Sequential reorganization of beta-sheet topology by insertion of a single strand (2006)
Sagermann, Martin, Baase, Walter A., Matthews, Brian W.
Insertions, duplications, and deletions of sequence segments are thought to be major evolutionary mechanisms that increase the structural and functional diversity of proteins. Alternative splicing,...
Addlagatta, Anthony, Matthews, Brian W.
Methionine aminopeptidases (MetAPs) remove the initiator methionine during protein biosynthesis. They exist in two isoforms, MetAP1 and MetAP2. The anti-angiogenic compound fumagillin binds tightly...
Yousef, Mohammad S., Bischoff, Nicole, Dyer, Collin M., Baase, Walter A., Matthews, Brian W.
The binding of guanidinium ion has been shown to promote a large-scale translation of a tandemly duplicated helix in an engineered mutant of T4 lysozyme. The guanidinium ion acts as a surrogate for...
Sequential reorganization of beta-sheet topology by insertion of a single strand (2006)
Sagermann, Martin, Baase, Walter A., Matthews, Brian W.
Insertions, duplications, and deletions of sequence segments are thought to be major evolutionary mechanisms that increase the structural and functional diversity of proteins. Alternative splicing,...
Sequential reorganization of beta-sheet topology by insertion of a single strand (2006)
Sagermann, Martin, Baase, Walter A., Matthews, Brian W.
Insertions, duplications, and deletions of sequence segments are thought to be major evolutionary mechanisms that increase the structural and functional diversity of proteins. Alternative splicing,...
Addlagatta, Anthony, Matthews, Brian W.
Methionine aminopeptidases (MetAPs) remove the initiator methionine during protein biosynthesis. They exist in two isoforms, MetAP1 and MetAP2. The anti-angiogenic compound fumagillin binds tightly...
CARMEL, ANDREW B., MATTHEWS, BRIAN W.
Most cellular processes requiring RNA structure rearrangement necessitate the action of Asp-Glu-Ala-Asp (DEAD) proteins. Members of the family, named originally for the conserved DEAD amino acid...
He, Molly M., Wood, Zachary A., Baase, Walter A., Xiao, Hong, Matthews, Brian W.
In general, &agr;-helical conformations in proteins depend in large part on the amino acid residues within the helix and their proximal interactions. For example, an alanine residue has a high...
He, Molly M., Wood, Zachary A., Baase, Walter A., Xiao, Hong, Matthews, Brian W.
In general, &agr;-helical conformations in proteins depend in large part on the amino acid residues within the helix and their proximal interactions. For example, an alanine residue has a high...
A test of proposed rules for helix capping: Implications for protein design (2002)
Sagermann, Martin, Mårtensson, Lars-Göran, Baase, Walter A., Matthews, Brian W.
α-helices within proteins are often terminated (capped) by distinctive configurations of the polypeptide chain. Two common arrangements are the Schellman motif and the alternative αL motif. Rose...
Xu, Jian, Baase, Walter A., Quillin, Michael L., Baldwin, Enoch P., Matthews, Brian W.
To investigate the structural and thermodynamic basis of the binding of solvent at internal sites within proteins a number of mutations were constructed in T4 lysozyme. Some of these were designed to...
A structural basis for processivity (2001)
Breyer, Wendy A., Matthews, Brian W.
The structures of a number of processive enzymes have been determined recently. These proteins remain attached to their polymeric substrates and may perform thousands of rounds of catalysis before...
Weaver, Larry H., Kwon, Keehwan, Beckett, Dorothy, Matthews, Brian W.
A model is suggested for the complex between the biotin repressor of Escherichia coli, BirA, and BCCP, the biotin carboxyl carrier protein to which BirA transfers biotin. The model is consistent with...
Use of a non-rigid region in T4 lysozyme to design an adaptable metal-binding site (2000)
Wray, Jonathan W., Baase, Walter A., Ostheimer, Gerard J., Zhang, Xue-jun, Matthews, Brian W.
It is not easy to find candidate sites within a given protein where the geometry of the polypeptide chain matches that of metal-binding sites in known protein structures. By choosing a location in T4...
Zhang, Xue-jun, Baase, Walter A., Shoichet, Brian K., Wilson, Keith P., Matthews, Brian W.
A number of mutations have been shown previously to stabilize T4 lysozyme. By combining up to seven such mutations in the same protein, the melting temperature was incrementally increased by up to...
Rapid crystallization of T4 lysozyme by intermolecular disulfide cross-linking (1994)
Heinz, Dirk W., Matthews, Brian W.
In an attempt to facilitate crystallization, engineered cysteines were used to promote formation of a ‘back–to–back’ dimer that occurs in different crystal forms of wild–type and mutant T4...
Dao-Pin, Sun, Alber, Tom, Bell, Jeffrey A., Weaver, Larry H., Matthews, Brian W.
Five different cysteine-containing mutants of the lysozyme from bacteriopbage T4 were used to explore the feasibility of using site-directed mutagenesis to generate isomorphous heavy-atom derivatives...
Weaver, Larry H., Rennell, Dale, Poteete, Anthony R., Matthews, Brian W.
The amino acid sequence of the lysozyme from phage P22 is shown to be homologous (26% identity) with the lysozyme from bacteriophage T4. The sequence correspondence suggests that the structure of P22...
Kuroki, Ryota, Weaver, Larry H., Matthews, Brian W.
In contrast to hen egg-white lysozyme, which retains the β-configuration of the substrate in the product, T4 lysozyme (T4L) is an inverting glycosidase. The substitution Thr-26 → His, however,...
Lowther, W. Todd, Brot, Nathan, Weissbach, Herbert, Honek, John F., Matthews, Brian W.
Peptide methionine sulfoxide reductase (MsrA; EC 1.8.4.6) reverses the inactivation of many proteins due to the oxidation of critical methionine residues by reducing methionine sulfoxide, Met(O), to...
Albright, Ronald A., Matthews, Brian W.
Knowledge of the three-dimensional structures of the λ-Cro and λ-repressor proteins in complex with DNA has made it possible to evaluate how these proteins discriminate between different operators...
Kovall, Rhett A., Matthews, Brian W.
λ-exonuclease participates in DNA recombination and repair. It binds a free end of double-stranded DNA and degrades one strand in the 5′ to 3′ direction. The primary sequence does not appear to...
Lowther, W. Todd, McMillen, Debra A., Orville, Allen M., Matthews, Brian W.
Methionine aminopeptidase (MetAP) exists in two forms (type I and type II), both of which remove the N-terminal methionine from proteins. It previously has been shown that the type II enzyme is the...
Hausrath, Andrew C., Grüber, Gerhard, Matthews, Brian W., Capaldi, Roderick A.
The F1 part of the F1FO ATP synthase from Escherichia coli has been crystallized and its structure determined to 4.4-Å resolution by using molecular replacement based on the structure of the...
Solid-state synthesis and mechanical unfolding of polymers of T4 lysozyme
Yang, Guoliang, Cecconi, Ciro, Baase, Walter A., Vetter, Ingrid R., Breyer, Wendy A., Haack, Julie A., ...
Recent advances in single molecule manipulation methods offer a novel approach to investigating the protein folding problem. These studies usually are done on molecules that are naturally organized...
Sagermann, Martin, Baase, Walter A., Matthews, Brian W.
To test a different approach to understanding the relationship between the sequence of part of a protein and its conformation in the overall folded structure, the amino acid sequence corresponding to...
Weaver, Larry H., Kwon, Keehwan, Beckett, Dorothy, Matthews, Brian W.
The Escherichia coli biotin repressor binds to the biotin operator to repress transcription of the biotin biosynthetic operon. In this work, a structure determined by x-ray crystallography of a...
Crystal structure of the regulatory subunit H of the V-type ATPase of Saccharomyces cerevisiae
Sagermann, Martin, Stevens, Tom H., Matthews, Brian W.
In contrast to the F-type ATPases, which use a proton gradient to generate ATP, the V-type enzymes use ATP to actively transport protons into organelles and extracellular compartments. We describe...
Long-distance conformational changes in a protein engineered by modulated sequence duplication
Sagermann, Martin, Gay, Leslie, Matthews, Brian W.
There are few, if any, known instances in which a biological signal is transmitted via a large conformational change through the body of a protein. We describe here a mutant of T4 lysozyme that was...
Structural basis for the attachment of a paramyxoviral polymerase to its template
Kingston, Richard L., Hamel, Damon J., Gay, Leslie S., Dahlquist, Frederick W., Matthews, Brian W.
The nucleocapsid of measles virus is the template for viral RNA synthesis and is generated through packaging of the genomic RNA by the nucleocapsid protein (N). The viral polymerase associates with...
Yousef, Mohammad S., Baase, Walter A., Matthews, Brian W.
We have designed a molecular switch in a T4 lysozyme construct that controls a large-scale translation of a duplicated helix. As shown by crystal structures of the construct with the switch on and...
CARMEL, ANDREW B., MATTHEWS, BRIAN W.
Most cellular processes requiring RNA structure rearrangement necessitate the action of Asp-Glu-Ala-Asp (DEAD) proteins. Members of the family, named originally for the conserved DEAD amino acid...
Collins, Marcus D., Hummer, Gerhard, Quillin, Michael L., Matthews, Brian W., Gruner, Sol M.
Formation of a water-expelling nonpolar core is the paradigm of protein folding and stability. Although experiment largely confirms this picture, water buried in “hydrophobic” cavities is...
Kuroki, Ryota, Weaver, Larry H., Matthews, Brian W.
In contrast to hen egg-white lysozyme, which retains the β-configuration of the substrate in the product, T4 lysozyme (T4L) is an inverting glycosidase. The substitution Thr-26 → His, however,...
Lowther, W. Todd, Brot, Nathan, Weissbach, Herbert, Honek, John F., Matthews, Brian W.
Peptide methionine sulfoxide reductase (MsrA; EC 1.8.4.6) reverses the inactivation of many proteins due to the oxidation of critical methionine residues by reducing methionine sulfoxide, Met(O), to...
Albright, Ronald A., Matthews, Brian W.
Knowledge of the three-dimensional structures of the λ-Cro and λ-repressor proteins in complex with DNA has made it possible to evaluate how these proteins discriminate between different operators...
Kovall, Rhett A., Matthews, Brian W.
λ-exonuclease participates in DNA recombination and repair. It binds a free end of double-stranded DNA and degrades one strand in the 5′ to 3′ direction. The primary sequence does not appear to...
Lowther, W. Todd, McMillen, Debra A., Orville, Allen M., Matthews, Brian W.
Methionine aminopeptidase (MetAP) exists in two forms (type I and type II), both of which remove the N-terminal methionine from proteins. It previously has been shown that the type II enzyme is the...
Hausrath, Andrew C., Grüber, Gerhard, Matthews, Brian W., Capaldi, Roderick A.
The F1 part of the F1FO ATP synthase from Escherichia coli has been crystallized and its structure determined to 4.4-Å resolution by using molecular replacement based on the structure of the...
Solid-state synthesis and mechanical unfolding of polymers of T4 lysozyme
Yang, Guoliang, Cecconi, Ciro, Baase, Walter A., Vetter, Ingrid R., Breyer, Wendy A., Haack, Julie A., ...
Recent advances in single molecule manipulation methods offer a novel approach to investigating the protein folding problem. These studies usually are done on molecules that are naturally organized...
Sagermann, Martin, Baase, Walter A., Matthews, Brian W.
To test a different approach to understanding the relationship between the sequence of part of a protein and its conformation in the overall folded structure, the amino acid sequence corresponding to...
Weaver, Larry H., Kwon, Keehwan, Beckett, Dorothy, Matthews, Brian W.
The Escherichia coli biotin repressor binds to the biotin operator to repress transcription of the biotin biosynthetic operon. In this work, a structure determined by x-ray crystallography of a...
Crystal structure of the regulatory subunit H of the V-type ATPase of Saccharomyces cerevisiae
Sagermann, Martin, Stevens, Tom H., Matthews, Brian W.
In contrast to the F-type ATPases, which use a proton gradient to generate ATP, the V-type enzymes use ATP to actively transport protons into organelles and extracellular compartments. We describe...
Long-distance conformational changes in a protein engineered by modulated sequence duplication
Sagermann, Martin, Gay, Leslie, Matthews, Brian W.
There are few, if any, known instances in which a biological signal is transmitted via a large conformational change through the body of a protein. We describe here a mutant of T4 lysozyme that was...
Structural basis for the attachment of a paramyxoviral polymerase to its template
Kingston, Richard L., Hamel, Damon J., Gay, Leslie S., Dahlquist, Frederick W., Matthews, Brian W.
The nucleocapsid of measles virus is the template for viral RNA synthesis and is generated through packaging of the genomic RNA by the nucleocapsid protein (N). The viral polymerase associates with...
Yousef, Mohammad S., Baase, Walter A., Matthews, Brian W.
We have designed a molecular switch in a T4 lysozyme construct that controls a large-scale translation of a duplicated helix. As shown by crystal structures of the construct with the switch on and...
Collins, Marcus D., Hummer, Gerhard, Quillin, Michael L., Matthews, Brian W., Gruner, Sol M.
Formation of a water-expelling nonpolar core is the paradigm of protein folding and stability. Although experiment largely confirms this picture, water buried in “hydrophobic” cavities is...
CARMEL, ANDREW B., MATTHEWS, BRIAN W.
Most cellular processes requiring RNA structure rearrangement necessitate the action of Asp-Glu-Ala-Asp (DEAD) proteins. Members of the family, named originally for the conserved DEAD amino acid...
Structure of aminopeptidase N from Escherichia coli suggests a compartmentalized, gated active site
Addlagatta, Anthony, Gay, Leslie, Matthews, Brian W.
Aminopeptidase N from Escherichia coli is a major metalloprotease that participates in the controlled hydrolysis of peptides in the proteolytic pathway. Determination of the 870-aa structure reveals...
Elucidation of the function of type 1 human methionine aminopeptidase during cell cycle progression
Hu, Xiaoyi, Addlagatta, Anthony, Lu, Jun, Matthews, Brian W., Liu, Jun O.
Processing of the N-terminal initiator methionine is an essential cellular process conserved from prokaryotes to eukaryotes. The enzymes that remove N-terminal methionine are known as methionine...
Determination of solvent content in cavities in IL-1β using experimentally phased electron density
Quillin, Michael L., Wingfield, Paul T., Matthews, Brian W.
The extent to which water is present within apolar cavities in proteins remains unclear. In the case of interleukin-1β (IL-1β), four independent structures solved by x-ray crystallography indicate...
Yousef, Mohammad S., Bischoff, Nicole, Dyer, Collin M., Baase, Walter A., Matthews, Brian W.
The binding of guanidinium ion has been shown to promote a large-scale translation of a tandemly duplicated helix in an engineered mutant of T4 lysozyme. The guanidinium ion acts as a surrogate for...
Sequential reorganization of β-sheet topology by insertion of a single strand
Sagermann, Martin, Baase, Walter A., Matthews, Brian W.
Insertions, duplications, and deletions of sequence segments are thought to be major evolutionary mechanisms that increase the structural and functional diversity of proteins. Alternative splicing,...
Addlagatta, Anthony, Matthews, Brian W.
Methionine aminopeptidases (MetAPs) remove the initiator methionine during protein biosynthesis. They exist in two isoforms, MetAP1 and MetAP2. The anti-angiogenic compound fumagillin binds tightly...
He, Molly M., Wood, Zachary A., Baase, Walter A., Xiao, Hong, Matthews, Brian W.
In general, α-helical conformations in proteins depend in large part on the amino acid residues within the helix and their proximal interactions. For example, an alanine residue has a high...
A structural basis for processivity
Breyer, Wendy A., Matthews, Brian W.
The structures of a number of processive enzymes have been determined recently. These proteins remain attached to their polymeric substrates and may perform thousands of rounds of catalysis before...
A test of proposed rules for helix capping: Implications for protein design
Sagermann, Martin, Mårtensson, Lars-Göran, Baase, Walter A., Matthews, Brian W.
α-helices within proteins are often terminated (capped) by distinctive configurations of the polypeptide chain. Two common arrangements are the Schellman motif and the alternative αL motif. Rose...
Weaver, Larry H., Kwon, Keehwan, Beckett, Dorothy, Matthews, Brian W.
A model is suggested for the complex between the biotin repressor of Escherichia coli, BirA, and BCCP, the biotin carboxyl carrier protein to which BirA transfers biotin. The model is consistent with...
Structural and thermodynamic analysis of the binding of solvent at internal sites in T4 lysozyme
Xu, Jian, Baase, Walter A., Quillin, Michael L., Baldwin, Enoch P., Matthews, Brian W.
To investigate the structural and thermodynamic basis of the binding of solvent at internal sites within proteins a number of mutations were constructed in T4 lysozyme. Some of these were designed to...
Liu, Lijun, Quillin, Michael L., Matthews, Brian W.
There is conflicting evidence as to whether cavities in proteins that are nonpolar and large enough to accommodate solvent are empty or are occupied by disordered water molecules. Here, we use...