Lustig, Brooke S

Publications & Presentations

Selected Publications/Proceedings at SJSU

Huynh , A. T., Nguyen, T.-T. N., Villegas. C. A., Montemorso, S., Strauss, B., Graham, J. G., Oribello, J. O., Suresh, R., Lustig, B. & Wang, N. Prediction and Confirmation of a Switch-like Region within the N-terminal Domain of hSIRT1. Biochem. Biophys. Rep. 30, 101275 (1-7).
Available online May 19, 2022 (https://doi.org/10.1016/j.bbrep.2022.101275) 

Kimura, T., Yasuo, N., Sekijima, M. & Lustig, B. “Statistical potentials for RNA-protein interactions optimized by CMA-ES” (2022) J. Mol. Graph. Model. 110, 108044(1-10). Available online October 7, 2021 (https://doi.org/10.1016/j.jmgm.2021.108044)

Liao, H., Yeh, W., Chiang, D., Jernigan, R. L. and Lustig, B. “Protein sequence entropy is closely related to packing density and hydrophobicity” (2005) Prot. Engr. 18, 59-64.

Wander, D. S., Yang, F., McNeil, M & Lustig, B. “Scoring DNA sequence alignment using energetics of hybridization” (2003) Proceedings of Annual Meeting of American Institute of Chemical Engineers T2/555b(1-8).

Hsieh, M., Collins, E. D., Blomquist, T. & Lustig, B. "Flexibility of BIV TAR-Tat: Models of peptide binding" (2002) J. Biomol. Struct. Dyn. 20, 243-251.

Lustig, B. & Jeang K.-T. "Biological applications of hammerhead ribozymes as anti-viral molecules" (2001) Current Medicinal Chemistry 8, 1181-1187.

Lustig, B., Bahar, I. & Jernigan, R. L. "RNA bulge entropies correlate with peptide binding strengths for HIV-1 and BIV TAR RNA because of improved conformational access" (1998) Nucleic Acids Res. 26, 5212-5217.

Lustig, B., Arora, S. & Jernigan, R. L. "RNA base-amino acid interaction strengths derived from structures and sequences" (1997) Nucleic Acids Res. 25, 2562-2565.

Lustig, B. & Jernigan, R. L. "Consistencies of individual DNA base-amino acid interactions in structures and sequences" (1995) Nucleic Acids Res. 23, 4707-4711.

Selected Presentations

Wang, N., Nguyen, T.-T., Armaya, C., Huynh, A., Montermoso, S., Strauss, B., Oribello, J. &  Lustig, B. "Identifying a switch-like region within the N-terminal domain of SIRT1" (2021) Annual Meeting of American Society for Biochemistry and Molecular Biology Abstracts. FASEB J. 35 (S1), 2952.

Oribello, J.  Strauss, B., Qi, C., Huynh, A., Millan, E., Cao, K., Wang, N. & Lustig, B. Identification of switch-like features in proteins using sequence-based descriptors modelled from regions identified in X-ray crystal structures. (2020) 64th Biophysical Society Meeting Abstracts Biophys. J. 18 (S1), 44A.

Wang, N., Nguyen, T.-T., Armaya, C., Huynh, A., Montermoso, S., Strauss, B., Oribello, J. &  Lustig, B.    Identifying a switch-like region within the N-terminal domain of SIRT1. (2021) Annual Meeting of American Society for Biochemistry and Molecular Biology Abstracts. FASEB J. 35 (S1), 2952.

Do, S., Lakkaraju, H., Potluri, S., Pham, K., Kantardjieff, K. and Lustig, B. “Protein Sequence Homology Parameters Applied to the Prediction of Solvent Accessible Residues” (2008) 52nd Biophysical Society Meeting Abstracts. Biophys. J. 94, Supplement, 3280-Pos.

Lustig, B. “CSU Cyberinfrastructure: How Much is Enough” Twentieth CSU Biotechnology Symposium (2008).

Theses and Thesis Project Reports (Research Advisor, since 2015)

Strauss, B. Predicting Switch-Like Behavior in Proteins Using Logistic Regression on Sequence-Based Descriptors M.S. Thesis. San Jose State University (published January 14 2020).

Ma, C. Exploring van der Waals and Other Interactions in the Development of RNA-Protein Statistical Potentials. M.S. Thesis Project Report. San Jose State University (2018). 

Graham, J. Computational Characterization of Sequences with Multiple Conformational Propensities in the Sirtuin Family of NAD+-Dependent Histone Deacetylases. M.S. Thesis Project Report (2018).

Le, T. Computational Models Exploring the Role of Flexibility in Binding Tat Peptide to TAR RNA. M.S. Thesis. San Jose State University (2018).

Rodriguez, M. Evaluation of a NovelPropensity-Based Statistical Potential. M.S, Thesis Project Report. San Jose State University (2017).

Kimura, T. RNA-Protein Structure Classifiers Incorporated into Second-Generation Statistical Potentials. M.S. Thesis. San Jose State University (2016).

Soshnikov, A. Analysis of Non-Covalent RNA-Protein Interactions. M.S. Thesis Project Report. San Jose State University (2016).

Nguyen, L. BIV TAR RNA Binding Glycine Mutant Peptides: An Integrated Modeling and Binding Assay Approach. M.S. Thesis. San Jose State University (2015).

Other Publications

Lustig, B., Lin, N. H., Smith, S. M., Jernigan, R. L. and Jeang, K.-T. "A small modified hammerhead ribozyme and its conformational characteristics determined by mutagenesis and lattice calculation" (1995) Nucleic Acids Res. 23, 3531-3538.

Lustig, B., Covell, D. G. & Jernigan, R. L. "Conformations of t-RNA: Base pairing and stacking" (1994) J. Biomol. Struct. Dyn. 12, 145-161.

Lustig, B. & Fink, A. L. "Secondary structure formation precedes tertiary structure in the refolding of ribonuclease A" (1992) Biochim. Biophys. Acta. 1121, 229-233.

Lustig, B. & Fink, A. L. "The thermal denaturation of ribonuclease A in aqueous methanol solvents" (1992) Biochim. Biophys. Acta. 1119, 205-210.

Fink, A. L., Anderson, W. D., Hattersly, J. E. & Lustig, B. "The effect of methanol and temperature on the kinetics of refolding of ribonuclease A" (1988) FEBS Lettr. 236, 190-194.

Other Presentations (since 2015)

Pearson, R., Strauss, B., Oribello, J., Le, Q., Wang, N. & Lustig, B. Prediction from Sequence of a Switch-like Region Within the N-Terminal Domain of SIRT1. 66th Biophysical Society Annual Meeting. San Francisco, CA. LB1-Pos.

Tong, H.,  Duong, L., Balaji, A. & Lustig, B. Characterization of Bridging Waters in a Diverse Set of RNA-Protein Complexes. (2021) Thirty-third CSU Annual Biotechnology Symposium, Poster-11.

Strauss, B., Qi, C., Oribello, J., Huynh, A., Millan, E., Cao, K., Wang, N. & Lustig, B. Switch-like Features in Proteins Using Logistic Regression with Sequence-Based Descriptors Compared to Regions Identified in X-ray Crystal Structures. (2020) Thirty-second CSU Annual Biotechnology Symposium, Poster-175.

Strauss, B., Huynh, A., Millan, E., Cao, K., Tran, P., Nguyen, M., Oribello, J., Montermoso, S., Wang, N. & Lustig, B. (2019) Predicting Switch-Like Features in Proteins Using Logistic Regression with Sequence-Based Descriptors. Thirty-First Annual American Chemical Society Northern California Undergraduate Research Symposium, Poster 23.

Le, T., Ma, C., Suwandi, E., Fozo, F., Le, T. T., Patel, M., Mir, V. & Lustig, B. Characterizing Alternative RNA-Protein Interactions for BIV Tat Peptide Binding to TAR. (2019) Thirty-First Annual American Chemical Society Northern California Undergraduate Research Symposium, Poster 75.

Huynh, A., Veeraklaew, M., Oribello, J., Montermoso, S., Buckley, D. Kuhn, M. & 
Lustig, B. Sequence Entropy and Flexibility Descriptors Identify a Possible Conformational Switch in Allosteric Dodecameric Polyamine Acetyltransferase SpeG. Thirtieth CSU Annual Biotechnology Symposium (2018). Poster 59.

Montermoso, S., Oribello, J., Huynh, A., Graham, J., Wang, N., Kuhn, M. L. & Lustig, B. Sequence Entropy and Other Descriptors Identify a Possible Conformational Switch: Case Study of an Allosteric Dodecameric Polyamine Acetyltransferase SpeG. 62nd Annual Meeting Biophysical Society (2018) Poster LB7. 

Soshnikov, A., Kimura, T., Rodriguez, M., Le, T. Park, A., Yu, D. & Lustig, B. Second-Generation RNA-Protein Statistical Potentials: Additional Refinements by Structure Class and Atom Type. (2017) Twenty-ninth CSU Annual Biotechnology Symposium, Poster 200.

Yu, D., Le, T., Rodriguez, M., Kimura, T., Soshnikov, A., Park, A. & Lustig, B. Computational Models Characterizing the Role of Flexibility in Binding Tat Peptides to TAR RNA. (2017) Twenty-ninth Annual American Chemical Society Northern California Undergraduate Research Symposium, Poster  7.

Montermoso, S., Oribello, J., Bagherinia, A. & Lustig, B. Topology-based Logistic Models for Predicting Interfacial Residues. (2016) Twenty-eighth Annual American Chemical Society Northern California Research Symposium, Poster 55.

Tran, P., Le, T. Q., Soshnikov, A., Kimura, T. & Lustig, B. Binding of Mutant Tat Peptides to TAR RNA as a Model for Developing Hierarchical Methods Utilizing RNA-Protein Statistical Potentials. (2016) Twenty-eighth Annual American Chemical Society Northern California Research Symposium, Poster 39.

Montermoso, S., Kadiyala, S., Oribello, J., Omictin, G., Tran, R., Pineda, L. C., Bros, S., Kantardjieff, K., Gottlieb, A. & Lustig, B. Exploring Sequence and Homology Signals in the Prediction of Protein Residue Solvent Accessibility with Logistic Regression Models. (2015) Annual Meeting Biology and Mathematics Bay Area, San Jose, CA, Poster.

Kimura, T., Tran, P. & Lustig, B. RNA-Protein Structure Classifiers Incorporated into Second-Generation Statistical Potentials. (2015) Annual Meeting Biology and Mathematics Bay Area, San Jose, CA, Poster.

Bhogal, G., Kamath, T., Omictin, G., Oribello, J., Gottlieb, A. & Lustig, B. Tertiary Contact Propensity as a Predictor in Logistic Regression for Determining Solvent Accessible Protein Regions (2015) 40th Annual West Coast Biological Sciences Undergraduate Research Conference, P63. 

Kamath, T., Bhogal, G., Poelman, T., Bros-Seeman, S., Kantardjieff, K., Gottlieb, A. & Lustig, B. Integration of Disordered Residue Propensity as a Predictor in Logistic Regression for Determining Solvent Accessible Elements. (2015) Twenty-seventh Annual CSU Biotechnology Symposium, Santa Clara, CA, Poster 50.

Nguyen, T., Tran, P., Kimura, T., Park, A., Cesare, A., Shalan, R. & Lustig, B. Development of Second Generation RNA-Protein Statistical Potentials. (2015) Twenty-seventh Annual CSU Biotechnology Symposium, Santa Clara, CA, Poster 51.