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  1. Article ; Online: In memoriam: Reflections on Charles Tanford (1921-2009).

    Pace, C Nick

    Protein science : a publication of the Protein Society

    2009  Volume 19, Issue 1, Page(s) 1–5

    MeSH term(s) Biochemistry ; Biophysics ; History, 20th Century ; History, 21st Century ; Humans ; Proteins
    Chemical Substances Proteins
    Language English
    Publishing date 2009-11-24
    Publishing country United States
    Document type Biography ; Historical Article ; Journal Article ; Portrait
    ZDB-ID 1106283-6
    ISSN 1469-896X ; 0961-8368
    ISSN (online) 1469-896X
    ISSN 0961-8368
    DOI 10.1002/pro.291
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  2. Article ; Online: Energetics of protein hydrogen bonds.

    Pace, C Nick

    Nature structural & molecular biology

    2009  Volume 16, Issue 7, Page(s) 681–682

    MeSH term(s) Hydrogen Bonding ; Molecular Structure ; Protein Conformation ; Proteins/chemistry
    Chemical Substances Proteins
    Language English
    Publishing date 2009-07-05
    Publishing country United States
    Document type Comment ; News
    ZDB-ID 2126708-X
    ISSN 1545-9985 ; 1545-9993
    ISSN (online) 1545-9985
    ISSN 1545-9993
    DOI 10.1038/nsmb0709-681
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  3. Article ; Online: Forces stabilizing proteins.

    Nick Pace, C / Scholtz, J Martin / Grimsley, Gerald R

    FEBS letters

    2014  Volume 588, Issue 14, Page(s) 2177–2184

    Abstract: The goal of this article is to summarize what has been learned about the major forces stabilizing proteins since the late 1980s when site-directed mutagenesis became possible. The following conclusions are derived from experimental studies of hydrophobic ...

    Abstract The goal of this article is to summarize what has been learned about the major forces stabilizing proteins since the late 1980s when site-directed mutagenesis became possible. The following conclusions are derived from experimental studies of hydrophobic and hydrogen bonding variants. (1) Based on studies of 138 hydrophobic interaction variants in 11 proteins, burying a -CH2- group on folding contributes 1.1±0.5 kcal/mol to protein stability. (2) The burial of non-polar side chains contributes to protein stability in two ways: first, a term that depends on the removal of the side chains from water and, more importantly, the enhanced London dispersion forces that result from the tight packing in the protein interior. (3) Based on studies of 151 hydrogen bonding variants in 15 proteins, forming a hydrogen bond on folding contributes 1.1±0.8 kcal/mol to protein stability. (4) The contribution of hydrogen bonds to protein stability is strongly context dependent. (5) Hydrogen bonds by side chains and peptide groups make similar contributions to protein stability. (6) Polar group burial can make a favorable contribution to protein stability even if the polar group is not hydrogen bonded. (7) Hydrophobic interactions and hydrogen bonds both make large contributions to protein stability.
    MeSH term(s) Cystine/chemistry ; Entropy ; Humans ; Hydrogen Bonding ; Hydrophobic and Hydrophilic Interactions ; Models, Molecular ; Protein Conformation ; Protein Stability ; Proteins/chemistry
    Chemical Substances Proteins ; Cystine (48TCX9A1VT)
    Language English
    Publishing date 2014-05-17
    Publishing country England
    Document type Journal Article ; Research Support, N.I.H., Extramural ; Research Support, Non-U.S. Gov't ; Review
    ZDB-ID 212746-5
    ISSN 1873-3468 ; 0014-5793
    ISSN (online) 1873-3468
    ISSN 0014-5793
    DOI 10.1016/j.febslet.2014.05.006
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  4. Article: Forces stabilizing proteins

    Nick Pace, C / J. Martin Scholtz / Gerald R. Grimsley

    Federation of European Biochemical Societies FEBS letters. 2014 June 27, v. 588, no. 14

    2014  

    Abstract: The goal of this article is to summarize what has been learned about the major forces stabilizing proteins since the late 1980s when site-directed mutagenesis became possible. The following conclusions are derived from experimental studies of hydrophobic ...

    Abstract The goal of this article is to summarize what has been learned about the major forces stabilizing proteins since the late 1980s when site-directed mutagenesis became possible. The following conclusions are derived from experimental studies of hydrophobic and hydrogen bonding variants. (1) Based on studies of 138 hydrophobic interaction variants in 11 proteins, burying a –CH2− group on folding contributes 1.1±0.5kcal/mol to protein stability. (2) The burial of non-polar side chains contributes to protein stability in two ways: first, a term that depends on the removal of the side chains from water and, more importantly, the enhanced London dispersion forces that result from the tight packing in the protein interior. (3) Based on studies of 151 hydrogen bonding variants in 15 proteins, forming a hydrogen bond on folding contributes 1.1±0.8kcal/mol to protein stability. (4) The contribution of hydrogen bonds to protein stability is strongly context dependent. (5) Hydrogen bonds by side chains and peptide groups make similar contributions to protein stability. (6) Polar group burial can make a favorable contribution to protein stability even if the polar group is not hydrogen bonded. (7) Hydrophobic interactions and hydrogen bonds both make large contributions to protein stability.
    Keywords hydrogen bonding ; hydrophobic bonding ; hydrophobicity ; proteins ; site-directed mutagenesis
    Language English
    Dates of publication 2014-0627
    Size p. 2177-2184.
    Publishing place Elsevier B.V.
    Document type Article
    ZDB-ID 212746-5
    ISSN 1873-3468 ; 0014-5793
    ISSN (online) 1873-3468
    ISSN 0014-5793
    DOI 10.1016/j.febslet.2014.05.006
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  5. Article: Cytotoxicity of RNase Sa to the acute myeloid leukemia Kasumi-1 cells depends on the net charge.

    Mitkevich, Vladimir A / Burnysheva, Ksenia M / Ilinskaya, Olga N / Pace, C Nick / Makarov, Alexander A

    Oncoscience

    2014  Volume 1, Issue 11, Page(s) 738–744

    Abstract: The majority of known cytotoxic RNases are basic proteins which destroy intracellular RNA. Cationization of RNases is considered to be an effective strategy for strengthening their antitumor properties. We constructed a set of RNase Sa variants ... ...

    Abstract The majority of known cytotoxic RNases are basic proteins which destroy intracellular RNA. Cationization of RNases is considered to be an effective strategy for strengthening their antitumor properties. We constructed a set of RNase Sa variants consisting of charge reversal mutants, charge neutralization mutants, and variants with positively charged cluster at the N-terminus. All constructs retain a high level of catalytic activity and differ in net charge. Using acute myeloid leukemia cells Kasumi-1 we have shown that (i) cytotoxicity of RNase Sa mutants is linearly enhanced by cationization, (ii) the ability of cytotoxic mutants to induce cell death is caused by induction of apoptosis and (iii) localization of positive charge on N-terminus does not contribute to RNase Sa cytotoxicity. Capacity to induce apoptosis in malignant cells and the absence of necrotic effects make the RNase Sa mutants with high positive charge a suitable anti-cancer agent.
    Language English
    Publishing date 2014-11-10
    Publishing country United States
    Document type Journal Article
    ISSN 2331-4737
    ISSN 2331-4737
    DOI 10.18632/oncoscience.97
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  6. Article: Protein ionizable groups: pK values and their contribution to protein stability and solubility.

    Pace, C Nick / Grimsley, Gerald R / Scholtz, J Martin

    The Journal of biological chemistry

    2009  Volume 284, Issue 20, Page(s) 13285–13289

    Abstract: The structure, stability, solubility, and function of proteins depend on their net charge and on the ionization state of the individual residues. Consequently, biochemists are interested in the pK values of the ionizable groups in proteins and how these ... ...

    Abstract The structure, stability, solubility, and function of proteins depend on their net charge and on the ionization state of the individual residues. Consequently, biochemists are interested in the pK values of the ionizable groups in proteins and how these pK values depend on their environment. We review what has been learned about pK values of ionizable groups in proteins from experimental studies and discuss the important contributions they make to protein stability and solubility.
    MeSH term(s) History, 20th Century ; Protein Conformation ; Protein Stability ; Proteins/chemistry ; Proteins/history ; Solubility ; Static Electricity
    Chemical Substances Proteins
    Language English
    Publishing date 2009-01-21
    Publishing country United States
    Document type Historical Article ; Journal Article ; Review
    ZDB-ID 2997-x
    ISSN 1083-351X ; 0021-9258
    ISSN (online) 1083-351X
    ISSN 0021-9258
    DOI 10.1074/jbc.R800080200
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  7. Article ; Online: Solvent denaturation of proteins and interpretations of the m value.

    Scholtz, J Martin / Grimsley, Gerald R / Pace, C Nick

    Methods in enzymology

    2009  Volume 466, Page(s) 549–565

    Abstract: The stability of globular proteins is important in medicine, proteomics, and basic research. The conformational stability of the folded state can be determined experimentally by analyzing urea, guanidinium chloride, and thermal denaturation curves. ... ...

    Abstract The stability of globular proteins is important in medicine, proteomics, and basic research. The conformational stability of the folded state can be determined experimentally by analyzing urea, guanidinium chloride, and thermal denaturation curves. Solvent denaturation curves in particular may give useful information about a protein such as the existence of domains or the presence of stable folding intermediates. The linear extrapolation method (LEM) for analyzing solvent denaturation curves gives the parameter m, which is a measure of the dependence of ΔG on denaturant concentration. There is much recent interest in the m value as it relates to the change in accessible surface area of a protein when it unfolds and what it may reveal about the denatured states of proteins.
    MeSH term(s) Animals ; Guanidine/chemistry ; Humans ; Linear Models ; Protein Conformation ; Protein Denaturation ; Protein Stability ; Proteins/chemistry ; Ribonuclease, Pancreatic/chemistry ; Ribonucleases/chemistry ; Thermodynamics ; Urea/chemistry
    Chemical Substances Proteins ; Urea (8W8T17847W) ; Ribonucleases (EC 3.1.-) ; ribonuclease Sa3 (EC 3.1.-) ; Ribonuclease, Pancreatic (EC 3.1.27.5) ; Guanidine (JU58VJ6Y3B)
    Language English
    Publishing date 2009
    Publishing country United States
    Document type Journal Article ; Research Support, N.I.H., Extramural ; Research Support, Non-U.S. Gov't
    ISSN 1557-7988 ; 0076-6879
    ISSN (online) 1557-7988
    ISSN 0076-6879
    DOI 10.1016/S0076-6879(09)66023-7
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  8. Article ; Online: Spectrophotometric determination of protein concentration.

    Grimsley, Gerald R / Pace, C Nick

    Current protocols in protein science

    2004  Volume Chapter 3, Page(s) Unit 3.1

    Abstract: ... using absorbance spectroscopy. The absorbance, A, is a linear function of the molar concentration, C ... according to the Beer-Lambert law: A = epsilon x l x c, where e is the molar absorption coefficient and l is ...

    Abstract The concentration of a purified protein in solution is most conveniently and accurately measured using absorbance spectroscopy. The absorbance, A, is a linear function of the molar concentration, C, according to the Beer-Lambert law: A = epsilon x l x c, where e is the molar absorption coefficient and l is the cell path length. This unit provides protocols for calculation of epsilon for a folded or unfolded protein, making use of the average epsilon values for the three contributing chromophores in proteins (the side chains of Trp, Tyr, and Cys). A basic protocol describes how to measure the concentration of a protein using the calculated epsilon and the Beer-Lambert law. A sensitive method is provided for measuring the concentration of proteins that contain few if any tryptophan or tyrosine residues, and a simple method is provided for estimating total protein concentration in crude extracts.
    MeSH term(s) Protein Folding ; Proteins/analysis ; Spectrophotometry, Ultraviolet/methods
    Chemical Substances Proteins
    Language English
    Publishing date 2004-11
    Publishing country United States
    Document type Journal Article
    ZDB-ID 2179077-2
    ISSN 1934-3663 ; 1934-3655
    ISSN (online) 1934-3663
    ISSN 1934-3655
    DOI 10.1002/0471140864.ps0301s33
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  9. Article ; Online: Measuring and increasing protein solubility.

    Trevino, Saul R / Scholtz, J Martin / Pace, C Nick

    Journal of pharmaceutical sciences

    2008  Volume 97, Issue 10, Page(s) 4155–4166

    Abstract: High concentration protein delivery is difficult to achieve for several protein pharmaceuticals due to low solubility. In this review, we discuss different types of low protein solubility, including low in vitro solubility, which is relevant to the ... ...

    Abstract High concentration protein delivery is difficult to achieve for several protein pharmaceuticals due to low solubility. In this review, we discuss different types of low protein solubility, including low in vitro solubility, which is relevant to the formulation of protein pharmaceuticals. We also discuss different methods of measuring protein solubility with an emphasis on the method of inducing amorphous precipitation using ammonium sulfate. Finally, we discuss strategies for increasing protein solubility, including site-directed mutagenesis. Evidence from solubility-changing mutations in the literature indicate that some hydrophilic residues (aspartic acid, glutamic acid, and serine) contribute significantly more favorably to protein solubility than other hydrophilic residues (asparagine, glutamine, threonine, lysine, and arginine). These findings should prove useful especially in cases where protein structure is not known. In these cases, instead of targeting hydrophobic residues that are often buried, one could target hydrophilic residues that do not contribute favorably to protein solubility and replace them with hydrophilic residues that contribute more favorably.
    MeSH term(s) Chemical Precipitation ; Mutagenesis, Site-Directed ; Pharmaceutical Preparations/chemistry ; Proteins/chemistry ; Proteins/genetics ; Solubility
    Chemical Substances Pharmaceutical Preparations ; Proteins
    Language English
    Publishing date 2008-10
    Publishing country United States
    Document type Journal Article ; Research Support, N.I.H., Extramural ; Research Support, Non-U.S. Gov't ; Review
    ZDB-ID 3151-3
    ISSN 1520-6017 ; 0022-3549
    ISSN (online) 1520-6017
    ISSN 0022-3549
    DOI 10.1002/jps.21327
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  10. Article ; Online: A summary of the measured pK values of the ionizable groups in folded proteins.

    Grimsley, Gerald R / Scholtz, J Martin / Pace, C Nick

    Protein science : a publication of the Protein Society

    2008  Volume 18, Issue 1, Page(s) 247–251

    Abstract: ... Lys side chains, and the C and N termini of 78 folded proteins. The majority of these values are ... His 6.6 +/- 1.0 (131); Cys 6.8 +/- 2.7 (25); Tyr 10.3 +/- 1.2 (20); Lys 10.5 +/- 1.1 (35); C-terminus 3 ...

    Abstract We tabulated 541 measured pK values reported in the literature for the Asp, Glu, His, Cys, Tyr, and Lys side chains, and the C and N termini of 78 folded proteins. The majority of these values are for the Asp, Glu, and His side chains. The average pK values are Asp 3.5 +/- 1.2 (139); Glu 4.2 +/- 0.9 (153); His 6.6 +/- 1.0 (131); Cys 6.8 +/- 2.7 (25); Tyr 10.3 +/- 1.2 (20); Lys 10.5 +/- 1.1 (35); C-terminus 3.3 +/- 0.8 (22) and N-terminus 7.7 +/- 0.5 (16). We compare these results with the measured pK values of these groups in alanine pentapeptides, and comment on our overall findings.
    MeSH term(s) Amino Acid Sequence/physiology ; Amino Acids/chemistry ; Aspartic Acid/chemistry ; Glutamic Acid/chemistry ; Histidine/chemistry ; Hydrogen-Ion Concentration ; Isoelectric Point ; Nuclear Magnetic Resonance, Biomolecular ; Protein Folding ; Protein Structure, Tertiary/physiology ; Proteins/chemistry ; Titrimetry
    Chemical Substances Amino Acids ; Proteins ; Aspartic Acid (30KYC7MIAI) ; Glutamic Acid (3KX376GY7L) ; Histidine (4QD397987E)
    Language English
    Publishing date 2008-12-27
    Publishing country United States
    Document type Journal Article ; Research Support, N.I.H., Extramural ; Research Support, Non-U.S. Gov't
    ZDB-ID 1106283-6
    ISSN 1469-896X ; 0961-8368
    ISSN (online) 1469-896X
    ISSN 0961-8368
    DOI 10.1002/pro.19
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