and additions.
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    PMC Citations indicate the number of times the publication was cited by articles in PubMed Central, and the Altmetric score represents citations in news articles and social media. (Note that publications are often cited in additional ways that are not shown here.) Fields are based on how the National Library of Medicine (NLM) classifies the publication's journal and might not represent the specific topic of the publication. Translation tags are based on the publication type and the MeSH terms NLM assigns to the publication. Some publications (especially newer ones and publications not in PubMed) might not yet be assigned Field or Translation tags.) Click a Field or Translation tag to filter the publications.
    1. Maurer M, Lazaridis T. Transmembrane ?-Barrel Models of a-Synuclein Oligomers. J Chem Inf Model. 2023 Nov 27; 63(22):7171-7179. PMID: 37963823.
      Citations:    Fields:    Translation:HumansCells
    2. Maurer M, Lazaridis T. Comparison of classical and ab?initio simulations of hydronium and aqueous proton transfer. J Chem Phys. 2023 Oct 07; 159(13). PMID: 37795787.
      Citations:    Fields:    
    3. Vasquez Rodriguez SY, Lazaridis T. Simulations suggest a scaffolding mechanism of membrane deformation by the caveolin 8S complex. Biophys J. 2023 10 17; 122(20):4082-4090. PMID: 37742070.
      Citations:    Fields:    Translation:Cells
    4. Lazaridis T. Proton Paths in Models of the Hv1 Proton Channel. J Phys Chem B. 2023 09 21; 127(37):7937-7945. PMID: 37695850.
      Citations:    Fields:    Translation:AnimalsCells
    5. Dutta A, Sepehri A, Lazaridis T. Putative Pore Structures of Amyloid ? 25-35 in Lipid Bilayers. Biochemistry. 2023 09 05; 62(17):2549-2558. PMID: 37582191.
      Citations:    Fields:    Translation:HumansCells
    6. Sepehri A, Lazaridis T. Putative Structures of Membrane-Embedded Amyloid ? Oligomers. ACS Chem Neurosci. 2022 Dec 16. PMID: 36525690.
      Citations: 2     Fields:    
    7. Lazaridis T. Molecular origins of asymmetric proton conduction in the influenza M2 channel. Biophys J. 2023 01 03; 122(1):90-98. PMID: 36403086.
      Citations:    Fields:    Translation:Cells
    8. Lazaridis T, Sepehri A. Amino acid deprotonation rates from classical force fields. J Chem Phys. 2022 Aug 28; 157(8):085101. PMID: 36050014.
      Citations: 1     Fields:    
    9. Nepal B, Sepehri A, Lazaridis T. Mechanism of negative membrane curvature generation by I-BAR domains. Structure. 2021 12 02; 29(12):1440-1452.e4. PMID: 34520736.
      Citations: 4     Fields:    Translation:HumansCells
    10. Sepehri A, Nepal B, Lazaridis T. Distinct Modes of Action of IAPP Oligomers on Membranes. J Chem Inf Model. 2021 09 27; 61(9):4645-4655. PMID: 34499498.
      Citations: 4     Fields:    Translation:HumansCells
    11. Sepehri A, Nepal B, Lazaridis T. Lipid interactions of an actinoporin pore-forming oligomer. Biophys J. 2021 04 20; 120(8):1357-1366. PMID: 33617834.
      Citations: 3     Fields:    Translation:Animals
    12. Dixit M, Lazaridis T. Free energy of hydrophilic and hydrophobic pores in lipid bilayers by free energy perturbation of a restraint. J Chem Phys. 2020 Aug 07; 153(5):054101. PMID: 32770888.
      Citations: 4     Fields:    Translation:Cells
    13. Rodnin MV, Vasquez-Montes V, Nepal B, Ladokhin AS, Lazaridis T. Correction to: Experimental and Computational Characterization of Oxidized and Reduced Protegrin Pores in Lipid Bilayers. J Membr Biol. 2020 Aug; 253(4):373. PMID: 32601712.
      Citations:    Fields:    
    14. Magana M, Pushpanathan M, Santos AL, Leanse L, Fernandez M, Ioannidis A, Giulianotti MA, Apidianakis Y, Bradfute S, Ferguson AL, Cherkasov A, Seleem MN, Pinilla C, de la Fuente-Nunez C, Lazaridis T, Dai T, Houghten RA, Hancock REW, Tegos GP. The value of antimicrobial peptides in the age of resistance. Lancet Infect Dis. 2020 09; 20(9):e216-e230. PMID: 32653070.
      Citations: 261     Fields:    Translation:Cells
    15. Rodnin MV, Vasquez-Montes V, Nepal B, Ladokhin AS, Lazaridis T. Experimental and Computational Characterization of Oxidized and Reduced Protegrin Pores in Lipid Bilayers. J Membr Biol. 2020 06; 253(3):287-298. PMID: 32500172.
      Citations: 5     Fields:    Translation:Cells
    16. Nepal B, Sepehri A, Lazaridis T. Mechanisms of negative membrane curvature sensing and generation by ESCRT III subunit Snf7. Protein Sci. 2020 06; 29(6):1473-1485. PMID: 32142182.
      Citations: 4     Fields:    Translation:HumansCells
    17. Sepehri A, PeBenito L, Pino-Angeles A, Lazaridis T. What Makes a Good Pore Former: A Study of Synthetic Melittin Derivatives. Biophys J. 2020 04 21; 118(8):1901-1913. PMID: 32183940.
      Citations: 4     Fields:    
    18. Pino-Angeles A, Lazaridis T. Effects of Peptide Charge, Orientation, and Concentration on Melittin Transmembrane Pores. Biophys J. 2018 06 19; 114(12):2865-2874. PMID: 29925023.
      Citations: 21     Fields:    Translation:Cells
    19. Nepal B, Leveritt J, Lazaridis T. Membrane Curvature Sensing by Amphipathic Helices: Insights from Implicit Membrane Modeling. Biophys J. 2018 05 08; 114(9):2128-2141. PMID: 29742406.
      Citations: 15     Fields:    Translation:Cells
    20. Lazaridis T, Hummer G. Classical Molecular Dynamics with Mobile Protons. J Chem Inf Model. 2017 11 27; 57(11):2833-2845. PMID: 29095613.
      Citations: 5     Fields:    Translation:Cells
    21. Lipkin R, Pino-Angeles A, Lazaridis T. Transmembrane Pore Structures of ?-Hairpin Antimicrobial Peptides by All-Atom Simulations. J Phys Chem B. 2017 10 05; 121(39):9126-9140. PMID: 28879767.
      Citations: 9     Fields:    Translation:Cells
    22. Lipkin R, Lazaridis T. Computational studies of peptide-induced membrane pore formation. Philos Trans R Soc Lond B Biol Sci. 2017 Aug 05; 372(1726). PMID: 28630158.
      Citations: 20     Fields:    Translation:Cells
    23. Lipkin R, Lazaridis T. Computational prediction of the optimal oligomeric state for membrane-inserted ?-barrels of protegrin-1 and related mutants. J Pept Sci. 2017 Apr; 23(4):334-345. PMID: 28382709.
      Citations: 3     Fields:    Translation:Cells
    24. Pino-Angeles A, Leveritt JM, Lazaridis T. Pore Structure and Synergy in Antimicrobial Peptides of the Magainin Family. PLoS Comput Biol. 2016 Jan; 12(1):e1004570. PMID: 26727376.
      Citations: 25     Fields:    Translation:Cells
    25. Versace RE, Lazaridis T. Modeling Protein-Micelle Systems in Implicit Water. J Phys Chem B. 2015 Jun 25; 119(25):8037-47. PMID: 26035001.
      Citations: 3     Fields:    Translation:Cells
    26. Leveritt JM, Pino-Angeles A, Lazaridis T. The structure of a melittin-stabilized pore. Biophys J. 2015 May 19; 108(10):2424-2426. PMID: 25992720.
      Citations: 32     Fields:    Translation:Cells
    27. Lipkin RB, Lazaridis T. Implicit Membrane Investigation of the Stability of Antimicrobial Peptide ?-Barrels and Arcs. J Membr Biol. 2015 Jun; 248(3):469-86. PMID: 25430621.
      Citations: 13     Fields:    Translation:Cells
    28. Rahaman A, Lazaridis T. A thermodynamic approach to alamethicin pore formation. Biochim Biophys Acta. 2014 May; 1838(5):1439-47. PMID: 24754058.
      Citations: 2     Fields:    Translation:Cells
    29. Brice AR, Lazaridis T. Structure and dynamics of a fusion peptide helical hairpin on the membrane surface: comparison of molecular simulations and NMR. J Phys Chem B. 2014 May 01; 118(17):4461-70. PMID: 24712538.
      Citations: 13     Fields:    Translation:Cells
    30. Lazaridis T, Leveritt JM, PeBenito L. Implicit membrane treatment of buried charged groups: application to peptide translocation across lipid bilayers. Biochim Biophys Acta. 2014 Sep; 1838(9):2149-59. PMID: 24525075.
      Citations: 9     Fields:    Translation:Cells
    31. Prieto L, He Y, Lazaridis T. Protein arcs may form stable pores in lipid membranes. Biophys J. 2014 Jan 07; 106(1):154-61. PMID: 24411247.
      Citations: 10     Fields:    Translation:Cells
    32. Rahaman A, Lazaridis T. A thermodynamic approach to alamethicin pore formation. Biochim Biophys Acta. 2014 Jan; 1838(1 Pt B):98-105. PMID: 24071593.
      Citations: 6     Fields:    Translation:Cells
    33. He Y, Lazaridis T. Activity determinants of helical antimicrobial peptides: a large-scale computational study. PLoS One. 2013; 8(6):e66440. PMID: 23776672.
      Citations: 9     Fields:    Translation:Cells
    34. He Y, Prieto L, Lazaridis T. Modeling peptide binding to anionic membrane pores. J Comput Chem. 2013 Jun 30; 34(17):1463-75. PMID: 23580260.
      Citations: 10     Fields:    Translation:Cells
    35. Lazaridis T, He Y, Prieto L. Membrane interactions and pore formation by the antimicrobial peptide protegrin. Biophys J. 2013 Feb 05; 104(3):633-42. PMID: 23442914.
      Citations: 22     Fields:    Translation:Cells
    36. Zhan H, Lazaridis T. Inclusion of lateral pressure/curvature stress effects in implicit membrane models. Biophys J. 2013 Feb 05; 104(3):643-54. PMID: 23442915.
      Citations: 13     Fields:    Translation:Cells
    37. Yuzlenko O, Lazaridis T. Membrane protein native state discrimination by implicit membrane models. J Comput Chem. 2013 Apr 05; 34(9):731-8. PMID: 23224861.
      Citations: 17     Fields:    Translation:HumansAnimalsCells
    38. Mihajlovic M, Lazaridis T. Charge distribution and imperfect amphipathicity affect pore formation by antimicrobial peptides. Biochim Biophys Acta. 2012 May; 1818(5):1274-83. PMID: 22290189.
      Citations: 34     Fields:    Translation:Cells
    39. Li Z, Lazaridis T. Computing the thermodynamic contributions of interfacial water. Methods Mol Biol. 2012; 819:393-404. PMID: 22183549.
      Citations: 24     Fields:    Translation:Cells
    40. Yuzlenko O, Lazaridis T. Interactions between ionizable amino acid side chains at a lipid bilayer-water interface. J Phys Chem B. 2011 Nov 24; 115(46):13674-84. PMID: 21985663.
      Citations: 9     Fields:    Translation:Cells
    41. Zhan H, Lazaridis T. Influence of the membrane dipole potential on peptide binding to lipid bilayers. Biophys Chem. 2012 Feb; 161:1-7. PMID: 22100997.
      Citations: 17     Fields:    Translation:Cells
    42. Madeo J, Mihajlovic M, Lazaridis T, Gunner MR. Slow dissociation of a charged ligand: analysis of the primary quinone Q(A) site of photosynthetic bacterial reaction centers. J Am Chem Soc. 2011 Nov 02; 133(43):17375-85. PMID: 21863833.
      Citations: 6     Fields:    Translation:Cells
    43. Ramos J, Lazaridis T. Computational analysis of residue contributions to coiled-coil topology. Protein Sci. 2011 Nov; 20(11):1845-55. PMID: 21858887.
      Citations: 5     Fields:    Translation:Cells
    44. Prieto L, Lazaridis T. Computational studies of colicin insertion into membranes: the closed state. Proteins. 2011 Jan; 79(1):126-41. PMID: 20941706.
      Citations: 2     Fields:    Translation:Cells
    45. Mihajlovic M, Lazaridis T. Antimicrobial peptides in toroidal and cylindrical pores. Biochim Biophys Acta. 2010 Aug; 1798(8):1485-93. PMID: 20403332.
      Citations: 51     Fields:    Translation:Cells
    46. Mihajlovic M, Lazaridis T. Antimicrobial peptides bind more strongly to membrane pores. Biochim Biophys Acta. 2010 Aug; 1798(8):1494-502. PMID: 20188066.
      Citations: 34     Fields:    Translation:AnimalsCells
    47. Zhang J, Lazaridis T. Transmembrane helix association affinity can be modulated by flanking and noninterfacial residues. Biophys J. 2009 Jun 03; 96(11):4418-27. PMID: 19486666.
      Citations: 14     Fields:    Translation:HumansCells
    48. Hajjar E, Mihajlovic M, Witko-Sarsat V, Lazaridis T, Reuter N. Computational prediction of the binding site of proteinase 3 to the plasma membrane. Proteins. 2008 Jun; 71(4):1655-69. PMID: 18076025.
      Citations: 19     Fields:    Translation:HumansAnimalsCells
    49. Mihajlovic M, Lazaridis T. Membrane-bound structure and energetics of alpha-synuclein. Proteins. 2008 Feb 15; 70(3):761-78. PMID: 17729279.
      Citations: 16     Fields:    Translation:Cells
    50. Mihajlovic M, Lazaridis T. Modeling fatty acid delivery from intestinal fatty acid binding protein to a membrane. Protein Sci. 2007 Sep; 16(9):2042-55. PMID: 17660261.
      Citations: 7     Fields:    Translation:AnimalsCells
    51. Ramos J, Lazaridis T. Energetic determinants of oligomeric state specificity in coiled coils. J Am Chem Soc. 2006 Dec 06; 128(48):15499-510. PMID: 17132017.
      Citations: 11     Fields:    Translation:Cells
    52. Li Z, Lazaridis T. Water at biomolecular binding interfaces. Phys Chem Chem Phys. 2007 Feb 07; 9(5):573-81. PMID: 17242738.
      Citations: 57     Fields:    Translation:Cells
    53. Sammalkorpi M, Lazaridis T. Modeling a spin-labeled fusion peptide in a membrane: implications for the interpretation of EPR experiments. Biophys J. 2007 Jan 01; 92(1):10-22. PMID: 17040984.
      Citations: 10     Fields:    Translation:Cells
    54. Zhang J, Lazaridis T. Calculating the free energy of association of transmembrane helices. Biophys J. 2006 Sep 01; 91(5):1710-23. PMID: 16766613.
      Citations: 14     Fields:    Translation:Cells
    55. Mottamal M, Lazaridis T. Voltage-dependent energetics of alamethicin monomers in the membrane. Biophys Chem. 2006 Jun 20; 122(1):50-7. PMID: 16542770.
      Citations: 21     Fields:    Translation:Cells
    56. Mottamal M, Zhang J, Lazaridis T. Energetics of the native and non-native states of the glycophorin transmembrane helix dimer. Proteins. 2006 Mar 01; 62(4):996-1009. PMID: 16395713.
      Citations: 13     Fields:    Translation:Cells
    57. Mihajlovic M, Lazaridis T. Calculations of pH-dependent binding of proteins to biological membranes. J Phys Chem B. 2006 Feb 23; 110(7):3375-84. PMID: 16494352.
      Citations: 7     Fields:    Translation:Cells
    58. Li Z, Lazaridis T. Thermodynamics of buried water clusters at a protein-ligand binding interface. J Phys Chem B. 2006 Jan 26; 110(3):1464-75. PMID: 16471698.
      Citations: 37     Fields:    Translation:Cells
    59. Lazaridis T, Mallik B, Chen Y. Implicit solvent simulations of DPC micelle formation. J Phys Chem B. 2005 Aug 11; 109(31):15098-106. PMID: 16852911.
      Citations: 28     Fields:    Translation:Cells
    60. Lazaridis T. Structural Determinants of Transmembrane ?-Barrels. J Chem Theory Comput. 2005 Jul; 1(4):716-22. PMID: 26641693.
      Citations: 16     Fields:    
    61. Lazaridis T. Implicit solvent simulations of peptide interactions with anionic lipid membranes. Proteins. 2005 Feb 15; 58(3):518-27. PMID: 15609352.
      Citations: 37     Fields:    Translation:AnimalsCells
    62. Mottamal M, Lazaridis T. The contribution of C alpha-H...O hydrogen bonds to membrane protein stability depends on the position of the amide. Biochemistry. 2005 Feb 08; 44(5):1607-13. PMID: 15683244.
      Citations: 11     Fields:    Translation:Cells
    63. Li Z, Lazaridis T. The effect of water displacement on binding thermodynamics: concanavalin A. J Phys Chem B. 2005 Jan 13; 109(1):662-70. PMID: 16851059.
      Citations: 35     Fields:    Translation:Cells
    64. Lazaridis T. Effective energy function for proteins in lipid membranes. Proteins. 2003 Aug 01; 52(2):176-92. PMID: 12833542.
      Citations: 132     Fields:    Translation:Cells
    65. Li Z, Lazaridis T. Thermodynamic contributions of the ordered water molecule in HIV-1 protease. J Am Chem Soc. 2003 Jun 04; 125(22):6636-7. PMID: 12769565.
      Citations: 31     Fields:    
    66. Madhusoodanan M, Lazaridis T. Investigation of pathways for the low-pH conformational transition in influenza hemagglutinin. Biophys J. 2003 Mar; 84(3):1926-39. PMID: 12609895.
      Citations: 9     Fields:    Translation:Cells
    67. Masunov A, Lazaridis T. Potentials of mean force between ionizable amino acid side chains in water. J Am Chem Soc. 2003 Feb 19; 125(7):1722-30. PMID: 12580597.
      Citations: 54     Fields:    Translation:Cells
    68. Lazaridis T, Karplus M. Thermodynamics of protein folding: a microscopic view. Biophys Chem. 2003; 100(1-3):367-95. PMID: 12646378.
      Citations: 27     Fields:    Translation:HumansAnimalsCells
    69. Mallik B, Masunov A, Lazaridis T. Distance and exposure dependent effective dielectric function. J Comput Chem. 2002 Aug; 23(11):1090-9. PMID: 12116395.
      Citations: 13     Fields:    
    70. Lazaridis T, Masunov A, Gandolfo F. Contributions to the binding free energy of ligands to avidin and streptavidin. Proteins. 2002 May 01; 47(2):194-208. PMID: 11933066.
      Citations: 38     Fields:    Translation:Cells
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