Amanda Liu - Academia.edu (original) (raw)

Papers by Amanda Liu

Proceedings of The National Academy of Sciences, 2010

Evolutionary relationships may exist among very diverse groups of proteins even though they perfo... more Evolutionary relationships may exist among very diverse groups of proteins even though they perform different functions and display little sequence similarity. The tailed bacteriophages present a uniquely amenable system for identifying such groups because of their huge diversity yet conserved genome structures. In this work, we used structural, functional, and genomic context comparisons to conclude that the head-tail connector protein and tail tube protein of bacteriophage λ diverged from a common ancestral protein. Further comparisons of tertiary and quaternary structures indicate that the baseplate hub and tail terminator proteins of bacteriophage may also be part of this same family. We propose that all of these proteins evolved from a single ancestral tail tube protein fold, and that gene duplication followed by differentiation led to the specialized roles of these proteins seen in bacteriophages today. Although this type of evolutionary mechanism has been proposed for other systems, our work provides an evolutionary mechanism for a group of proteins with different functions that bear no sequence similarity. Our data also indicate that the addition of a structural element at the N terminus of the λ head-tail connector protein endows it with a distinctive protein interaction capability compared with many of its putative homologues. macromolecular assembly | protein evolution | unstructured protein A s the proteins existing in nature arose through diversification from a small primordial set, many evolutionarily related groups of proteins must exist that no longer share a common function or detectable sequence identity. However, the identification of such related groups is challenging because sequence similarity is the major criterion for establishing evolutionary connections between proteins. Comparative analysis of bacteriophage (phage) genomes provides a unique opportunity for tracing distant evolutionary relationships. Phage proteins are tremendously diverse and many that are clearly related through evolution bear no sequence similarity. Nevertheless, the conserved genome organization among highly diverged phages allows functional and evolutionary connections to be made even in the absence of sequence similarity (1-3). Furthermore, the sequences of tens of thousands of phage and prophage proteins are present in the databases, providing a superb resource for bioinformatic and evolutionary studies. The advantages of phage-based investigations are exemplified by studies on phage Cro proteins, which provided a description of one of the few clearly documented cases of protein fold evolution (4). In the work presented here, we investigated two phage λ virion proteins that bear no detectable sequence similarity and perform different functions, yet possess the same fold. This structural similarity prompted us to address the question of whether these proteins arose from a common ancestral protein.

Journal of Molecular Biology, 2009

The tail terminator protein (TrP) plays an essential role in phage tail assembly by capping the r... more The tail terminator protein (TrP) plays an essential role in phage tail assembly by capping the rapidly polymerizing tail once it has reached its requisite length and serving as the interaction surface for phage heads. Here, we present the 2.7-Å crystal structure of a hexameric ring of gpU, the TrP of phage λ. Using sequence alignment analysis and site-directed mutagenesis, we have shown that this multimeric structure is biologically relevant and we have delineated its functional surfaces. Comparison of the hexameric crystal structure with the solution structure of gpU that we previously solved using NMR spectroscopy shows large structural changes occurring upon multimerization and suggests a mechanism that allows gpU to remain monomeric at high concentrations on its own, yet polymerize readily upon contact with an assembled tail tube. The gpU hexamer displays several flexible loops that play key roles in head and tail binding, implying a role for disorder-to-order transitions in controlling assembly as has been observed with other λ morphogenetic proteins. Finally, we have found that the hexameric structure of gpU is very similar to the structure of a putative TrP from a contractile phage tail even though it displays no detectable sequence similarity. This finding coupled with further bioinformatic investigations has led us to conclude that the TrPs of non-contractiletailed phages, such as λ, are evolutionarily related to those of contractiletailed phages, such as P2 and Mu, and that all long-tailed phages may utilize a conserved mechanism for tail termination.

Journal of Molecular Biology, 2007

During the late stages of lambda bacteriophage assembly, the protein gpU terminates tail polymeri... more During the late stages of lambda bacteriophage assembly, the protein gpU terminates tail polymerization and participates at the interface between the mature capsid and tail components. When it engages the lambda tail, gpU undergoes a monomer-hexamer transition to achieve its biologically active form. Towards understanding how gpU participates in multiple protein-protein interactions, we have solved the structure of gpU in its monomeric state using NMR methods. The structure reveals a mixed alpha/beta motif with several dynamic loops at the periphery. Addition of 20 mM MgCl(2) is known to oligomerize gpU in the absence of its protein partners. Multiple image analysis of electron micrographs revealed ring-like structures of magnesium ion saturated gpU with a 30 A pore, consistent with its function as a portal for the passage of viral DNA into the host bacterium. The ability of magnesium ions to promote oligomerization was lost when substitutions were made at a cluster of acidic amino acids in the vicinity of helix alpha2 and the beta1-beta2 loop. Furthermore, substitutions at these sites abolished the biological activity of gpU.

Journal of Biomolecular Nmr, 2005

... Lizbeth Edmondsa, Ramanan Thirumoorthya, Amanda Liub, Alan Davidsonb & Logan Donaldsona,*... more ... Lizbeth Edmondsa, Ramanan Thirumoorthya, Amanda Liub, Alan Davidsonb & Logan Donaldsona,* aDepartment of Biology, Biomolecular Expression and ... a Bruker Avance DRX 600 MHz equipped with a room temperature triple resonance probehead and a Varian Unity Inova ...

Proceedings of The National Academy of Sciences, 2010

Evolutionary relationships may exist among very diverse groups of proteins even though they perfo... more Evolutionary relationships may exist among very diverse groups of proteins even though they perform different functions and display little sequence similarity. The tailed bacteriophages present a uniquely amenable system for identifying such groups because of their huge diversity yet conserved genome structures. In this work, we used structural, functional, and genomic context comparisons to conclude that the head-tail connector protein and tail tube protein of bacteriophage λ diverged from a common ancestral protein. Further comparisons of tertiary and quaternary structures indicate that the baseplate hub and tail terminator proteins of bacteriophage may also be part of this same family. We propose that all of these proteins evolved from a single ancestral tail tube protein fold, and that gene duplication followed by differentiation led to the specialized roles of these proteins seen in bacteriophages today. Although this type of evolutionary mechanism has been proposed for other systems, our work provides an evolutionary mechanism for a group of proteins with different functions that bear no sequence similarity. Our data also indicate that the addition of a structural element at the N terminus of the λ head-tail connector protein endows it with a distinctive protein interaction capability compared with many of its putative homologues. macromolecular assembly | protein evolution | unstructured protein A s the proteins existing in nature arose through diversification from a small primordial set, many evolutionarily related groups of proteins must exist that no longer share a common function or detectable sequence identity. However, the identification of such related groups is challenging because sequence similarity is the major criterion for establishing evolutionary connections between proteins. Comparative analysis of bacteriophage (phage) genomes provides a unique opportunity for tracing distant evolutionary relationships. Phage proteins are tremendously diverse and many that are clearly related through evolution bear no sequence similarity. Nevertheless, the conserved genome organization among highly diverged phages allows functional and evolutionary connections to be made even in the absence of sequence similarity (1-3). Furthermore, the sequences of tens of thousands of phage and prophage proteins are present in the databases, providing a superb resource for bioinformatic and evolutionary studies. The advantages of phage-based investigations are exemplified by studies on phage Cro proteins, which provided a description of one of the few clearly documented cases of protein fold evolution (4). In the work presented here, we investigated two phage λ virion proteins that bear no detectable sequence similarity and perform different functions, yet possess the same fold. This structural similarity prompted us to address the question of whether these proteins arose from a common ancestral protein.

Journal of Molecular Biology, 2009

The tail terminator protein (TrP) plays an essential role in phage tail assembly by capping the r... more The tail terminator protein (TrP) plays an essential role in phage tail assembly by capping the rapidly polymerizing tail once it has reached its requisite length and serving as the interaction surface for phage heads. Here, we present the 2.7-Å crystal structure of a hexameric ring of gpU, the TrP of phage λ. Using sequence alignment analysis and site-directed mutagenesis, we have shown that this multimeric structure is biologically relevant and we have delineated its functional surfaces. Comparison of the hexameric crystal structure with the solution structure of gpU that we previously solved using NMR spectroscopy shows large structural changes occurring upon multimerization and suggests a mechanism that allows gpU to remain monomeric at high concentrations on its own, yet polymerize readily upon contact with an assembled tail tube. The gpU hexamer displays several flexible loops that play key roles in head and tail binding, implying a role for disorder-to-order transitions in controlling assembly as has been observed with other λ morphogenetic proteins. Finally, we have found that the hexameric structure of gpU is very similar to the structure of a putative TrP from a contractile phage tail even though it displays no detectable sequence similarity. This finding coupled with further bioinformatic investigations has led us to conclude that the TrPs of non-contractiletailed phages, such as λ, are evolutionarily related to those of contractiletailed phages, such as P2 and Mu, and that all long-tailed phages may utilize a conserved mechanism for tail termination.

Journal of Molecular Biology, 2007

During the late stages of lambda bacteriophage assembly, the protein gpU terminates tail polymeri... more During the late stages of lambda bacteriophage assembly, the protein gpU terminates tail polymerization and participates at the interface between the mature capsid and tail components. When it engages the lambda tail, gpU undergoes a monomer-hexamer transition to achieve its biologically active form. Towards understanding how gpU participates in multiple protein-protein interactions, we have solved the structure of gpU in its monomeric state using NMR methods. The structure reveals a mixed alpha/beta motif with several dynamic loops at the periphery. Addition of 20 mM MgCl(2) is known to oligomerize gpU in the absence of its protein partners. Multiple image analysis of electron micrographs revealed ring-like structures of magnesium ion saturated gpU with a 30 A pore, consistent with its function as a portal for the passage of viral DNA into the host bacterium. The ability of magnesium ions to promote oligomerization was lost when substitutions were made at a cluster of acidic amino acids in the vicinity of helix alpha2 and the beta1-beta2 loop. Furthermore, substitutions at these sites abolished the biological activity of gpU.

Journal of Biomolecular Nmr, 2005

... Lizbeth Edmondsa, Ramanan Thirumoorthya, Amanda Liub, Alan Davidsonb & Logan Donaldsona,*... more ... Lizbeth Edmondsa, Ramanan Thirumoorthya, Amanda Liub, Alan Davidsonb & Logan Donaldsona,* aDepartment of Biology, Biomolecular Expression and ... a Bruker Avance DRX 600 MHz equipped with a room temperature triple resonance probehead and a Varian Unity Inova ...