Thomas James, PhD

What I do

I retired from full-time service at UCSF at the end of June, 2012. However, I went on Recall status a month later to do research, which diminishes each year. I needed to finish some projects that were still funded via grants during the initial year and continue with another funded project subsequently.

Departmental research area

My research expertise

nuclear magnetic resonance (NMR), structural biology, nucleic acids, computational drug discovery


1. We aim to understand the role of RNA in selected biological processes and, in certain cases, to modify those biological processes if therapy for a disease can result. In practice, that means we study (a) RNA/protein systems, (b) small molecule-macromolecule interactions, and (c) use of three-dimensional RNA structures and computational search algorithms to discover novel ligands that can serve as lead compounds for drug discovery.

2. We extend the methodologies of using computational search algorithms and NMR in tandem to find novel ligands to bind to important protein targets. These ligands can serve as leads for drug therapy or diagnostics.

There are several reasons for RNA as a fascinating subject for study: importance for biology, dearth of information extant, applicability of NMR and x-ray crystallography given recent methodological and labeling developments, and (perhaps most important) challenge. Studies on a few different systems have been carried out in our lab but, in the waning years of my research career, I have narrowed our lab’s current research interest to Retroviral Packaging. Replication of retroviruses, such as human immunodeficiency virus type-1 (HIV-1), entails packaging of two identical, noncovalently linked copies of full length genomic RNA into each new virus particle. This 'dimer packaging' is governed by specific sequences and their interaction with the nucleocapsid moiety of the Gag polyprotein. The RNA strands first interact by base-pairing via a six-base palindrome in the loop of a stem-loop, SL1, to form a “kissing dimer” and subsequently rearrange into a mature form of the packaged dimer (“extended dimer” or “linear dimer”). Using NMR we have solved the structures of the intermediate loop-loop homodimer (KD) formed by a truncated version of SL1 as well as other structures more similar to the mature dimer (ED), yielding some insight into the crucial, but complicated, packaging process. We have also used NMR and other techniques to investigate the mechanism of the conversion from the KD to ED forms.
We have been developing a strategy to discover novel ligands based on detailed three-dimensional RNA or protein structure. While there has been much effort to design diagnostic and therapeutic agents that bind to protein receptors based on their three-dimensional structure, there has been little effort to design drugs rationally on the basis of the sequence-dependent three-dimensional structure of DNA or RNA. We have been working on a rapid, cost-effective means of identifying novel ligands that can bind to selected RNA targets that apparently have unique 3D structure. The tandem approach utilizes computational screening of a selected database of small molecules followed by screening of the most promising computational “hits” by NMR. In this regard, we have developed the docking program MORDOR, which has the capability for induced fitting of ligand to receptor by permitting flexibility in both ligand and receptor during the docking procedure. To date, we have found novel small molecules that can bind with preference for the selected target in the HIV-1 genome and in the human telomerase RNA.

In a collaborative study, we have also been exploring appropriate use of computational screening together with NMR and SPR (surface plasmon resonance) to find small molecules that can bind to AAA ATPase p97/VCP. p97 is a key player in the endoplasmic reticulum-associated degradation (ERAD) of misfolded secretory and membrane proteins as well as ubiquitin-dependent turnover of a certain cytoplasmic substrates of the ubiquitin-proteasome system (UPS). As such, it is a target for developing drugs that may be useful anticancer agents.

Research keywords

  • Brain Chemistry
  • DNA
  • Phenothiazines
  • Nucleic Acid Conformation
  • Magnetic Resonance Spectroscopy
  • Viral RNA
  • Gene Products, tat
  • RNA-Binding Proteins
  • Oligodeoxyribonucleotides
  • Dimerization
  • Molecular Models
  • Nuclear Magnetic Resonance, Biomolecular
  • HIV-1
  • HIV Long Terminal Repeat
  • RNA