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# Laboratory of Molecular Biology

Susan K. Buchanan, Ph.D.
Chief
**susan.buchanan2@nih.gov

Yihong Ye, Ph.D.
Deputy Chief
**yihong.ye@nih.gov

About the Lab

- Lab Sections
-  About the Lab 

## Lab Sections and Chiefs

          -  Developmental Biology Section                      Michael W. Krause, Ph.D.                
          -  Genetic Mechanisms Section                      Kiyoshi Mizuuchi, Ph.D., NIH Distinguished Investigator                
          -  Mechanism of DNA Repair, Replication, and Recombination Section                      Wei Yang, Ph.D., NIH Distinguished Investigator                
          -  Molecular Genetics Section                      Martin Gellert, Ph.D., NIH Distinguished Investigator                
          -  Molecular Virology Section                      Robert Craigie, Ph.D.                
          -  Protein Stability and Quality Control Section                      Yihong Ye, Ph.D.                
          -  Section on Nuclear Mechanotransduction and Cell Fate Dynamics                      Yekaterina (Kate) Miroshnikova, Ph.D., Stadtman Tenure-Track Investigator                
          -  Structural Biochemistry Section                      Frederick Dyda, Ph.D.                
          -  Structural Biology of Membrane Proteins Section                      Susan K. Buchanan, Ph.D.                
          -  Structural Biology of Noncoding RNAs and Ribonucleoproteins Section                      Jinwei Zhang, Ph.D.                

### Developmental Biology Section

Michael W. Krause, Ph.D.,Section Chief        

        The Developmental Biology Section investigates the transcriptional regulation of cell fate determination during metazoan development. Using the *C. elegans* system, we exploit forward and reverse genetic approaches to identify and characterize transcription factor function required for proper development of specific cell types, at single-cell resolution. Historically, our interest has primarily been directed at understanding muscle cell specification and differentiation as a model for both embryonic and postembryonic development. Our goal is to fully describe the transcriptional cascade that orchestrates the formation of this tissue from just after fertilization, throughout embryogenesis, and into adulthood.    

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### Genetic Mechanisms Section

Kiyoshi Mizuuchi, Ph.D., NIH Distinguished Investigator,Section Chief        

        The Genetic Mechanisms Section investigates the mechanics of cellular processes that impact the genomic structure and the heritance of the genomic material. We study mechanisms of reactions that impact the stability of the linear organization of the genome, as well as the 3-dimensional dynamics involved in the heritance of bacterial chromosomes.    

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### Mechanism of DNA Repair, Replication, and Recombination Section

Wei Yang, Ph.D., NIH Distinguished Investigator,Section Chief        

        The Mechanism of DNA Repair, Replication, and Recombination Section is interested in studying DNA recombination, repair, and replication. In particular, we are interested in V(D)J recombination, mismatch repair, nucleotide excision repair, and translesion DNA synthesis. We use X-ray crystallography, molecular biology, and various biochemical and biophysical approaches to find out the molecular mechanisms in these biological processes.    

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### Molecular Genetics Section

Martin Gellert, Ph.D., NIH Distinguished Investigator,Section Chief        

        The Molecular Genetics Section studies the rearrangement of immunoglobulin and T-cell receptor genes (known as V(D)J recombination). This process is essential for the development of lymphoid cells and is unique in sharing some properties with site-specific recombination and with the repair of radiation damage to DNA. Our aim is to understand V(D)J recombination in detail and to apply this knowledge to the immune system. Our research has shown that recombination begins with site-specific DNA breaks, which can be made by the isolated RAG1 and RAG2 proteins, and that a DNA hairpin is produced on one side of each break. This reaction shares many properties with mobile genetic elements (transposons), and we are interested in the potential role of transposition in causing chromosomal translocations of the types found in leukemias and lymphomas. Researchers in this section are also investigating the separate ubiquitin ligase activity of RAG1 and its covalent modification by auto-ubiquitylation.    

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### Molecular Virology Section

Robert Craigie, Ph.D.,Section Chief        

        The Molecular Virology Section focuses on mechanistic aspects of retroviral DNA integration. After entering the host cell, a DNA copy of the viral genome is made by reverse transcription. Integration of this viral DNA into a chromosome of the host cell is an essential step in the retroviral replication cycle. The key player in the retroviral DNA integration process is the virally encoded integrase protein. Integrase processes the ends of the viral DNA and covalently inserts these processed ends into host DNA. We study the molecular mechanism of these reactions using biochemical, biophysical, and structural techniques. Researchers in this section collaborate closely with NIDDK colleagues who use X-ray crystallography and NMR.  Our work also investigates cellular proteins that play important accessory roles in the integration process. Of particular interest is the mechanism that prevents integrase using the viral DNA as a target for integration. Such autointegration would result in destruction of the viral DNA. We have identified a cellular protein, which we called barrier-to-autointegration factor (BAF) that prevents integration of the viral DNA into itself. Our studies suggest that compaction of the viral DNA by BAF makes it inaccessible as a target for integration.    

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### Protein Stability and Quality Control Section

Yihong Ye, Ph.D.,Section Chief        

        The Protein Stability and Quality Control Section (1) performs research using in vitro reconstitution and cell-based assays to elucidate the cellular mechanisms underlying protein quality control at the endoplasmic reticulum (ER); (2) develops reagents and tools to disrupt ER protein homeostasis and evaluates their activities in anti-cancer therapy; (3) studies the catalysis mechanisms for various enzymes in the ubiquitin proteasome system; (4) extends our studies to address fundamental questions in other protein quality control systems; and (5) supports the career development of research trainees in scientific or biomedical pursuits.    

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### Section on Nuclear Mechanotransduction and Cell Fate Dynamics

Yekaterina (Kate) Miroshnikova, Ph.D., Stadtman Tenure-Track Investigator,Acting Section Chief        

We study how cells sense and integrate mechanical and chemical information from their environment to control cell state and behavior. We are particularly interested how the nucleus responds to these mechanochemical signals to alter chromatin architecture and gene expression. Our interdisciplinary research combines scale-bridging tools ranging from tissue-level live imaging, mechanical manipulation, and various genomics approaches to nanoscale atomic force microscopy to understand fundamental principles of cell and tissue maintenance and how this regulation becomes perturbed in cancer.

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### Structural Biochemistry Section

Frederick Dyda, Ph.D.,Section Chief        

        The Structural Biochemistry Section studies the molecular mechanisms underlying protein activity modulation. To function properly, cells must coordinate and choreograph a large number of simultaneous events and processes. Proteins carry out these essential processes. We primarily use X-ray crystallography to study how cells regulate the activity and function of protein-protein and protein-DNA complexes. X-ray crystallography produces high-resolution "snapshots" to visualize subtle changes in protein structure that often accompany functional regulation. With these snapshots in hand, we use a variety of biochemical, biophysical and simulation approaches to relate their structures and biological functions. Specific projects investigate how proteins control the movement of mobile genetic elements, such as transposons or viruses. One of our current areas of emphasis is the Rep protein of adeno-associated virus (AAV). This protein catalyzes the integration of the AAV genome into a specific locus in human chromosome 19, making it an extremely useful tool for gene therapy studies. In addition, we are studying how a ubiquitous group of chaperone proteins known as 14-3-3s are able to direct when and where in a cell to deliver proteins that regulate gene expression.    

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### Structural Biology of Membrane Proteins Section

Susan K. Buchanan, Ph.D.,Section Chief        

        The Structural Biology of Membrane Biology Section focuses on the structure determination of integral membrane proteins by x-ray crystallography and functional analysis of these proteins using biophysical, biochemical, and cell biological techniques. We study transporters embedded in the outer membranes of Gram-negative bacteria, which are surface accessible and therefore have the potential to be good vaccine and/or drug targets against infectious diseases. We also study the membrane-associated, or soluble protein, partners that interact with outer membrane transporters to better understand how these systems function in vivo. Current topics in the lab include (1) small molecule and protein import across the bacterial outer membrane, (2) protein secretion by pathogenic bacteria, and (3) protein import across mitochondrial outer membranes. Our lab currently studies several distinct proteins.  Some are common to many different kinds of bacteria and are required for their survival, while others are uniquely involved in the development of *E. coli* or *Yersinia pestis* (the bacteria that causes the plague) infections. Recently, we have also started to study mammalian proteins, which may play a role in the progression of neurodegenerative states like Alzheimer’s and Parkinson’s diseases.    

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### Structural Biology of Noncoding RNAs and Ribonucleoproteins Section

Jinwei Zhang, Ph.D.,Section Chief        

        The Structural Biochemistry of Noncoding RNAs and Ribonucleoproteins Section performs research to gain a detailed structural and mechanistic understanding of cellular and viral noncoding RNAs and their associated ribonucleoprotein complexes involved in gene regulation and human diseases. We are working to uncover general motifs and principles that govern RNA tertiary structure formation, RNA recognition by another RNA or protein, and how dynamic RNA structures contribute to the regulation of gene expression and human pathophysiology. Current research topics include: [1] Structure, mechanism, targeting, and engineering of gene-regulatory riboswitches. [2] tRNA-mediated stress sensing and response pathways in eukaryotes. [3] HIV and other viral RNA structures and their protein complexes.    

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