Peter Von Hipel - Academia.edu (original) (raw)

Papers by Peter Von Hipel

Research paper thumbnail of Components of multiprotein-RNA complex that controls transcription elongation in Escherichia coli phage lambda

Methods in Enzymology, 1996

Research paper thumbnail of Electronic transition moments of 6-methyl isoxanthopterin--a fluorescent analogue of the nucleic acid base guanine

Nucleic Acids Research, 2013

Research paper thumbnail of Opening of a monomer-monomer interface of the trimeric bacteriophage T4-coded GP45 sliding clamp is required for clamp loading onto DNA

Proceedings of the National Academy of Sciences, 1999

Research paper thumbnail of A two-metal ion mechanism operates in the hammerhead ribozyme-mediated cleavage of an RNA substrate

Proceedings of the National Academy of Sciences, 1998

A two-metal ion mechanism operates in the hammerhead ribozyme-mediated cleavage of an RNA substra... more A two-metal ion mechanism operates in the hammerhead ribozyme-mediated cleavage of an RNA substrate (ribozyme function͞metal ion activation͞RNA cleavage͞magnesium ion͞lanthanum ion)

Research paper thumbnail of The Destabilizing Effect of Ribonuclease on the Helical Dna Structure

Proceedings of the National Academy of Sciences, 1963

There has been considerable recent interest in the possible effects of proteins upon the biologic... more There has been considerable recent interest in the possible effects of proteins upon the biological properties of DNA; the role of histones in regulation of RNA synthesis has been discussed by a number of workers,1'2 while Monod and his colleagues3 have suggested that in inducible enzyme synthesis the regulatory substance acting upon DNA is a protein. All of these studies have been concerned with the ways in which protein may regulate the stability of the helical DNA structure, making the bases more or less accessible for their potential roles in DNA and RNA synthesis.

Research paper thumbnail of Nonspecific DNA binding of genome-regulating proteins as a biological control mechanism: Measurement of DNA-bound Escherichia coli lac repressor in vivo

Proceedings of the National Academy of Sciences, 1977

ABSTBACr Binding of genome regulatory proteins to nonspecific DNA sites may play an important rol... more ABSTBACr Binding of genome regulatory proteins to nonspecific DNA sites may play an important role in controlling the thermodynamics and kinetics of the interactions of these proteins with their specific target DNA sequences. An estimate of the fraction of Escherchia colilac repressor molecules bound in vivo to the operator region and to nonoperator sites on the E coli chromosome is derived by measurement of the distribution of repressor between a minicell-producing E. coli strain (P678-54) and the DNA-free minicells derived therefrom. Assuming the minicell cytoplasm to be representative of that of the parent E. coli cells, we find that less than 10% of the repressor tetramers of the average cell are free in solution; the remainder are presumed to be bound to the bacterial chromosome. The minimum in vivo value of the association constant for repressor to bulk nonoperator DNA (Kim) calculated from these results is about 103 Mel, and analysis of the sources of error in the minicell experiment suggests that the actual in vivo value of KRD could be substantially greater. The value of KRD,

Research paper thumbnail of Thinking quantitatively about transcriptional regulation

Nature Reviews Molecular Cell Biology, 2005

Transcription is the primary regulatory process that is used by cells, tissues and organisms to f... more Transcription is the primary regulatory process that is used by cells, tissues and organisms to facilitate and control the complex programmes of gene expression, cellular metabolism, and organ and tissue development. Many aberrant events that lead to the development of tumours and cancer also depend on transcription. At the chemical level, transcription means 'copying' into RNA transcripts (mRNA, tRNA or rRNA) the portions of the template strand of the DNA genome that correspond to genes. In effect, monomeric ribonucleotides are bound specifically and sequentially to the DNA template at the 3′ end of the growing RNA chain by Watson-Crick base pairing and are polymerized into covalently linked transcripts by enzymes, known as RNA polymerases, that advance processively along the DNA template and catalyse inter-nucleotide-bond formation. Inter-and intracellular signalling networkswhich control transcription factors that operate directly on the regulatory DNA sequences surrounding the PROMOTERS of specific genes -direct the function of the RNA polymerases and therefore control which genes are activated and transcribed, and which are not, at various stages of the cell cycle.

Research paper thumbnail of Proton exchange of N-methylacetamide in concentrated aqueous electrolyte solutions. I. Acid catalysis

Journal of the American Chemical Society, 1968

ABSTRACT

Research paper thumbnail of Transcriptional activation via DNA-looping: visualization of intermediates in the activation pathway of E. coli RNA polymerase·σ54 holoenzyme by scanning force microscopy

Journal of Molecular Biology, 1997

Scanning force microscopy (SFM) has been used to study transcriptional activation of Escherichia ... more Scanning force microscopy (SFM) has been used to study transcriptional activation of Escherichia coli RNA polymerase Ás 54 (RNAP Á s 54 ) at the glnA promoter by the constitutive mutant NtrC D54E,S160F of the NtrC Protein (nitrogen regulatory protein C). DNA-protein complexes were deposited on mica and images were recorded in air. The DNA template was a 726 bp linear fragment with two NtrC binding sites located at the end and about 460 bp away from the RNAP Á s 54 glnA promoter. By choosing appropriate conditions the structure of various intermediates in the transcription process could be visualized and analyzed: (1) different multimeric complexes of NtrC D54E,S160F dimers bound to the DNA template; (2) the closed complex of RNAP Á s 54 at the glnA promoter; (3) association between DNA bound RNAP Á s 54 and NtrC D54E,S160F with the intervening DNA looped out; and the activated open promoter complex of RNAP Á s 54 . Measurements of the DNA bending angle of RNAP Á s 54 closed promoter complexes yielded an apparent bending angle of 49(AE24) . Under conditions that allowed the formation of the open promoter complex, the distribution of bending angles displayed two peaks at 50(AE24) and 114(AE18) , suggesting that the transition from the RNAP Ás 54 closed complex to the open complex is accompanied by an increase of the DNA bending angle. # 1997 Academic Press Limited

Research paper thumbnail of Assembly of the N-dependent antitermination complex of phage λ: NusA and RNA bind independently to different unfolded domains of the N protein

Journal of Molecular Biology, 1997

The N protein of bacteriophage l activates expression of the delayed early genes of this phage by... more The N protein of bacteriophage l activates expression of the delayed early genes of this phage by modifying RNA polymerase (RNAP) into a form that is resistant to termination signals. N binds to the boxB hairpin that forms in the nascent RNA transcript upon transcription of the nut regulatory element, and then interacts with RNAP by RNA looping. The binding of the N-boxB subassembly to the transcription complex is further stabilized by interaction with the Escherichia coli NusA protein. N, free in solution, exists as an unfolded protein that becomes partially structured upon binding speci®cally to boxB RNA. Because NusA does not assist in antitermination unless N is speci®cally bound to boxB, we have asked whether the structural change induced by binding to boxB affects the interaction of N with NusA. Using¯uorescence spectroscopy, we have measured the af®nity of N for NusA in the presence and absence of boxB RNA. We ®nd that NusA binds to the unfolded N protein with a dissociation constant (K d ) of %70 nM, and although N undergoes a signi®cant structural change upon binding to boxB, the binding af®nity of NusA for a N protein complexed with boxB is not altered. We have also shown that the boxA element of nut does not affect NusA binding to N-boxB. These results demonstrate that the interaction of N with NusA is independent of RNA binding, arguing that NusA must interact with an unfolded region of the polypeptide that remains unstructured even when N binds to boxB RNA. To further establish this point we isolated a truncated peptide containing the amino-terminal 36 residues of the N protein. Binding of boxB RNA to this peptide showed that all of the structural change in N that occurs upon binding to boxB RNA is localized within the amino-terminal 36 residues of N, therefore the C terminus of N, including the regions necessary for NusA binding and RNAP activation, remains unfolded when the full length N binds to boxB RNA. Thus it appears that N can be described as an unfolded multi-domain protein that becomes ordered in a modular fashion as it encounters its various binding partners within the N-dependent antitermination complex.

Research paper thumbnail of Regulation of the elongation-termination decision at intrinsic terminators by antitermination protein N of phage λ

Journal of Molecular Biology, 1997

The mechanisms that control N-protein-dependent antitermination in the phage l life cycle have co... more The mechanisms that control N-protein-dependent antitermination in the phage l life cycle have counterparts in the regulatory systems of other organisms. Here we examine N-dependent antitermination at the intrinsic tR H terminator of l to elucidate the regulatory principles involved. The tR H terminator consists of a sequence of six base-pairs along the template at which the transcription complex is suf®ciently destabilized to make RNA release possible. Within this``zone of opportunity'' for termination the termination ef®ciency (TE) at each template position is determined by a kinetic competition between alternative reaction pathways that lead either to elongation or to termination. TE values at each position within tR H have been mapped as a function of NTP concentration, and it is shown that N protein (in the presence of NusA and a nut site; the minimal system for N-dependent antitermination) can offset increases in TE that are induced by limiting the concentrations of each of the next required NTPs. By limiting NTP concentrations or working at low temperature we show that a signi®cant effect of N within the minimal system is to increase the rate of transcript elongation three-to ®vefold at most positions along the template. Assuming that a comparable increase in elongation rate applies at template positions within the terminator, we show that an increase of this magnitude is not suf®cient to account for the antitermination ef®ciency observed and that an $100-fold stabilization of the transcription complex at intrinsic termination sites as a consequence of binding the N-containing antitermination sub-assembly must be invoked as well. A general method for partitioning TE effects in antitermination between changes in elongation rate and termination complex stability is demonstrated, based on competing free energy of activation barriers for the elongation and termination reactions. The analysis and utility of such mixed modes of transcriptional regulation are considered in general terms.

Research paper thumbnail of The Effect of Ions on the Kinetics of Formation and the Stability of the Collagen-Fold *

Biochemistry, 1962

Page 1. 664 PETER H. VON HIPPEL AND KWOK-YING WONG Biochemistry The Effect of Ions on the Kinetic... more Page 1. 664 PETER H. VON HIPPEL AND KWOK-YING WONG Biochemistry The Effect of Ions on the Kinetics of Formation and the Stability of the Collagen-Fold* PETER H. VON HIPPEL AND KWOK-YING WONG ...

Research paper thumbnail of Effects of methylation on the stability of nucleic acid conformations. Monomer level

Research paper thumbnail of Structure and function of the bacteriophage T4 DNA polymerase holoenzyme

Biochemistry, 1992

Page 1. 0 Copyright 1992 by the American Chemical Society Volume 31, Number 37 September 22, 1992... more Page 1. 0 Copyright 1992 by the American Chemical Society Volume 31, Number 37 September 22, 1992 Perspectives in Biochemistry Structure and Function of the Bacteriophage T4 DNA Polymerase Holoenzyme+ Mark C ...

Research paper thumbnail of Molecular parameters characterizing the interaction of Escherichia coli lac repressor with non-operator DNA and inducer

Biochemistry, 1977

The stoichiometries of binding of non-operator DNA and inducer to lac repressor, as well as some ... more The stoichiometries of binding of non-operator DNA and inducer to lac repressor, as well as some conformational aspects of these interactions, are described in this paper. It is shown that the circular dichroism (CD) spectrum of the repressor-non-operator DNA complex is appreciably different from that obtained by summing the spectra of the separate components; the major change is a substantial enhancement of the positive (-275 nm) lobe of the originally conservative DNA B form pattern. These CD spectral changes appear to reflect a change in DNA conformation on repressor binding and are interpreted in terms of tilting (relative to the DNA axis) of some of the base pairs of the native structure, or perhaps some twisting of the overall structure resulting in a tighter coupling of vicinal base transition moments. These changes in the CD spectrum of non-operator DNA on repressor binding have been monitored as a function of added repressor concentration, under tight-binding conditions, to establish that the site size (n) for binding to non-operator DNA is -12 base pairs per repressor tetramer (-24 base pairs if repressor binds to both sides of the double helical DNA lattice). This value of n is confirmed both by calculation from binding isotherms , Biochemistry 16 (following paper in this issue), and by titration of repressor T h e lac repressor recognizes (and binds tightly to) a particular sequence of base pairs in the Escherichia coli chromosome which is defined, on this basis, as the lac operator. By virtue of this specific binding the repressor exerts negative control over the expression of the lactose operon (Jacob and . The interaction of lac repressor with operator has been subjected to intense scrutiny by both biochemical and genetic means, and a great deal of information is now available State University, East Lansing, Mich. 48824. sulfhydryl groups as a function of added DNA concentration. The measured site size is discussed in terms of the relationship between operator and non-operator DNA binding of repressor, and of various features of the known operator sequence, to suggest alternative models for the geometry of the repressoroperator interaction. Investigation of the repressor-inducer interaction by equilibrium dialysis, fluorescence, and gel permeation chromatography shows, in confirmation of the results of Ohshima, Y., et al. , that different repressor preparations exhibit different (average) numbers of "active" inducer binding sites per repressor tetramer (nl); values of nl between two and four have been obtained. The effects on n~ of a variety of environmental conditions have been examined, and the results, together with relevant data from the literature, are discussed in terms of conformational equilibria between forms of repressor subunits which bind strongly to inducer and weakly to operator (RI), and forms which bind strongly to operator and weakly to inducer (Ro). Thermodynamic parameters for the binding of inducer to repressor subunits (in the RI form) have also been determined. At pH 7.6 (4-25 "C), AGO = -7.7 kcal/mol (25 "C), AH" = -6.2 kcal/mol, and AS" = +5 cal mol-' deg-' for this reaction. about both the protein and the operator (for a recent review, see .

Research paper thumbnail of Corrections - Measurement of Macromolecular Equilibrium Binding Constants by a Sucrose Gradient Band Sedimentation Method. Application to Protein-Nucleic Acid Interactions

Biochemistry, 1979

lines 3-5 should read as follows: identified as 1,2-di-O-acyl-3-0-[ 0-a-D-glucopyranosyl-(~-+)-a-... more lines 3-5 should read as follows: identified as 1,2-di-O-acyl-3-0-[ 0-a-D-glucopyranosyl-(~-+)-a-D-glucopyranosyl]g~ycerol and 1,2-di-O-acyl-3-0-[ O-a-D-glucopyranosy1-( 1 +2)-(6-0-acyl-a-~-glucopyrano-sy1)lglycerol.

Research paper thumbnail of Components of multiprotein-RNA complex that controls transcription elongation in Escherichia coli phage lambda

Methods in Enzymology, 1996

... Asis Das, Mahadeb Pal, Jaime Garcia Mena, William Whalen, Krystyna Wolska, Robin Crossley, Wi... more ... Asis Das, Mahadeb Pal, Jaime Garcia Mena, William Whalen, Krystyna Wolska, Robin Crossley, William Rees, Peter H. von Hippel, Nina Costantino, Donald Court, Marie Mazzulla, Amanda S. Altieri, R.Andrew Byrd, Samit Chattopadhyay, Joseph DeVito and Balaram Ghosh. ...

Research paper thumbnail of Components of multiprotein-RNA complex that controls transcription elongation in Escherichia coli phage lambda

Methods in Enzymology, 1996

Research paper thumbnail of Electronic transition moments of 6-methyl isoxanthopterin--a fluorescent analogue of the nucleic acid base guanine

Nucleic Acids Research, 2013

Research paper thumbnail of Opening of a monomer-monomer interface of the trimeric bacteriophage T4-coded GP45 sliding clamp is required for clamp loading onto DNA

Proceedings of the National Academy of Sciences, 1999

Research paper thumbnail of A two-metal ion mechanism operates in the hammerhead ribozyme-mediated cleavage of an RNA substrate

Proceedings of the National Academy of Sciences, 1998

A two-metal ion mechanism operates in the hammerhead ribozyme-mediated cleavage of an RNA substra... more A two-metal ion mechanism operates in the hammerhead ribozyme-mediated cleavage of an RNA substrate (ribozyme function͞metal ion activation͞RNA cleavage͞magnesium ion͞lanthanum ion)

Research paper thumbnail of The Destabilizing Effect of Ribonuclease on the Helical Dna Structure

Proceedings of the National Academy of Sciences, 1963

There has been considerable recent interest in the possible effects of proteins upon the biologic... more There has been considerable recent interest in the possible effects of proteins upon the biological properties of DNA; the role of histones in regulation of RNA synthesis has been discussed by a number of workers,1'2 while Monod and his colleagues3 have suggested that in inducible enzyme synthesis the regulatory substance acting upon DNA is a protein. All of these studies have been concerned with the ways in which protein may regulate the stability of the helical DNA structure, making the bases more or less accessible for their potential roles in DNA and RNA synthesis.

Research paper thumbnail of Nonspecific DNA binding of genome-regulating proteins as a biological control mechanism: Measurement of DNA-bound Escherichia coli lac repressor in vivo

Proceedings of the National Academy of Sciences, 1977

ABSTBACr Binding of genome regulatory proteins to nonspecific DNA sites may play an important rol... more ABSTBACr Binding of genome regulatory proteins to nonspecific DNA sites may play an important role in controlling the thermodynamics and kinetics of the interactions of these proteins with their specific target DNA sequences. An estimate of the fraction of Escherchia colilac repressor molecules bound in vivo to the operator region and to nonoperator sites on the E coli chromosome is derived by measurement of the distribution of repressor between a minicell-producing E. coli strain (P678-54) and the DNA-free minicells derived therefrom. Assuming the minicell cytoplasm to be representative of that of the parent E. coli cells, we find that less than 10% of the repressor tetramers of the average cell are free in solution; the remainder are presumed to be bound to the bacterial chromosome. The minimum in vivo value of the association constant for repressor to bulk nonoperator DNA (Kim) calculated from these results is about 103 Mel, and analysis of the sources of error in the minicell experiment suggests that the actual in vivo value of KRD could be substantially greater. The value of KRD,

Research paper thumbnail of Thinking quantitatively about transcriptional regulation

Nature Reviews Molecular Cell Biology, 2005

Transcription is the primary regulatory process that is used by cells, tissues and organisms to f... more Transcription is the primary regulatory process that is used by cells, tissues and organisms to facilitate and control the complex programmes of gene expression, cellular metabolism, and organ and tissue development. Many aberrant events that lead to the development of tumours and cancer also depend on transcription. At the chemical level, transcription means 'copying' into RNA transcripts (mRNA, tRNA or rRNA) the portions of the template strand of the DNA genome that correspond to genes. In effect, monomeric ribonucleotides are bound specifically and sequentially to the DNA template at the 3′ end of the growing RNA chain by Watson-Crick base pairing and are polymerized into covalently linked transcripts by enzymes, known as RNA polymerases, that advance processively along the DNA template and catalyse inter-nucleotide-bond formation. Inter-and intracellular signalling networkswhich control transcription factors that operate directly on the regulatory DNA sequences surrounding the PROMOTERS of specific genes -direct the function of the RNA polymerases and therefore control which genes are activated and transcribed, and which are not, at various stages of the cell cycle.

Research paper thumbnail of Proton exchange of N-methylacetamide in concentrated aqueous electrolyte solutions. I. Acid catalysis

Journal of the American Chemical Society, 1968

ABSTRACT

Research paper thumbnail of Transcriptional activation via DNA-looping: visualization of intermediates in the activation pathway of E. coli RNA polymerase·σ54 holoenzyme by scanning force microscopy

Journal of Molecular Biology, 1997

Scanning force microscopy (SFM) has been used to study transcriptional activation of Escherichia ... more Scanning force microscopy (SFM) has been used to study transcriptional activation of Escherichia coli RNA polymerase Ás 54 (RNAP Á s 54 ) at the glnA promoter by the constitutive mutant NtrC D54E,S160F of the NtrC Protein (nitrogen regulatory protein C). DNA-protein complexes were deposited on mica and images were recorded in air. The DNA template was a 726 bp linear fragment with two NtrC binding sites located at the end and about 460 bp away from the RNAP Á s 54 glnA promoter. By choosing appropriate conditions the structure of various intermediates in the transcription process could be visualized and analyzed: (1) different multimeric complexes of NtrC D54E,S160F dimers bound to the DNA template; (2) the closed complex of RNAP Á s 54 at the glnA promoter; (3) association between DNA bound RNAP Á s 54 and NtrC D54E,S160F with the intervening DNA looped out; and the activated open promoter complex of RNAP Á s 54 . Measurements of the DNA bending angle of RNAP Á s 54 closed promoter complexes yielded an apparent bending angle of 49(AE24) . Under conditions that allowed the formation of the open promoter complex, the distribution of bending angles displayed two peaks at 50(AE24) and 114(AE18) , suggesting that the transition from the RNAP Ás 54 closed complex to the open complex is accompanied by an increase of the DNA bending angle. # 1997 Academic Press Limited

Research paper thumbnail of Assembly of the N-dependent antitermination complex of phage λ: NusA and RNA bind independently to different unfolded domains of the N protein

Journal of Molecular Biology, 1997

The N protein of bacteriophage l activates expression of the delayed early genes of this phage by... more The N protein of bacteriophage l activates expression of the delayed early genes of this phage by modifying RNA polymerase (RNAP) into a form that is resistant to termination signals. N binds to the boxB hairpin that forms in the nascent RNA transcript upon transcription of the nut regulatory element, and then interacts with RNAP by RNA looping. The binding of the N-boxB subassembly to the transcription complex is further stabilized by interaction with the Escherichia coli NusA protein. N, free in solution, exists as an unfolded protein that becomes partially structured upon binding speci®cally to boxB RNA. Because NusA does not assist in antitermination unless N is speci®cally bound to boxB, we have asked whether the structural change induced by binding to boxB affects the interaction of N with NusA. Using¯uorescence spectroscopy, we have measured the af®nity of N for NusA in the presence and absence of boxB RNA. We ®nd that NusA binds to the unfolded N protein with a dissociation constant (K d ) of %70 nM, and although N undergoes a signi®cant structural change upon binding to boxB, the binding af®nity of NusA for a N protein complexed with boxB is not altered. We have also shown that the boxA element of nut does not affect NusA binding to N-boxB. These results demonstrate that the interaction of N with NusA is independent of RNA binding, arguing that NusA must interact with an unfolded region of the polypeptide that remains unstructured even when N binds to boxB RNA. To further establish this point we isolated a truncated peptide containing the amino-terminal 36 residues of the N protein. Binding of boxB RNA to this peptide showed that all of the structural change in N that occurs upon binding to boxB RNA is localized within the amino-terminal 36 residues of N, therefore the C terminus of N, including the regions necessary for NusA binding and RNAP activation, remains unfolded when the full length N binds to boxB RNA. Thus it appears that N can be described as an unfolded multi-domain protein that becomes ordered in a modular fashion as it encounters its various binding partners within the N-dependent antitermination complex.

Research paper thumbnail of Regulation of the elongation-termination decision at intrinsic terminators by antitermination protein N of phage λ

Journal of Molecular Biology, 1997

The mechanisms that control N-protein-dependent antitermination in the phage l life cycle have co... more The mechanisms that control N-protein-dependent antitermination in the phage l life cycle have counterparts in the regulatory systems of other organisms. Here we examine N-dependent antitermination at the intrinsic tR H terminator of l to elucidate the regulatory principles involved. The tR H terminator consists of a sequence of six base-pairs along the template at which the transcription complex is suf®ciently destabilized to make RNA release possible. Within this``zone of opportunity'' for termination the termination ef®ciency (TE) at each template position is determined by a kinetic competition between alternative reaction pathways that lead either to elongation or to termination. TE values at each position within tR H have been mapped as a function of NTP concentration, and it is shown that N protein (in the presence of NusA and a nut site; the minimal system for N-dependent antitermination) can offset increases in TE that are induced by limiting the concentrations of each of the next required NTPs. By limiting NTP concentrations or working at low temperature we show that a signi®cant effect of N within the minimal system is to increase the rate of transcript elongation three-to ®vefold at most positions along the template. Assuming that a comparable increase in elongation rate applies at template positions within the terminator, we show that an increase of this magnitude is not suf®cient to account for the antitermination ef®ciency observed and that an $100-fold stabilization of the transcription complex at intrinsic termination sites as a consequence of binding the N-containing antitermination sub-assembly must be invoked as well. A general method for partitioning TE effects in antitermination between changes in elongation rate and termination complex stability is demonstrated, based on competing free energy of activation barriers for the elongation and termination reactions. The analysis and utility of such mixed modes of transcriptional regulation are considered in general terms.

Research paper thumbnail of The Effect of Ions on the Kinetics of Formation and the Stability of the Collagen-Fold *

Biochemistry, 1962

Page 1. 664 PETER H. VON HIPPEL AND KWOK-YING WONG Biochemistry The Effect of Ions on the Kinetic... more Page 1. 664 PETER H. VON HIPPEL AND KWOK-YING WONG Biochemistry The Effect of Ions on the Kinetics of Formation and the Stability of the Collagen-Fold* PETER H. VON HIPPEL AND KWOK-YING WONG ...

Research paper thumbnail of Effects of methylation on the stability of nucleic acid conformations. Monomer level

Research paper thumbnail of Structure and function of the bacteriophage T4 DNA polymerase holoenzyme

Biochemistry, 1992

Page 1. 0 Copyright 1992 by the American Chemical Society Volume 31, Number 37 September 22, 1992... more Page 1. 0 Copyright 1992 by the American Chemical Society Volume 31, Number 37 September 22, 1992 Perspectives in Biochemistry Structure and Function of the Bacteriophage T4 DNA Polymerase Holoenzyme+ Mark C ...

Research paper thumbnail of Molecular parameters characterizing the interaction of Escherichia coli lac repressor with non-operator DNA and inducer

Biochemistry, 1977

The stoichiometries of binding of non-operator DNA and inducer to lac repressor, as well as some ... more The stoichiometries of binding of non-operator DNA and inducer to lac repressor, as well as some conformational aspects of these interactions, are described in this paper. It is shown that the circular dichroism (CD) spectrum of the repressor-non-operator DNA complex is appreciably different from that obtained by summing the spectra of the separate components; the major change is a substantial enhancement of the positive (-275 nm) lobe of the originally conservative DNA B form pattern. These CD spectral changes appear to reflect a change in DNA conformation on repressor binding and are interpreted in terms of tilting (relative to the DNA axis) of some of the base pairs of the native structure, or perhaps some twisting of the overall structure resulting in a tighter coupling of vicinal base transition moments. These changes in the CD spectrum of non-operator DNA on repressor binding have been monitored as a function of added repressor concentration, under tight-binding conditions, to establish that the site size (n) for binding to non-operator DNA is -12 base pairs per repressor tetramer (-24 base pairs if repressor binds to both sides of the double helical DNA lattice). This value of n is confirmed both by calculation from binding isotherms , Biochemistry 16 (following paper in this issue), and by titration of repressor T h e lac repressor recognizes (and binds tightly to) a particular sequence of base pairs in the Escherichia coli chromosome which is defined, on this basis, as the lac operator. By virtue of this specific binding the repressor exerts negative control over the expression of the lactose operon (Jacob and . The interaction of lac repressor with operator has been subjected to intense scrutiny by both biochemical and genetic means, and a great deal of information is now available State University, East Lansing, Mich. 48824. sulfhydryl groups as a function of added DNA concentration. The measured site size is discussed in terms of the relationship between operator and non-operator DNA binding of repressor, and of various features of the known operator sequence, to suggest alternative models for the geometry of the repressoroperator interaction. Investigation of the repressor-inducer interaction by equilibrium dialysis, fluorescence, and gel permeation chromatography shows, in confirmation of the results of Ohshima, Y., et al. , that different repressor preparations exhibit different (average) numbers of "active" inducer binding sites per repressor tetramer (nl); values of nl between two and four have been obtained. The effects on n~ of a variety of environmental conditions have been examined, and the results, together with relevant data from the literature, are discussed in terms of conformational equilibria between forms of repressor subunits which bind strongly to inducer and weakly to operator (RI), and forms which bind strongly to operator and weakly to inducer (Ro). Thermodynamic parameters for the binding of inducer to repressor subunits (in the RI form) have also been determined. At pH 7.6 (4-25 "C), AGO = -7.7 kcal/mol (25 "C), AH" = -6.2 kcal/mol, and AS" = +5 cal mol-' deg-' for this reaction. about both the protein and the operator (for a recent review, see .

Research paper thumbnail of Corrections - Measurement of Macromolecular Equilibrium Binding Constants by a Sucrose Gradient Band Sedimentation Method. Application to Protein-Nucleic Acid Interactions

Biochemistry, 1979

lines 3-5 should read as follows: identified as 1,2-di-O-acyl-3-0-[ 0-a-D-glucopyranosyl-(~-+)-a-... more lines 3-5 should read as follows: identified as 1,2-di-O-acyl-3-0-[ 0-a-D-glucopyranosyl-(~-+)-a-D-glucopyranosyl]g~ycerol and 1,2-di-O-acyl-3-0-[ O-a-D-glucopyranosy1-( 1 +2)-(6-0-acyl-a-~-glucopyrano-sy1)lglycerol.

Research paper thumbnail of Components of multiprotein-RNA complex that controls transcription elongation in Escherichia coli phage lambda

Methods in Enzymology, 1996

... Asis Das, Mahadeb Pal, Jaime Garcia Mena, William Whalen, Krystyna Wolska, Robin Crossley, Wi... more ... Asis Das, Mahadeb Pal, Jaime Garcia Mena, William Whalen, Krystyna Wolska, Robin Crossley, William Rees, Peter H. von Hippel, Nina Costantino, Donald Court, Marie Mazzulla, Amanda S. Altieri, R.Andrew Byrd, Samit Chattopadhyay, Joseph DeVito and Balaram Ghosh. ...