Andersen Research Group

Publications

2008

The Trp-cage: optimizing the stability of a globular miniprotein

B Barua, JC Lin, DV Williams, P Kummler, JW Neidigh, NH Andersen The Trp-cage: optimizing the stability of a globular miniprotein Protein Engineering Design & Selection, 21, 2008, 171-185.

2007

A Pre-existing Hydrophobic Collapse in the Unfolded State of an Ultrafast Folding Protein

KH Mok, LT Kuhn, M Goez, IJ Day, JC Lin, NH Andersen, PJ Hore A Pre-existing Hydrophobic Collapse in the Unfolded State of an Ultrafast Folding Protein Nature, 255, 2007, 106-109.

2006

Measuring Cooperativity in the Formation of a Three-stranded β-sheet (Double Hairpin)

FM Hudson, NH Andersen Measuring Cooperativity in the Formation of a Three-stranded β-sheet (Double Hairpin) Biopolymers, 83, 2006, 424-433.

Minimization and Optimization of Designed beta-Hairpin Folds

NH Andersen, KA Olsen, RM Fesinmeyer, X Tan, FM Hudson, LA Eidenschink, SR Farazi Minimization and Optimization of Designed beta-Hairpin Folds Journal of the American Chemical Society, 128, 2006, 6101-6110.

2005

Chemical Shifts Provide Fold Populations and Register of β Hairpins and β Sheets

RM Fesinmeyer, FM Hudson, KA Olsen, GWN White, A Euser, NH Andersen Chemical Shifts Provide Fold Populations and Register of β Hairpins and β Sheets Journal of Biomolecular NMR, 33, 2005, 213-231.

A Slow, Tight-binding Inhibitor of the Zinc-Depedent Deacetylase LpxC in the Lipid A Biosynthetic Pathway

AL McClerren, SA Endsley, JL Bowman, NH Andersen, Z Guan, J Rudolph, CRH Raetz A Slow, Tight-binding Inhibitor of the Zinc-Depedent Deacetylase LpxC in the Lipid A Biosynthetic Pathway Biochemistry, 44, 2005, 16574-16583.

Hairpin Folding Rates Reflect Mutations Within and Remote from the Turn Region

KA Olsen, RM Fesinmeyer, JM Stewart, NH Andersen Hairpin Folding Rates Reflect Mutations Within and Remote from the Turn Region Proceedings of the National Academy of Sciences, USA, 102, 2005, 15483-15487.

Studies of helix fraying and solvation using 13C’ isotopomers

RM Fesinmeyer, ES Peterson, RB Dyer, NH Andersen Studies of helix fraying and solvation using 13C’ isotopomers Protein Science, 14, 2005, 2324-2332.

Hairpin Folding Dynamics: The Cold-Denatured State Is Predisposed for Rapid Refolding

RB Dyer, SJ Maness, S Franzen, RM Fesinmeyer, KA Olsen, NH Andersen Hairpin Folding Dynamics: The Cold-Denatured State Is Predisposed for Rapid Refolding Biochemistry, 44, 2005, 10406-10415.

2004

The Helical Alanine Controversy: An (Ala)6 Insertion Dramatically Increases Helicity

JC Lin, B Barua, NH Andersen The Helical Alanine Controversy: An (Ala)6 Insertion Dramatically Increases Helicity Journal of the American Chemical Society, 126, 2004, 13679-13684.

Exenatide: NMR/CD evaluation of the medium dependence of conformation and aggregation state

FM Hudson, NH Andersen Exenatide: NMR/CD evaluation of the medium dependence of conformation and aggregation state Biopolymers (Peptide Science), 76, 2004, 298-308.

The Mechanism of Beta-Hairpin Formation

RB Dyer, SJ Maness, ES Peterson, S Franzen, RM Fesinmeyer, NH Andersen The Mechanism of Beta-Hairpin Formation Biochemistry, 43, 2004, 11560-11566.

Enhanced Hairpin Stability through Loop Design: The Case of the Protein G B1 Domain Hairpin

RM Fesinmeyer, FM Hudson, NH Andersen Enhanced Hairpin Stability through Loop Design: The Case of the Protein G B1 Domain Hairpin Journal of the American Chemical Society, 126, 2004, 7238-7243.

2003

A Low-barrier Hydrogen Bond Between Histidine of Secreted Phospholipase A2 and a Transition State Analog Inhibitor

MJ Poi, J Tomaszewski, C Yuan, CA Dunlap, NH Andersen, MH Gelb, MD Tsai A Low-barrier Hydrogen Bond Between Histidine of Secreted Phospholipase A2 and a Transition State Analog Inhibitor Journal of Molecular Biology, 255, 2003, 997-1009.

Possible Locally Driven Folding Pathways of TC5b, a 20-residue Protein

GV Nikifororvich, NH Andersen, RM Fesinmeyer, C Frieden Possible Locally Driven Folding Pathways of TC5b, a 20-residue Protein Proteins, 52, 2003, 292-302.

2002

19F NMR Studies of Tryptophan/Serum Albumin Binding

B Cao, SA Endsley, NH Andersen 19F NMR Studies of Tryptophan/Serum Albumin Binding Bioorganic and Medicinal Chemistry, 11, 2002, 69-75.

Potent, Novel in Vitro Inhibitors of the Pseudomonas aeruginosa Deacetylase LpxC

T Kline, NH Andersen, EA Harwood, J Bowman, A Malanda, SA Endsley, AL Erwin, M Doyle, S Fong, AL Harris, B Mendelsohn, K Mdluli, CRH Raetz, CK Stover, PR Witte, A Yabannavar, and S Zhu Potent, Novel in Vitro Inhibitors of the Pseudomonas aeruginosa Deacetylase LpxC Journal of Medicinal Chemistry, 45, 2002, 3112-3129.

Designing a 20-Residue Protein

JW Neidigh, RM Fesinmeyer, NH Andersen Designing a 20-Residue Protein Nature Structural Biology, 9, 2002, 425-430.

Activation of Erythropoietin Receptor through a Novel Extracellular Binding Site

T Naranda, RI Kaufman, J Li, K Wong, A Boge, D Hallen, KYC Fung, MW Duncan, NH Andersen, A Goldstein, L Olsson Activation of Erythropoietin Receptor through a Novel Extracellular Binding Site Endocrinology, 143, 2002, 2293-2302.

Medium-Dependence of the secondary structure of exendin-4 and glucagon-like-peptide-1

NH Andersen, Y Brodsky, JW Neidigh, and KS Prickett Medium-Dependence of the secondary structure of exendin-4 and glucagon-like-peptide-1 Bioorganic and Medicinal Chemistry, 10, 2002, 79-85.

2001

Protein Structure, Stability, and Folding. Methods in Molecular Biology. Volume 168 Edited by Kenneth P. Murphy. Book Review

NH Andersen Protein Structure, Stability, and Folding. Methods in Molecular Biology. Volume 168 Edited by Kenneth P. Murphy. Book Review Journal of the American Chemical Society, 123, 2001, 12933-12934.

Peptide Conformational Changes Induced by Tryptophan-Thosphocholine Interactions in a Micelle

JW Neidigh, NH Andersen Peptide Conformational Changes Induced by Tryptophan-Thosphocholine Interactions in a Micelle Biopolymers, 65, 2002, 354-361.

Dynamics of the Primary Processes of Protein Folding: Helix Nucleation

JH Werner, RB Dyer, RM Fesinmeyer, NH Andersen Dynamics of the Primary Processes of Protein Folding: Helix Nucleation Journal of Physical Chemistry, B, 106, 2002, 487-494.

Determinants of Miniprotein Stability: Can Anything Replace a Buried H-bonded Trp Sidechain?

B Barua, NH Andersen Determinants of Miniprotein Stability: Can Anything Replace a Buried H-bonded Trp Sidechain? Letters in Peptide Science, 8, 2002, 221-226.

Exendin-4 and Glucagon-like-peptide-1: NMR Structural Comparisons in the Solution and Micelle-Associated States

JW Neidigh, RM Fesinmeyer, KS Prickett, and NH Andersen Exendin-4 and Glucagon-like-peptide-1: NMR Structural Comparisons in the Solution and Micelle-Associated States Biochemistry, 40, 2001, 13188-13200.

1999

Effect of Hexafluoroisopropanol on the Thermodynamics of Peptide Secondary Structure Formation

NH Andersen, RB Dyer, RM Fesinmeyer, F Gai, Z Liu, JW Neidigh, and H Tong Effect of Hexafluoroisopropanol on the Thermodynamics of Peptide Secondary Structure Formation Journal of the American Chemical Society, 121, 1999, 9879-9880.

1997

Empirical Parameterization of a Model for Predicting Peptide Helix/Coil Equilibrium Populations

NH Andersen and H Tong Empirical Parameterization of a Model for Predicting Peptide Helix/Coil Equilibrium Populations Protein Science, 6, 1997, 1920-1936.

Formation of a Molten-Globule-Like State of Myoglobin in Aqueous Hexafluoroisopropanol

JR Cort and NH Andersen Formation of a Molten-Globule-Like State of Myoglobin in Aqueous Hexafluoroisopropanol Biochemical and Biophysical Research Communications, 233, 1997, 687-691.

Extracting Information from the Temperature Gradients of Polypeptide NH Chemical Shifts: I. The Importance of Conformational Averaging

NH Andersen, JW Neidigh, SM Harris, GM Lee, Z Liu, and H Tong Extracting Information from the Temperature Gradients of Polypeptide NH Chemical Shifts: I. The Importance of Conformational Averaging Journal of the American Chemical Society, 119, 1997, 8547-8561.

1996

Efforts Toward Deriving the CD Spectrum of a 3-10 Helix in Aqueous Medium

NH Andersen, Z Liu, and KS Prickett Efforts Toward Deriving the CD Spectrum of a 3-10 Helix in Aqueous Medium FEBS Letters, 255, 1996, 140-146.

Synthesis and X-ray Crystal Structure of 1,4-Dihydro-2,6-dimethyl-4-(2'-isopropylphenyl)-3,5-pyridine-dicarboxylic acid dimethyl ester: A Nifedipine Analogue

RB Palmer and NH Andersen Synthesis and X-ray Crystal Structure of 1,4-Dihydro-2,6-dimethyl-4-(2'-isopropylphenyl)-3,5-pyridine-dicarboxylic acid dimethyl ester: A Nifedipine Analogue Bioorganic and Medicinal Chemistry Letters, 6, 1996, 2173-2176.

Cold Denaturation of Monomeric Peptide Helices

NH Andersen, JR Cort, Z Liu, S Sjoberg, and H Tong Cold Denaturation of Monomeric Peptide Helices Journal of the American Chemical Society, 118, 1996, 10309-10310.

Conformational Dynamics of 4-Aryl-1,4-dihydropyridine Calcium Channel Antagonists. 1. Quantitation of C4-C1' Bond Rotation Barriers

RB Palmer, TM Andro, NR Natale, and NH Andersen Conformational Dynamics of 4-Aryl-1,4-dihydropyridine Calcium Channel Antagonists. 1. Quantitation of C4-C1' Bond Rotation Barriers Tetrahedron, 52, 1996, 9665-9680.

Conformational Preferences and Dynamics of 4-Isoxazolyl-1,4-dihydropyridine Calcium Channel Antagonists as Determined by Variable Temperature NMR and NOE Experiments

RB Palmer, TM Andro, NR Natale, and NH Andersen Conformational Preferences and Dynamics of 4-Isoxazolyl-1,4-dihydropyridine Calcium Channel Antagonists as Determined by Variable Temperature NMR and NOE Experiments Magnetic Resonance in Chemistry, 34, 1996, 495-504.

1995

Structural and Dynamic Properties of a b-Hairpin-Forming Linear Peptide. I. Modeling Using Ensemble- Averaged Constraints

KL Constantine, L Mueller, NH Andersen, H Tong, CF Wandler, MS Friedrichs, and RE Bruccoleri Structural and Dynamic Properties of a b-Hairpin-Forming Linear Peptide. I. Modeling Using Ensemble- Averaged Constraints Journal of the American Chemical Society, 117, 1995, 10841-10854.

Aryl-Dihydropyridine Rotational Barriers and Rotameric Preferences in Dihydropyridine Calcium Channel Antagonists

RB Palmer and NH Andersen Aryl-Dihydropyridine Rotational Barriers and Rotameric Preferences in Dihydropyridine Calcium Channel Antagonists Trends in Organic Chemistry, 5, 1995, 171-187.

The Endothelin C-Terminal Signal Fragment: Determinants of the Conformational Equilibrium in situ and Detached

NH Andersen, C Chen, and GM Lee The Endothelin C-Terminal Signal Fragment: Determinants of the Conformational Equilibrium in situ and Detached Protein and Peptide Letters, 1, 1995, 215-222.

The Receptor Binding Affinity of Monocyclic [Ala3, Xaa11]-Endothelin-1 Analogs Correlates with Inducible Helix Length

NH Andersen, SM Harris, VG Lee, ECK Liu, S Moreland, and JT Hunt The Receptor Binding Affinity of Monocyclic [Ala3, Xaa11]-Endothelin-1 Analogs Correlates with Inducible Helix Length Bioorganic and Medicinal Chemistry, 3, 1995, 113-124.

1994

b-Structure in Human Amylin and Two Designer b-Peptides: CD and NMR Spectroscopic Comparisons Suggest Soluble b-Oligomers and the Absence of Significant Populations of b-Strand Dimers

JR Cort, Z Liu, GM Lee, SM Harris, KS Prickett, LSL Gaeta, and NH Andersen b-Structure in Human Amylin and Two Designer b-Peptides: CD and NMR Spectroscopic Comparisons Suggest Soluble b-Oligomers and the Absence of Significant Populations of b-Strand Dimers Biochemical and Biophysical Research Communications, 204, 1994, 1088-1095.

Does the solid-state structure of endothelin-1 provide insights concerning the solution-state conformational equilibrium?

GM Lee, C Chen, TM Marschner, and NH Andersen Does the solid-state structure of endothelin-1 provide insights concerning the solution-state conformational equilibrium? FEBS Letters, 255, 1994, 140-146.

CD Studies of a Peptide Mimetic of L-Type Calcium Channels

NH Andersen and RB Palmer CD Studies of a Peptide Mimetic of L-Type Calcium Channels Bioorganic and Medicinal Chemistry Letters, 4, 1994, 817-822.

1993

A Comparison of BKCALC-Adjusted Constraints and Those from Program DISCON using Simulated Data for a B-DNA Structure

X Lai, B Reid, and NH Andersen A Comparison of BKCALC-Adjusted Constraints and Those from Program DISCON using Simulated Data for a B-DNA Structure Journal of Magnetic Resonance, Series B, 101, 1993, 288-293.

The DISCON Algorithm, an Accurate and Robust Alternative to an Eigenvalue Solution for Extracting Experimental Distances from NOESY Data

X Lai, C Chen, and NH Andersen The DISCON Algorithm, an Accurate and Robust Alternative to an Eigenvalue Solution for Extracting Experimental Distances from NOESY Data Journal of Magnetic Resonance, Series B, 101, 1993, 271-287.

Dactylocyclines: Novel Tetracycline Glycosides Active Against Tetracycline-resistant Bacteria

AA Tymiak, C Aklonis, MS Bolger, AD Kahle, DR Kirsch, J O'Sullivan, MA Porubcan, P Principe, WH Trejo. HA Ax, JS Wells, NH Andersen, P Devasthale, H Telikepalli, DV Velde, J-Y Zou and LA Mitsche Dactylocyclines: Novel Tetracycline Glycosides Active Against Tetracycline-resistant Bacteria Journal of Organic Chemistry, 58, 1993, 535-537.

Hevein: The NMR Assignment and an Assessment of Solution-state Folding for the Agglutinin-Toxin Motif

NH Andersen, B Cao, A Rodriguez, and B Arreguin Hevein: The NMR Assignment and an Assessment of Solution-state Folding for the Agglutinin-Toxin Motif Biochemistry, 32, 1993, 1407-1422.

1992

Peptide/Protein Structure Analysis using the Chemical Shift Index Method: Upfield a-CH Values Reveal Dynamic Helices and aL Sites

NH Andersen, B Cao, and C Chen Peptide/Protein Structure Analysis using the Chemical Shift Index Method: Upfield a-CH Values Reveal Dynamic Helices and aL Sites Biochemical and Biophysical Research Communications, 184, 1992, 1008-1014.

Dactylocyclines, Novel Tetracycline Derivatives Produced by a Dactylosporangium sp. II. Structure Elucidation

AA Tymiak, HA Ax, MS Bolger, AD Kahle, MA Porubcan, and NH Andersen Dactylocyclines, Novel Tetracycline Derivatives Produced by a Dactylosporangium sp. II. Structure Elucidation Journal of Antibiotics, 45, 1992, 1899-1906.

Solution Conformation of a Cyclic Pentapeptide Endothelin Antagonist: Comparison of Structures Obtained from Constrained Dynamics and Conformational Search

SR Krystek Jr., DA Bassolino, RE Bruccoleri, JT Hunt, MA Porubcan, CF Wandler and NH Andersen Solution Conformation of a Cyclic Pentapeptide Endothelin Antagonist: Comparison of Structures Obtained from Constrained Dynamics and Conformational Search FEBS Letters, 255, 1992, 255-261.

A Preparation of Imidazolyl Acids Tethered to Agarose Gels and Assessment of the Degree of Coupling for Affinity Chromatography

J Rhee and NH Andersen A Preparation of Imidazolyl Acids Tethered to Agarose Gels and Assessment of the Degree of Coupling for Affinity Chromatography Bulletin of the Korean Chemical Society, 13, 1992, 208-210.

An Approach to Isolation of Thromboxane Synthase by Ligand Tethered Affinity Techniques

NH Andersen and J Rhee An Approach to Isolation of Thromboxane Synthase by Ligand Tethered Affinity Techniques Bulletin of the Korean Chemical Society, 13, 1992, 119-122.

Conformational Isomerism of Endothelin in Acidic Aqueous Media: A Quantitative NOESY Analysis

NH Andersen, C Chen, TM Marschner, SR Krystek, and D Bassolino Conformational Isomerism of Endothelin in Acidic Aqueous Media: A Quantitative NOESY Analysis Biochemistry, 31, 1992, 1280-1295.

1991

Quantitative NOESY-Based Conformational Analysis of Endothelin-1 in Aqueous Media

NH Andersen, C Chen, TM Marschner, SR Krystek, D Bassolino, and J Novotny Quantitative NOESY-Based Conformational Analysis of Endothelin-1 in Aqueous Media Journal of Cellular Biochemistry, 15, 1991, 83.

A Conformation-Preference/Potency Correlation for GnRH analogs: NMR Evidence

NH Andersen and PK Hammen A Conformation-Preference/Potency Correlation for GnRH analogs: NMR Evidence Bioorganic and Medicinal Chemistry Letters, 1, 1991, 263-266.

Conformation of Endothelin in Aqueous Glycol Determined by 1H-NMR and molecular Dynamics Simulations

SR Krystek Jr., DA Bassolino, J Novotny, C Chen, TM Marschner and NH Andersen Conformation of Endothelin in Aqueous Glycol Determined by 1H-NMR and molecular Dynamics Simulations FEBS Letters, 255, 1991, 212-218.

Active Conformation of 1,4-Dihydropyridine Calcium Entry Blockers: Effect of Size of 2-Aryl Substituent on Aryl Rotamer Preference

G Rovnyak, NH Andersen, J Gougoutas, A Hedberg, SD Kimball, M Malley, S Moreland, M Porubcan and A Pudzianowski Active Conformation of 1,4-Dihydropyridine Calcium Entry Blockers: Effect of Size of 2-Aryl Substituent on Aryl Rotamer Preference Journal of Medicinal Chemistry, 34, 1991, 2521-2524.

1990

Computer-Aided Conformational Analysis Based on NOESY Signal Intensities

NH Andersen, X Lai, PK Hammen, and TM Marschner Computer-Aided Conformational Analysis Based on NOESY Signal Intensities NMR Applications in Biopolymers, 0, 1990, 95-134.