About

Lorena Sue Beese is the James B. Duke Distinguished Professor of Biochemistry at Duke University and a Professor of Biochemistry. She is a member of the Duke Cancer Institute. Her primary affiliation is with the Duke Department of Biochemistry, where she is involved in research and teaching activities. Her work focuses on biochemistry, and she is part of the faculty contributing to the academic and research missions of Duke University.

Research topics

• Computer Science
• Biology
• Chemistry
• Programming language
• Genetics
• Microbiology
• Biochemistry
• Pharmacology
• Molecular biology

Selected publications

• Library Screening, In Vivo Confirmation, and Structural and Bioinformatic Analysis of Pentapeptide Sequences as Substrates for Protein Farnesyltransferase

  International Journal of Molecular Sciences · 2024-05-13 · 4 citations

  articleOpen access

  Protein farnesylation is a post-translational modification where a 15-carbon farnesyl isoprenoid is appended to the C-terminal end of a protein by farnesyltransferase (FTase). This process often causes proteins to associate with the membrane and participate in signal transduction pathways. The most common substrates of FTase are proteins that have C-terminal tetrapeptide CaaX box sequences where the cysteine is the site of modification. However, recent work has shown that five amino acid sequences can also be recognized, including the pentapeptides CMIIM and CSLMQ. In this work, peptide libraries were initially used to systematically vary the residues in those two parental sequences using an assay based on Matrix Assisted Laser Desorption Ionization-Mass Spectrometry (MALDI-MS). In addition, 192 pentapeptide sequences from the human proteome were screened using that assay to discover additional extended CaaaX-box motifs. Selected hits from that screening effort were rescreened using an in vivo yeast reporter protein assay. The X-ray crystal structure of CMIIM bound to FTase was also solved, showing that the C-terminal tripeptide of that sequence interacted with the enzyme in a similar manner as the C-terminal tripeptide of CVVM, suggesting that the tripeptide comprises a common structural element for substrate recognition in both tetrapeptide and pentapeptide sequences. Molecular dynamics simulation of CMIIM bound to FTase further shed light on the molecular interactions involved, showing that a putative catalytically competent Zn(II)-thiolate species was able to form. Bioinformatic predictions of tetrapeptide (CaaX-box) reactivity correlated well with the reactivity of pentapeptides obtained from in vivo analysis, reinforcing the importance of the C-terminal tripeptide motif. This analysis provides a structural framework for understanding the reactivity of extended CaaaX-box motifs and a method that may be useful for predicting the reactivity of additional FTase substrates bearing CaaaX-box sequences.

  PublisherOA PDFDOI

• Accurate Identification of Periplasmic Urea-binding Proteins by Structure- and Genome Context-assisted Functional Analysis

  Journal of Molecular Biology · 2024-09-04 · 1 citations

  articleOpen access

  ABC transporters are ancient and ubiquitous nutrient transport systems in bacteria and play a central role in defining lifestyles. Periplasmic solute-binding proteins (SBPs) are components that deliver ligands to their translocation machinery. SBPs have diversified to bind a wide range of ligands with high specificity and affinity. However, accurate assignment of cognate ligands remains a challenging problem in SBPs. Urea metabolism plays an important role in the nitrogen cycle; anthropogenic sources account for more than half of global nitrogen fertilizer. We report identification of urea-binding proteins within a large SBP sequence family that encodes diverse functions. By combining genetic linkage between SBPs, ABC transporter components, enzymes or transcription factors, we accurately identified cognate ligands, as we verified experimentally by biophysical characterization of ligand binding and crystallographic determination of the urea complex of a thermostable urea-binding homolog. Using three-dimensional structure information, these functional assignments were extrapolated to other members in the sequence family lacking genetic linkage information, which revealed that only a fraction bind urea. Using the same combined approaches, we also inferred that other family members bind various short-chain amides, aliphatic amino acids (leucine, isoleucine, valine), γ-aminobutyrate, and as yet unknown ligands. Comparative structural analysis revealed structural adaptations that encode diversification in these SBPs. Systematic assignment of ligands to SBP sequence families is key to understanding bacterial lifestyles, and also provides a rich source of biosensors for clinical and environmental analysis, such as the thermostable urea-binding protein identified here.

  PublisherDOI

• Chromophore carbonyl twisting in fluorescent biosensors encodes direct readout of protein conformations with multicolor switching

  Communications Chemistry · 2023-08-19 · 2 citations

  articleOpen access

  Fluorescent labeling of proteins is a powerful tool for probing structure-function relationships with many biosensing applications. Structure-based rules for systematically designing fluorescent biosensors require understanding ligand-mediated fluorescent response mechanisms which can be challenging to establish. We installed thiol-reactive derivatives of the naphthalene-based fluorophore Prodan into bacterial periplasmic glucose-binding proteins. Glucose binding elicited paired color exchanges in the excited and ground states of these conjugates. X-ray structures and mutagenesis studies established that glucose-mediated color switching arises from steric interactions that couple protein conformational changes to twisting of the Prodan carbonyl relative to its naphthalene plane. Mutations of residues contacting the carbonyl can optimize color switching by altering fluorophore conformational equilibria in the apo and glucose-bound proteins. A commonly accepted view is that Prodan derivatives report on protein conformations via solvatochromic effects due to changes in the dielectric of their local environment. Here we show that instead Prodan carbonyl twisting controls color switching. These insights enable structure-based biosensor design by coupling ligand-mediated protein conformational changes to internal chromophore twists through specific steric interactions between fluorophore and protein.

  PublisherOA PDFDOI

• Thermally controlled intein splicing of engineered DNA polymerases provides a robust and generalizable solution for accurate and sensitive molecular diagnostics

  Nucleic Acids Research · 2023-05-11 · 8 citations

  articleOpen accessSenior author

  DNA polymerases are essential for nucleic acid synthesis, cloning, sequencing and molecular diagnostics technologies. Conditional intein splicing is a powerful tool for controlling enzyme reactions. We have engineered a thermal switch into thermostable DNA polymerases from two structurally distinct polymerase families by inserting a thermally activated intein domain into a surface loop that is integral to the polymerase active site, thereby blocking DNA or RNA template access. The fusion proteins are inactive, but retain their structures, such that the intein excises during a heat pulse delivered at 70-80°C to generate spliced, active polymerases. This straightforward thermal activation step provides a highly effective, one-component 'hot-start' control of PCR reactions that enables accurate target amplification by minimizing unwanted by-products generated by off-target reactions. In one engineered enzyme, derived from Thermus aquaticus DNA polymerase, both DNA polymerase and reverse transcriptase activities are controlled by the intein, enabling single-reagent amplification of DNA and RNA under hot-start conditions. This engineered polymerase provides high-sensitivity detection for molecular diagnostics applications, amplifying 5-6 copies of the tested DNA and RNA targets with >95% certainty. The design principles used to engineer the inteins can be readily applied to construct other conditionally activated nucleic acid processing enzymes.

  PublisherOA PDFDOI

• Structure-Guided Discovery of Potent Antifungals that Prevent Ras Signaling by Inhibiting Protein Farnesyltransferase

  Journal of Medicinal Chemistry · 2022 · 12 citations

  Senior authorCorresponding
  • Chemistry
  • Biochemistry
  • Pharmacology

  levels of enzyme and farnesyl substrate. We elucidated how chemical modifications of the antifungals encode desired inhibitor conformation and concomitant inhibitory mechanism.

  PublisherOA PDFDOI

• Structure-guided design of <i>Cryptococcus neoformans</i> protein farnesyltransferase inhibitors with antifungal activity

  Acta Crystallographica Section A Foundations and Advances · 2021-07-30

  articleOpen accessSenior author

  Invasive fungal infections are pervasive and often life threatening, resulting in over 11.5 million life-threatening infections. Cryptococcus neoformans is a major human fungal pathogen causing over 160,000 deaths each year. The options for threating C. neoformans infections are limited and the drug resistance is emerging and spreading. Therefore, there is a need for new therapeutics. Protein farnesyltransferase (FTase) is essential for the virulence of C. neoformans, providing opportunities to develop species specific FTase inhibitors for treating infectious diseases.

  PublisherOA PDFDOI

• Structural basis for the 3′ – 5′ exonuclease activity of <i>Escherichia coli</i> DNA polymerase I: a two metal ion mechanism

  WORLD SCIENTIFIC eBooks · 2020-08-29

  book-chapter1st authorCorresponding
  PublisherDOI

• Cocrystal structure of an editing complex of klenow fragment with dna (3'-5' exonuclease dna polymerase protein-dna interaction x-ray crystallography/metal ion catalysis)

  2020-01-01

  article
  Publisher

• Investigation of ATP-induced global motions of the human DNA mismatch repair sensor complex using time-lapse crystallography 

  Acta Crystallographica Section A Foundations and Advances · 2020-08-02

  articleOpen accessSenior author

  Over 1 in 300 people in the US have Lynch syndrome (hereditary nonpolyposis colorectal cancer, HNPCC), which is caused by mutations in DNA mismatch repair (MMR) genes. Over 40% of the Lynch syndrome mutations are found in the human MSH2 gene, which is the common subunit that forms the key MMR lesion sensors MutS (MSH2-MSH6) and MutS (MSH2-MSH3). MSH2 mutations are also identified in over ten other cancer types. The MutS proteins are members of the ABC ATPase family that undergo large conformational rearrangements upon binding/hydrolysis of ADP/ATP. Here we present our time-lapse X-ray crystallography studies to demonstrate the conformational changes of MSH2 as it transitions from ATP to ADP bound states. A dramatic and global conformational rearrangement is triggered after ATP hydrolysis, which spans over 150 and causes over 60-degree domain rotations. Time-lapse crystallographic results reveal a network of interactions that link the ABC ATPase center to the DNA binding domains. Moreover, a nascent globular domain formed only in specific nucleotide states has been identified, which is stabilized by residues that are variants of unknown significance in Lynch syndrome and other cancers. Our findings provide new insights into the mechanism of MMR and could aid the development of better colorectal cancer risk prediction models and personalized therapeutic strategies. These results may also extend the understanding of the mechanism of other ABC ATPase family proteins.

  PublisherOA PDFDOI

• Cocrystal structure of an editing complex of Klenow fragment with DNA

  WORLD SCIENTIFIC eBooks · 2020 · 15 citations

  • Computer Science
  • Programming language
  • Computer Science
  PublisherDOI

Recent grants

• NIH Grant R01GM091487

  NIH · $647k · 2012

• NIH Grant R37GM052382

  NIH · $3.5M · 2016

• NIH Grant R01GM052382

  NIH · $1.8M · 2004

• Transdisciplinary Program to Identify Novel Antifungal Targets and Inhibitors

  NIH · $3.8M · 2015–2020

Frequent coauthors

• Homme W. Hellinga

  Duke University Hospital

  57 shared

• Patrick J. Casey

  Geological Survey of Sweden

  50 shared

• Michael A. Hast

  30 shared

• Stephen B. Long

  Memorial Sloan Kettering Cancer Center

  25 shared

• Paul Modrich

  Howard Hughes Medical Institute

  25 shared

• K.L. Terry

  Duke University Hospital

  21 shared

• Anita Changela

  National Institutes of Health

  21 shared

• Thomas A. Steitz

  Yale University

  21 shared

Labs

• Beese LabPI