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Themis Lazaridis

TitleInvestigator
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. 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:    Fields:    Translation:Cells
    2. 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:    
    3. 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: 21     Fields:    Translation:Cells
    4. 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: 2     Fields:    
    5. 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: 1     Fields:    
    6. 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: 1     Fields:    
    7. 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: 6     Fields:    Translation:Cells
    8. 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: 6     Fields:    Translation:Cells
    9. Lazaridis T, Hummer G. Classical Molecular Dynamics with Mobile Protons. J Chem Inf Model. 2017 11 27; 57(11):2833-2845. PMID: 29095613.
      Citations: 3     Fields:    Translation:Cells
    10. Lipkin R, Pino-Angeles A, Lazaridis T. Transmembrane Pore Structures of ß-Hairpin Antimicrobial Peptides by All-Atom Simulations. J Phys Chem B. 2017 10 05; 121(39):9126-9140. PMID: 28879767.
      Citations: 7     Fields:    Translation:Cells
    11. 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: 9     Fields:    Translation:Cells
    12. Lipkin R, Lazaridis T. Computational prediction of the optimal oligomeric state for membrane-inserted ß-barrels of protegrin-1 and related mutants. J Pept Sci. 2017 Apr; 23(4):334-345. PMID: 28382709.
      Citations: 3     Fields:    Translation:Cells
    13. 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: 13     Fields:    Translation:Cells
    14. 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
    15. 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: 18     Fields:    Translation:Cells
    16. Lipkin RB, Lazaridis T. Implicit Membrane Investigation of the Stability of Antimicrobial Peptide ß-Barrels and Arcs. J Membr Biol. 2015 Jun; 248(3):469-86. PMID: 25430621.
      Citations: 8     Fields:    Translation:Cells
    17. Rahaman A, Lazaridis T. A thermodynamic approach to alamethicin pore formation. Biochim Biophys Acta. 2014 May; 1838(5):1439-47. PMID: 24754058.
      Citations:    Fields:    Translation:Cells
    18. 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: 7     Fields:    Translation:Cells
    19. 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: 6     Fields:    Translation:Cells
    20. 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: 9     Fields:    Translation:Cells
    21. 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: 5     Fields:    Translation:Cells
    22. He Y, Lazaridis T. Activity determinants of helical antimicrobial peptides: a large-scale computational study. PLoS One. 2013; 8(6):e66440. PMID: 23776672.
      Citations: 7     Fields:    Translation:Cells
    23. 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: 8     Fields:    Translation:Cells
    24. 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: 16     Fields:    Translation:Cells
    25. 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: 10     Fields:    Translation:Cells
    26. 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: 13     Fields:    Translation:HumansAnimalsCells
    27. 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: 21     Fields:    Translation:Cells
    28. Li Z, Lazaridis T. Computing the thermodynamic contributions of interfacial water. Methods Mol Biol. 2012; 819:393-404. PMID: 22183549.
      Citations: 16     Fields:    Translation:Cells
    29. 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: 8     Fields:    Translation:Cells
    30. 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: 11     Fields:    Translation:Cells
    31. 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
    32. Ramos J, Lazaridis T. Computational analysis of residue contributions to coiled-coil topology. Protein Sci. 2011 Nov; 20(11):1845-55. PMID: 21858887.
      Citations: 4     Fields:    Translation:Cells
    33. Prieto L, Lazaridis T. Computational studies of colicin insertion into membranes: the closed state. Proteins. 2011 Jan; 79(1):126-41. PMID: 20941706.
      Citations: 1     Fields:    Translation:Cells
    34. Mihajlovic M, Lazaridis T. Antimicrobial peptides in toroidal and cylindrical pores. Biochim Biophys Acta. 2010 Aug; 1798(8):1485-93. PMID: 20403332.
      Citations: 38     Fields:    Translation:Cells
    35. Mihajlovic M, Lazaridis T. Antimicrobial peptides bind more strongly to membrane pores. Biochim Biophys Acta. 2010 Aug; 1798(8):1494-502. PMID: 20188066.
      Citations: 29     Fields:    Translation:AnimalsCells
    36. 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: 12     Fields:    Translation:HumansCells
    37. 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: 17     Fields:    Translation:HumansAnimalsCells
    38. Mihajlovic M, Lazaridis T. Membrane-bound structure and energetics of alpha-synuclein. Proteins. 2008 Feb 15; 70(3):761-78. PMID: 17729279.
      Citations: 14     Fields:    Translation:Cells
    39. 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: 6     Fields:    Translation:AnimalsCells
    40. 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: 9     Fields:    Translation:Cells
    41. Li Z, Lazaridis T. Water at biomolecular binding interfaces. Phys Chem Chem Phys. 2007 Feb 07; 9(5):573-81. PMID: 17242738.
      Citations: 49     Fields:    Translation:Cells
    42. 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: 9     Fields:    Translation:Cells
    43. 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: 12     Fields:    Translation:Cells
    44. 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: 20     Fields:    Translation:Cells
    45. 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: 12     Fields:    Translation:Cells
    46. 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: 6     Fields:    Translation:Cells
    47. 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: 31     Fields:    Translation:Cells
    48. 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: 25     Fields:    Translation:Cells
    49. Lazaridis T. Structural Determinants of Transmembrane ß-Barrels. J Chem Theory Comput. 2005 Jul; 1(4):716-22. PMID: 26641693.
      Citations: 15     Fields:    
    50. Lazaridis T. Implicit solvent simulations of peptide interactions with anionic lipid membranes. Proteins. 2005 Feb 15; 58(3):518-27. PMID: 15609352.
      Citations: 35     Fields:    Translation:AnimalsCells
    51. 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: 10     Fields:    Translation:Cells
    52. 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: 27     Fields:    Translation:Cells
    53. Lazaridis T. Effective energy function for proteins in lipid membranes. Proteins. 2003 Aug 01; 52(2):176-92. PMID: 12833542.
      Citations: 113     Fields:    Translation:Cells
    54. 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: 24     Fields:    
    55. 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: 7     Fields:    Translation:Cells
    56. 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: 44     Fields:    Translation:Cells
    57. Lazaridis T, Karplus M. Thermodynamics of protein folding: a microscopic view. Biophys Chem. 2003; 100(1-3):367-95. PMID: 12646378.
      Citations: 20     Fields:    Translation:HumansAnimalsCells
    58. 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: 12     Fields:    
    59. 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: 37     Fields:    Translation:Cells
    60. Lazaridis T. Solvent size vs cohesive energy as the origin of hydrophobicity. Acc Chem Res. 2001 Dec; 34(12):931-7. PMID: 11747410.
      Citations: 9     Fields:    
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