Peter Beernink, PhD

Our research lies at the intersection between vaccinology and structural biology. We use X-ray crystallography and other biochemical and biophysical approaches to aid in developing vaccines against the mucosal bacterial pathogens meningococcus and gonococcus. Meningococci cause potentially fatal cases of sepsis and meningitis and gonococcus causes sexually-transmitted infections, which are increasingly resistant to antibiotics. Our vaccine approaches against these pathogens include mutant Factor H binding protein (FHbp) and Neisserial surface protein A (NspA) antigens designed to disrupt the interaction with human complement Factor H, as well as outer membrane vesicles that have increased abundance of the mutant antigens. We are also collaborating on a gonococcal vaccine based on a peptide that mimics a sugar on the surface of the bacteria. From the structures of antibodies bound to vaccine antigens, we gain information both to develop improved antigens and to understand the human antibody repertoire induced by vaccination.
Education
Postdoc, 03/1999 - Physical Biochemistry, University of California
Ph.D., 06/1995 - Molecular Biology and Biochemistry, Boston University
A.B., 05/1988 - Microbial Genetics, Cornell University
Honors and Awards
  • Scientific Career Achievement Award, UCSF Benioff Children's Hospital Oakland, 2021
  • Clorox Endowed Chair of Immunobiology and Vaccine Development, UCSF Benioff Children's Hospital Oakland, 2020
  • Scientific Achievement Award, Children's Hospital & Research Center at Oakland, 2016
  • Individual National Research Service Award (F32), U.C. Berkeley, 1998-2000

  1. Beernink PT, Di Carluccio C, Marchetti R, Cerofolini L, Carillo S, Cangiano A, Cowieson N, Bones J, Molinaro A, Paduano L, Fragai M, Beernink BP, Gulati S, Shaughnessy J, Rice PA, Ram S, Silipo A. Gonococcal Mimitope Vaccine Candidate Forms a Beta-Hairpin Turn and Binds Hydrophobically to a Therapeutic Monoclonal Antibody. JACS Au 2024. PMID: 39055159


  2. Dold C, Marsay L, Wang N, Silva-Reyes L, Clutterbuck E, Paterson GK, Sharkey K, Wyllie D, Beernink PT, Hill AV, Pollard AJ, Rollier CS. An adenoviral-vectored vaccine confers seroprotection against capsular group B meningococcal disease. Science translational medicine 2023. PMID: 37343082


  3. Sands NA, Beernink PT. Two human antibodies to a meningococcal serogroup B vaccine antigen enhance binding of complement Factor H by stabilizing the Factor H binding site. PLoS pathogens 2021. PMID: 34125873


  4. Findlow J, Bayliss CD, Beernink PT, Borrow R, Liberator P, Balmer P. Broad vaccine protection against Neisseria meningitidis using factor H binding protein. Vaccine 2020. PMID: 32878710


  5. Beernink PT. Effect of complement Factor H on antibody repertoire and protection elicited by meningococcal capsular group B vaccines containing Factor H binding protein. Human vaccines & immunotherapeutics 2019. PMID: 31526219


  6. Sharkey K, Beernink PT, Langley JM, Gantt S, Quach C, Dold C, Liu Q, Galvan M, Granoff DM. Anti-Factor H Antibody Reactivity in Young Adults Vaccinated with a Meningococcal Serogroup B Vaccine Containing Factor H Binding Protein. mSphere 2019. PMID: 31270173


  7. Beernink PT, Vianzon V, Lewis LA, Moe GR, Granoff DM. A Meningococcal Outer Membrane Vesicle Vaccine with Overexpressed Mutant FHbp Elicits Higher Protective Antibody Responses in Infant Rhesus Macaques than a Licensed Serogroup B Vaccine. mBio 2019. PMID: 31213564


  8. Beernink PT, Ispasanie E, Lewis LA, Ram S, Moe GR, Granoff DM. A Meningococcal Native Outer Membrane Vesicle Vaccine With Attenuated Endotoxin and Overexpressed Factor H Binding Protein Elicits Gonococcal Bactericidal Antibodies. The Journal of infectious diseases 2019. PMID: 30346576


  9. Lo Passo C, Zippilli L, Angiolillo A, Costa I, Pernice I, Galbo R, Felici F, Beernink PT. Molecular characterization of two sub-family specific monoclonal antibodies to meningococcal Factor H binding protein. Heliyon 2018. PMID: 29644339


  10. López-Sagaseta J, Beernink PT, Bianchi F, Santini L, Frigimelica E, Lucas AH, Pizza M, Bottomley MJ. Crystal structure reveals vaccine elicited bactericidal human antibody targeting a conserved epitope on meningococcal fHbp. Nature communications 2018. PMID: 29410413


  11. Endrizzi JA, Beernink PT. Charge neutralization in the active site of the catalytic trimer of aspartate transcarbamoylase promotes diverse structural changes. Protein science : a publication of the Protein Society 2017. PMID: 28833948


  12. Malito E, Lo Surdo P, Veggi D, Santini L, Stefek H, Brunelli B, Luzzi E, Bottomley MJ, Beernink PT, Scarselli M. Neisseria meningitidis factor H-binding protein bound to monoclonal antibody JAR5: implications for antibody synergy. The Biochemical journal 2016. PMID: 27784765


  13. Granoff DM, Giuntini S, Gowans FA, Lujan E, Sharkey K, Beernink PT. Enhanced protective antibody to a mutant meningococcal factor H-binding protein with low-factor H binding. JCI insight 2016. PMID: 27668287


  14. Giuntini S, Granoff DM, Beernink PT, Ihle O, Bratlie D, Michaelsen TE. Human IgG1, IgG3, and IgG3 Hinge-Truncated Mutants Show Different Protection Capabilities against Meningococci Depending on the Target Antigen and Epitope Specificity. Clinical and vaccine immunology : CVI 2016. PMID: 27307451


  15. Rossi R, Konar M, Beernink PT. Meningococcal Factor H Binding Protein Vaccine Antigens with Increased Thermal Stability and Decreased Binding of Human Factor H. Infection and immunity 2016. PMID: 27021245


  16. Konar M, Pajon R, Beernink PT. A meningococcal vaccine antigen engineered to increase thermal stability and stabilize protective epitopes. Proceedings of the National Academy of Sciences of the United States of America 2015. PMID: 26627237


  17. Giuntini S, Beernink PT, Granoff DM. Effect of complement Factor H on anti-FHbp serum bactericidal antibody responses of infant rhesus macaques boosted with a licensed meningococcal serogroup B vaccine. Vaccine 2015. PMID: 26562320


  18. Rossi R, Beernink PT, Giuntini S, Granoff DM. Susceptibility of Meningococcal Strains Responsible for Two Serogroup B Outbreaks on U.S. University Campuses to Serum Bactericidal Activity Elicited by the MenB-4C Vaccine. Clinical and vaccine immunology : CVI 2015. PMID: 26424832


  19. Konar M, Beernink PT, Granoff DM. A Newly-Identified Polymorphism in Rhesus Macaque Complement Factor H Modulates Binding Affinity for Meningococcal FHbp. PloS one 2015. PMID: 26285122


  20. Beernink PT, Giuntini S, Costa I, Lucas AH, Granoff DM. Functional Analysis of the Human Antibody Response to Meningococcal Factor H Binding Protein. mBio 2015. PMID: 26106082


  21. Konar M, Rossi R, Walter H, Pajon R, Beernink PT. A Mutant Library Approach to Identify Improved Meningococcal Factor H Binding Protein Vaccine Antigens. PloS one 2015. PMID: 26057742


  22. Granoff DM, Costa I, Konar M, Giuntini S, Van Rompay KK, Beernink PT. Binding of Complement Factor H (FH) Decreases Protective Anti-FH Binding Protein Antibody Responses of Infant Rhesus Macaques Immunized With a Meningococcal Serogroup B Vaccine. The Journal of infectious diseases 2015. PMID: 25676468


  23. Beernink PT, Shaughnessy J, Stefek H, Ram S, Granoff DM. Heterogeneity in rhesus macaque complement factor H binding to meningococcal factor H binding protein (FHbp) informs selection of primates to assess immunogenicity of FHbp-based vaccines. Clinical and vaccine immunology : CVI 2014. PMID: 25185576


  24. Rossi R, Granoff DM, Beernink PT. Meningococcal factor H-binding protein vaccines with decreased binding to human complement factor H have enhanced immunogenicity in human factor H transgenic mice. Vaccine 2013. PMID: 24035433


  25. Granoff DM, Ram S, Beernink PT. Does binding of complement factor H to the meningococcal vaccine antigen, factor H binding protein, decrease protective serum antibody responses? Clinical and vaccine immunology : CVI 2013. PMID: 23740919


  26. Konar M, Granoff DM, Beernink PT. Importance of inhibition of binding of complement factor H for serum bactericidal antibody responses to meningococcal factor H-binding protein vaccines. The Journal of infectious diseases 2013. PMID: 23715659


  27. Pajon R, Beernink PT, Granoff DM. Design of meningococcal factor H binding protein mutant vaccines that do not bind human complement factor H. Infection and immunity 2012. PMID: 22615247


  28. Beernink PT, Shaughnessy J, Pajon R, Braga EM, Ram S, Granoff DM. The effect of human factor H on immunogenicity of meningococcal native outer membrane vesicle vaccines with over-expressed factor H binding protein. PLoS pathogens 2012. PMID: 22589720


  29. Giuntini S, Beernink PT, Reason DC, Granoff DM. Monoclonal antibodies to meningococcal factor H binding protein with overlapping epitopes and discordant functional activity. PloS one 2012. PMID: 22461909


  30. Beernink PT, Shaughnessy J, Braga EM, Liu Q, Rice PA, Ram S, Granoff DM. A meningococcal factor H binding protein mutant that eliminates factor H binding enhances protective antibody responses to vaccination. Journal of immunology (Baltimore, Md. : 1950) 2011. PMID: 21325619


  31. Dunphy KY, Beernink PT, Brogioni B, Granoff DM. Effect of factor H-binding protein sequence variation on factor H binding and survival of Neisseria meningitidis in human blood. Infection and immunity 2010. PMID: 21041484


  32. Beernink PT, Shaughnessy J, Ram S, Granoff DM. Impaired immunogenicity of a meningococcal factor H-binding protein vaccine engineered to eliminate factor h binding. Clinical and vaccine immunology : CVI 2010. PMID: 20519444


  33. Pajon R, Beernink PT, Harrison LH, Granoff DM. Frequency of factor H-binding protein modular groups and susceptibility to cross-reactive bactericidal activity in invasive meningococcal isolates. Vaccine 2009. PMID: 20044056


  34. Beernink PT, Granoff DM. The modular architecture of meningococcal factor H-binding protein. Microbiology (Reading, England) 2009. PMID: 19574307


  35. Beernink PT, Caugant DA, Welsch JA, Koeberling O, Granoff DM. Meningococcal factor H-binding protein variants expressed by epidemic capsular group A, W-135, and X strains from Africa. The Journal of infectious diseases 2009. PMID: 19302008


  36. Beernink PT, LoPasso C, Angiolillo A, Felici F, Granoff D. A region of the N-terminal domain of meningococcal factor H-binding protein that elicits bactericidal antibody across antigenic variant groups. Molecular immunology 2009. PMID: 19286260


  37. Beernink PT, Welsch JA, Bar-Lev M, Koeberling O, Comanducci M, Granoff DM. Fine antigenic specificity and cooperative bactericidal activity of monoclonal antibodies directed at the meningococcal vaccine candidate factor h-binding protein. Infection and immunity 2008. PMID: 18591239


  38. Beernink PT, Granoff DM. Bactericidal antibody responses induced by meningococcal recombinant chimeric factor H-binding protein vaccines. Infection and immunity 2008. PMID: 18362128


  39. Cosman M, Pesavento JB, Zemla A, Beernink PT, Balhorn R, Barsky D. Identification of a thermo-regulated glutamine-binding protein from Yersinia pestis. Protein and peptide letters 2008. PMID: 18991762


  40. Beernink PT, Welsch JA, Harrison LH, Leipus A, Kaplan SL, Granoff DM. Prevalence of factor H-binding protein variants and NadA among meningococcal group B isolates from the United States: implications for the development of a multicomponent group B vaccine. The Journal of infectious diseases 2007. PMID: 17436227


  41. Coleman MA, Beernink PT, Camarero JA, Albala JS. Applications of functional protein microarrays: identifying protein-protein interactions in an array format. Methods in molecular biology (Clifton, N.J.) 2007. PMID: 18365708


  42. Beernink PT, Leipus A, Granoff DM. Rapid genetic grouping of factor h-binding protein (genome-derived neisserial antigen 1870), a promising group B meningococcal vaccine candidate. Clinical and vaccine immunology : CVI 2006. PMID: 16829612


  43. Beernink PT, Hwang M, Ramirez M, Murphy MB, Doyle SA, Thelen MP. Specificity of protein interactions mediated by BRCT domains of the XRCC1 DNA repair protein. The Journal of biological chemistry 2005. PMID: 15987676


  44. Coleman MA, Lao VH, Segelke BW, Beernink PT. High-throughput, fluorescence-based screening for soluble protein expression. Journal of proteome research 2004. PMID: 15473692


  45. Coleman MA, Miller KA, Beernink PT, Yoshikawa DM, Albala JS. Identification of chromatin-related protein interactions using protein microarrays. Proteomics 2003. PMID: 14595808


  46. Tolan DR, Schuler B, Beernink PT, Jaenicke R. Thermodynamic analysis of the dissociation of the aldolase tetramer substituted at one or both of the subunit interfaces. Biological chemistry 2003. PMID: 14669989


  47. Pezza JA, Choi KH, Berardini TZ, Beernink PT, Allen KN, Tolan DR. Spatial clustering of isozyme-specific residues reveals unlikely determinants of isozyme specificity in fructose-1,6-bisphosphate aldolase. The Journal of biological chemistry 2003. PMID: 12611890


  48. Beernink PT, Krupka SS, Lao V, Martin G, Coleman MA. Application of In Vitro Protein Expression to Human Prote. TheScientificWorldJournal 2002. PMID: 29973809


  49. Doyle SA, Beernink PT, Koshland DE. Structural basis for a change in substrate specificity: crystal structure of S113E isocitrate dehydrogenase in a complex with isopropylmalate, Mg2+, and NADP. Biochemistry 2001. PMID: 11284679


  50. Beernink PT, Segelke BW, Hadi MZ, Erzberger JP, Wilson DM, Rupp B. Two divalent metal ions in the active site of a new crystal form of human apurinic/apyrimidinic endonuclease, Ape1: implications for the catalytic mechanism. Journal of molecular biology 2001. PMID: 11286553


  51. Beernink PT, Yang YR, Graf R, King DS, Shah SS, Schachman HK. Random circular permutation leading to chain disruption within and near alpha helices in the catalytic chains of aspartate transcarbamoylase: effects on assembly, stability, and function. Protein science : a publication of the Protein Society 2001. PMID: 11344321


  52. Endrizzi JA, Beernink PT, Alber T, Schachman HK. Binding of bisubstrate analog promotes large structural changes in the unregulated catalytic trimer of aspartate transcarbamoylase: implications for allosteric regulation. Proceedings of the National Academy of Sciences of the United States of America 2000. PMID: 10805770


  53. Beernink PT, Endrizzi JA, Alber T, Schachman HK. Assessment of the allosteric mechanism of aspartate transcarbamoylase based on the crystalline structure of the unregulated catalytic subunit. Proceedings of the National Academy of Sciences of the United States of America 1999. PMID: 10318893


  54. Beernink PT, Tolan DR. Disruption of the aldolase A tetramer into catalytically active monomers. Proceedings of the National Academy of Sciences of the United States of America 1996. PMID: 8643582


  55. Beernink PT, Tolan DR. Subunit interface mutants of rabbit muscle aldolase form active dimers. Protein science : a publication of the Protein Society 1994. PMID: 7833800


  56. Beernink PT, Tolan DR. Construction of a high-copy "ATG vector" for expression in Escherichia coli. Protein expression and purification 1992. PMID: 1422227