A systematic study of minima in alanine dipeptide

Mironov, Vladimir; Alexeev, Yuri; Mulligan, Vikram Khipple; Fedorov, Dmitri G.

doi:10.1002/jcc.25589

Title: A systematic study of minima in alanine dipeptide

Journal Article · Tue Oct 23 00:00:00 EDT 2018 · Journal of Computational Chemistry

DOI:https://doi.org/10.1002/jcc.25589· OSTI ID:1510055

^[1]; Alexeev, Yuri ^[2]; Mulligan, Vikram Khipple ^[3];

^[4]

Lomonosov Moscow State Univ., Moscow (Russian Federation). Dept. of Chemistry
Argonne National Lab. (ANL), Argonne, IL (United States). Computational Science Division
Univ. of Washington, Seattle, WA (United States). Dept. of Biochemistry
National Inst. of Advanced Industrial Science and Technology (AIST), Tsukuba (Japan)

The alanine dipeptide is a standard system to model dihedral angles in proteins. It is shown that obtaining the Ramachandran plot accurately is a hard problem because of many local minima; depending on the details of geometry optimizations, different Ramachandran plots can be obtained. To locate all energy minima, starting from geometries from MD simulations, 250,000 geometry optimizations were performed at the level of RHF/6‐31G*, followed by re‐optimizations of the located 827 minima at the level of MP2/6–311++G**, yielding 30 unique minima, most of which were not previously reported in literature. Both in vacuo and solvated structures are discussed. The minima are systematically categorized based on four backbone dihedral angles. The Gibbs energies are evaluated and the structural factors determining the relative stabilities of conformers are discussed. © 2018 Wiley Periodicals, Inc.

View Accepted Manuscript (DOE)

View Accepted Manuscript (Publisher)

Cite

Export

Save

Research Organization:: Argonne National Laboratory (ANL), Argonne, IL (United States)

Sponsoring Organization:: Russian Science Foundation; USDOE

Grant/Contract Number:: AC02-06CH11357

OSTI ID:: 1510055

Alternate ID(s):: OSTI ID: 1485691

Journal Information:: Journal of Computational Chemistry, Vol. 40, Issue 2; ISSN 0192-8651

Publisher:: WileyCopyright Statement

Country of Publication:: United States

Language:: English

Citation Metrics:

Cited by: 22 works

Citation information provided by
Web of Science

References (66)

A fresh look at the Ramachandran plot and the occurrence of standard structures in proteins Hollingsworth, Scott A.; Karplus, P. Andrew BioMolecular Concepts, Vol. 1, Issue 3-4 https://doi.org/10.1515/bmc.2010.022	journal	January 2010
Conformational Study of the Alanine Dipeptide at the MP2 and DFT Levels Vargas, Rubicelia; Garza, Jorge; Hay, Benjamin P. The Journal of Physical Chemistry A, Vol. 106, Issue 13 https://doi.org/10.1021/jp013952f	journal	April 2002
Accurate de novo design of hyperstable constrained peptides Bhardwaj, Gaurav; Mulligan, Vikram Khipple; Bahl, Christopher D. Nature, Vol. 538, Issue 7625 https://doi.org/10.1038/nature19791	journal	September 2016
Temperature dependence of the hydrophobic interaction in protein folding. Baldwin, R. L. Proceedings of the National Academy of Sciences, Vol. 83, Issue 21 https://doi.org/10.1073/pnas.83.21.8069	journal	November 1986
Evaluation of the performance of four molecular docking programs on a diverse set of protein-ligand complexes Li, Xun; Li, Yan; Cheng, Tiejun Journal of Computational Chemistry, Vol. 31, Issue 11 https://doi.org/10.1002/jcc.21498	journal	February 2010
Unfolding and refolding occur much faster for a proline-free proteins than for most proline-containing proteins. Brandts, J. F.; Brennan, M. Proceedings of the National Academy of Sciences, Vol. 74, Issue 10 https://doi.org/10.1073/pnas.74.10.4178	journal	October 1977
Modeling Water, the Hydrophobic Effect, and Ion Solvation Dill, Ken A.; Truskett, Thomas M.; Vlachy, Vojko Annual Review of Biophysics and Biomolecular Structure, Vol. 34, Issue 1 https://doi.org/10.1146/annurev.biophys.34.040204.144517	journal	June 2005
Conformational studies into N-methylation of alanine diamide models: A quantitative approach Siodłak, Dawid; Gajewska, Monika; Macedowska, Agnieszka Journal of Molecular Structure: THEOCHEM, Vol. 775, Issue 1-3 https://doi.org/10.1016/j.theochem.2006.07.021	journal	November 2006
Accurate ab Initio Quantum Chemical Determination of the Relative Energetics of Peptide Conformations and Assessment of Empirical Force Fields Beachy, Michael D.; Chasman, David; Murphy, Robert B. Journal of the American Chemical Society, Vol. 119, Issue 25 https://doi.org/10.1021/ja962310g	journal	June 1997
Conformational Preferences and Vibrational Frequency Distributions of Short Peptides in Relation to Multidimensional Infrared Spectroscopy Gnanakaran, S.; Hochstrasser, R. M. Journal of the American Chemical Society, Vol. 123, Issue 51 https://doi.org/10.1021/ja011088z	journal	December 2001
Ab initio SCF calculations on low-energy conformers of N-acetyl-N'-methylalaninamide and N-acetyl-N'-methylglycinamide Boehm, Hans Joachim; Brode, Stefan Journal of the American Chemical Society, Vol. 113, Issue 19 https://doi.org/10.1021/ja00019a007	journal	September 1991
Solvation effects on alanine dipeptide: A MP2/cc-pVTZ//MP2/6-31G** study of (?, ?) energy maps and conformers in the gas phase, ether, and water Wang, Zhi-Xiang; Duan, Yong Journal of Computational Chemistry, Vol. 25, Issue 14 https://doi.org/10.1002/jcc.20092	journal	January 2004
Non-proline Cis peptide bonds in proteins Jabs, Andreas; Weiss, Manfred S.; Hilgenfeld, Rolf Journal of Molecular Biology, Vol. 286, Issue 1 https://doi.org/10.1006/jmbi.1998.2459	journal	February 1999
Origins of structure in globular proteins. Chan, H. S.; Dill, K. A. Proceedings of the National Academy of Sciences, Vol. 87, Issue 16 https://doi.org/10.1073/pnas.87.16.6388	journal	August 1990
Is Alanine Dipeptide a Good Model for Representing the Torsional Preferences of Protein Backbones? Feig, Michael Journal of Chemical Theory and Computation, Vol. 4, Issue 9 https://doi.org/10.1021/ct800153n	journal	July 2008
GAMESS As a Free Quantum-Mechanical Platform for Drug Research Alexeev, Yuri; P. Mazanetz, Michael; Ichihara, Osamu Current Topics in Medicinal Chemistry, Vol. 12, Issue 18 https://doi.org/10.2174/156802612804910269	journal	September 2012
Populations of the three major backbone conformations in 19 amino acid dipeptides Grdadolnik, Joze; Mohacek-Grosev, Vlasta; Baldwin, Robert L. Proceedings of the National Academy of Sciences, Vol. 108, Issue 5 https://doi.org/10.1073/pnas.1017317108	journal	January 2011
The Rosetta All-Atom Energy Function for Macromolecular Modeling and Design Douglas, Renfrew, P.; J., O'Meara, Matthew; Philip, Bradley, The University of North Carolina at Chapel Hill University Libraries https://doi.org/10.17615/6sk2-v510	text	January 2017
The structure of proteins: Two hydrogen-bonded helical configurations of the polypeptide chain Pauling, L.; Corey, R. B.; Branson, H. R. Proceedings of the National Academy of Sciences, Vol. 37, Issue 4, p. 205-211 https://doi.org/10.1073/pnas.37.4.205	journal	April 1951
Structure and Dynamics of the Homologous Series of Alanine Peptides: A Joint Molecular Dynamics/NMR Study Graf, Jürgen; Nguyen, Phuong H.; Stock, Gerhard Journal of the American Chemical Society, Vol. 129, Issue 5 https://doi.org/10.1021/ja0660406	journal	February 2007
Cis proline mutants of ribonuclease A. II. Elimination of the slow-folding forms by mutation Schultz, David A.; Baldwin, Robert L.; Schmid, Franz X. Protein Science, Vol. 1, Issue 7 https://doi.org/10.1002/pro.5560010710	journal	July 1992
The alanine dipeptide free energy surface in solution Smith, Paul E. The Journal of Chemical Physics, Vol. 111, Issue 12 https://doi.org/10.1063/1.479860	journal	September 1999
A theoretical study of alanine dipeptide and analogs Head-Gordon, Teresa; Head-Gordon, Martin; Frisch, Michael J. International Journal of Quantum Chemistry, Vol. 36, Issue S16 https://doi.org/10.1002/qua.560360725	journal	April 1989
Ab initio studies of molecular geometries. 27. Optimized molecular structures and conformational analysis of N.alpha.-acetyl-N-methylalaninamide and comparison with peptide crystal data and empirical calculations Scarsdale, J. N.; Van Alsenoy, C.; Klimkowski, V. J. Journal of the American Chemical Society, Vol. 105, Issue 11 https://doi.org/10.1021/ja00349a010	journal	June 1983
Stereochemical Criteria for Polypeptide and Protein Chain Conformations Ramakrishnan, C.; Ramachandran, G. N. Biophysical Journal, Vol. 5, Issue 6 https://doi.org/10.1016/S0006-3495(65)86759-5	journal	November 1965
N-Acetyl-L-alanine N′-methylamide: a density functional analysis of the vibrational absorption and vibrational circular dichroism spectra Jalkanen, K. J.; Suhai, S. Chemical Physics, Vol. 208, Issue 1 https://doi.org/10.1016/0301-0104(96)00042-0	journal	July 1996
Large-Scale Computations in Chemistry: A Bird’s Eye View of a Vibrant Field Akimov, Alexey V.; Prezhdo, Oleg V. Chemical Reviews, Vol. 115, Issue 12 https://doi.org/10.1021/cr500524c	journal	April 2015
Perspective: Ab initio force field methods derived from quantum mechanics Xu, Peng; Guidez, Emilie B.; Bertoni, Colleen The Journal of Chemical Physics, Vol. 148, Issue 9 https://doi.org/10.1063/1.5009551	journal	March 2018
Structure of the Alanine Dipeptide in Condensed Phases Determined by ¹³ C NMR Mehta, Manish A.; Fry, Elizabeth A.; Eddy, Matthew T. The Journal of Physical Chemistry B, Vol. 108, Issue 9 https://doi.org/10.1021/jp037871q	journal	March 2004
Replacement of proline-76 with alanine eliminates the slowest kinetic phase in thioredoxin folding Kelley, Robert F.; Richards, Frederic M. Biochemistry, Vol. 26, Issue 21 https://doi.org/10.1021/bi00395a028	journal	October 1987
A Test on Peptide Stability of AMBER Force Fields with Implicit Solvation Shell, M. Scott; Ritterson, Ryan; Dill, Ken A. The Journal of Physical Chemistry B, Vol. 112, Issue 22 https://doi.org/10.1021/jp800282x	journal	June 2008
Theory of the Cooperative Transition between Two Ordered Conformations of Poly(L-proline). II. Molecular Theory in the Absence of Solvent Tanaka, Seiji; Scheraga, Harold A. Macromolecules, Vol. 8, Issue 4 https://doi.org/10.1021/ma60046a024	journal	July 1975
Density Functional Theory and Biomolecules: A Study of Glycine, Alanine, and Their Oligopeptides Kaschner, R.; Hohl, D. The Journal of Physical Chemistry A, Vol. 102, Issue 26 https://doi.org/10.1021/jp980975u	journal	June 1998
Empirical force fields for biological macromolecules: Overview and issues Mackerell, Alexander D. Journal of Computational Chemistry, Vol. 25, Issue 13 https://doi.org/10.1002/jcc.20082	journal	January 2004
The Rosetta All-Atom Energy Function for Macromolecular Modeling and Design Alford, Rebecca F.; Leaver-Fay, Andrew; Jeliazkov, Jeliazko R. Journal of Chemical Theory and Computation, Vol. 13, Issue 6 https://doi.org/10.1021/acs.jctc.7b00125	journal	May 2017
Conformational Analysis of Alanine Dipeptide from Dipolar Couplings in a Water-Based Liquid Crystal Weise, Christoph F.; Weisshaar, James C. The Journal of Physical Chemistry B, Vol. 107, Issue 14 https://doi.org/10.1021/jp026854i	journal	April 2003
One type of gamma-turn, rather than the other gives rise to chain-reversal in proteins Milner-White, E. James; Ross, Brian M.; Ismail, Roslan Journal of Molecular Biology, Vol. 204, Issue 3 https://doi.org/10.1016/0022-2836(88)90368-3	journal	December 1988
Dominant forces in protein folding Dill, Ken A. Biochemistry, Vol. 29, Issue 31 https://doi.org/10.1021/bi00483a001	journal	August 1990
Chemical aspects of peptide bond isomerisation Fischer, Gunter Chemical Society Reviews, Vol. 29, Issue 2 https://doi.org/10.1039/a803742f	journal	January 2000
The amino acid dipeptide: Small but still influential after 50 years Hermans, J. Proceedings of the National Academy of Sciences, Vol. 108, Issue 8 https://doi.org/10.1073/pnas.1019470108	journal	February 2011
A quantum Mechanical Investigation of the Conformational Energetics of the Alanine and Glycine Dipeptides in the Gas Phase and in Aqueous Solution Gould, Ian R.; Cornell, Wendy D.; Hillier, Ian H. Journal of the American Chemical Society, Vol. 116, Issue 20 https://doi.org/10.1021/ja00099a048	journal	October 1994
GAMESS As a Free Quantum-Mechanical Platform for Drug Research Alexeev, Yuri; Mazanetz, Michael P.; Ichihara, Osamu Current Topics in Medicinal Chemistry, Vol. 12, Issue 18 https://doi.org/10.2174/1568026611212180008	journal	January 2013
Comparison of a QM/MM force field and molecular mechanics force fields in simulations of alanine and glycine “dipeptides” (Ace-Ala-Nme and Ace-Gly-Nme) in water in relation to the problem of modeling the unfolded peptide backbone in solution Hu, Hao; Elstner, Marcus; Hermans, Jan Proteins: Structure, Function, and Bioinformatics, Vol. 50, Issue 3 https://doi.org/10.1002/prot.10279	journal	January 2003
Extending the treatment of backbone energetics in protein force fields: Limitations of gas-phase quantum mechanics in reproducing protein conformational distributions in molecular dynamics simulations Mackerell, Alexander D.; Feig, Michael; Brooks, Charles L. Journal of Computational Chemistry, Vol. 25, Issue 11 https://doi.org/10.1002/jcc.20065	journal	August 2004
General atomic and molecular electronic structure system Schmidt, Michael W.; Baldridge, Kim K.; Boatz, Jerry A. Journal of Computational Chemistry, Vol. 14, Issue 11, p. 1347-1363 https://doi.org/10.1002/jcc.540141112	journal	November 1993
Unravelling the Conformational Dynamics of the Aqueous Alanine Dipeptide with First-Principle Molecular Dynamics Gaigeot, M. -P. The Journal of Physical Chemistry B, Vol. 113, Issue 30 https://doi.org/10.1021/jp903745r	journal	July 2009
Analytic second derivatives of the energy in the fragment molecular orbital method Nakata, Hiroya; Nagata, Takeshi; Fedorov, Dmitri G. The Journal of Chemical Physics, Vol. 138, Issue 16 https://doi.org/10.1063/1.4800990	journal	April 2013
Phosphorylation Effects on cis/trans Isomerization and the Backbone Conformation of Serine−Proline Motifs: Accelerated Molecular Dynamics Analysis Hamelberg, Donald; Shen, Tongye; McCammon, J. Andrew Journal of the American Chemical Society, Vol. 127, Issue 6 https://doi.org/10.1021/ja0446707	journal	February 2005
Dictionary of protein secondary structure: Pattern recognition of hydrogen-bonded and geometrical features Kabsch, Wolfgang; Sander, Christian Biopolymers, Vol. 22, Issue 12 https://doi.org/10.1002/bip.360221211	journal	December 1983
Evolutionary Origin of a Secondary Structure: π-Helices as Cryptic but Widespread Insertional Variations of α-Helices That Enhance Protein Functionality Cooley, Richard B.; Arp, Daniel J.; Karplus, P. Andrew Journal of Molecular Biology, Vol. 404, Issue 2 https://doi.org/10.1016/j.jmb.2010.09.034	journal	November 2010
Structure validation by Cα geometry: ϕ,ψ and Cβ deviation Lovell, Simon C.; Davis, Ian W.; Arendall, W. Bryan Proteins: Structure, Function, and Bioinformatics, Vol. 50, Issue 3 https://doi.org/10.1002/prot.10286	journal	January 2003
Tests of the simple model of Lin and Brandts for the folding kinetics of ribonuclease A Schmid, Franz X.; Buonocore, Michael H.; Baldwin, Robert L. Biochemistry, Vol. 23, Issue 15 https://doi.org/10.1021/bi00310a002	journal	July 1984
Conformational transitions of thioredoxin in guanidine hydrochloride Kelley, Robert F.; Stellwagen, Earle Biochemistry, Vol. 23, Issue 22 https://doi.org/10.1021/bi00317a003	journal	October 1984
Ion Mobility Analysis of Molecular Dynamics Wyttenbach, Thomas; Pierson, Nicholas A.; Clemmer, David E. Annual Review of Physical Chemistry, Vol. 65, Issue 1 https://doi.org/10.1146/annurev-physchem-040513-103644	journal	April 2014
Ab initio SCF and MP2 calculations on four low-energy conformers of N-acetyl-N'-methylalaninamide Gould, Ian R.; Kollman, Peter A. The Journal of Physical Chemistry, Vol. 96, Issue 23 https://doi.org/10.1021/j100202a035	journal	November 1992
Situations of gamma-turns in proteins Milner-White, E. James Journal of Molecular Biology, Vol. 216, Issue 2 https://doi.org/10.1016/S0022-2836(05)80329-8	journal	November 1990
Assessment of density functionals with long-range and/or empirical dispersion corrections for conformational energy calculations of peptides Kang, Young Kee; Byun, Byung Jin Journal of Computational Chemistry, Vol. 31, Issue 16 https://doi.org/10.1002/jcc.21587	journal	June 2010
Mixedab initio QM/MM modeling using frozen orbitals and tests with alanine dipeptide and tetrapeptide Philipp, Dean M.; Friesner, Richard A. Journal of Computational Chemistry, Vol. 20, Issue 14 https://doi.org/10.1002/(SICI)1096-987X(19991115)20:14<1468::AID-JCC2>3.0.CO;2-0	journal	November 1999
Advances in electronic structure theory Gordon, Mark S.; Schmidt, Michael W. Theory and Applications of Computational Chemistry https://doi.org/10.1016/B978-044451719-7/50084-6	book	January 2005
Role of proline isomerization in folding of ribonuclease A at low temperatures Cook, K. H.; Schmid, F. X.; Baldwin, R. L. Proceedings of the National Academy of Sciences, Vol. 76, Issue 12 https://doi.org/10.1073/pnas.76.12.6157	journal	December 1979
Theoretical study of blocked glycine and alanine peptide analogs Head-Gordon, Teresa; Head-Gordon, Martin; Frisch, Michael J. Journal of the American Chemical Society, Vol. 113, Issue 16 https://doi.org/10.1021/ja00016a010	journal	July 1991
Comprehensive computational design of ordered peptide macrocycles Hosseinzadeh, Parisa; Bhardwaj, Gaurav; Mulligan, Vikram Khipple Science, Vol. 358, Issue 6369 https://doi.org/10.1126/science.aap7577	journal	December 2017
Two-Dimensional Infrared Spectroscopy of the Alanine Dipeptide in Aqueous Solution Kim, Yung Sam; Wang, Jianping; Hochstrasser, Robin M. The Journal of Physical Chemistry B, Vol. 109, Issue 15 https://doi.org/10.1021/jp044989d	journal	April 2005
Solvation Effect on the Conformations of Alanine Dipeptide: Integral Equation Approach Ishizuka, Ryosuke; Huber, Gary A.; McCammon, J. Andrew The Journal of Physical Chemistry Letters, Vol. 1, Issue 15 https://doi.org/10.1021/jz100665c	journal	July 2010
Energy gradients in combined fragment molecular orbital and polarizable continuum model (FMO/PCM) calculation Li, Hui; Fedorov, Dmitri G.; Nagata, Takeshi Journal of Computational Chemistry https://doi.org/10.1002/jcc.21363	journal	January 2009
STEREOCHEMICAL CRITERIA FOR POLYPEPTIDE AND PROTEIN CHAIN CONFORMATIONS.: VIII. Energy Maps for a Pair of Non-Planar Peptide Units Having Distortion of Bond Angle at the α-Carbon Atom* Balasubramanian, R.; Ramakrishnan, C. International Journal of Peptide and Protein Research, Vol. 4, Issue 2 https://doi.org/10.1111/j.1399-3011.1972.tb03404.x	journal	March 1972

Similar Records

Conformational Study of the Alanine Dipeptide at the MP2 and DFT Levels

Journal Article · Thu Apr 04 00:00:00 EST 2002 · Journal of Physical Chemistry A, 106(13):3213-3218 · OSTI ID:1510055

Vargas, Rubicelia; Garza, Jorge; Hay, Benjamin P; +1 more

A theoretical study of alanine dipeptide and analogs

Conference · Sun Jan 01 00:00:00 EST 1989 · International Journal of Quantum Chemistry; (USA) · OSTI ID:1510055

Head-Gordon, T; Head-Gordon, M; Brooks, C III; +2 more

Ab initio molecular orbital study of cation-{pi} binding between the alkali-metal cations and benzene

Journal Article · Thu Mar 11 00:00:00 EST 1999 · Journal of Physical Chemistry A: Molecules, Spectroscopy, Kinetics, Environment, amp General Theory · OSTI ID:1510055

Nicholas, J B; Hay, B P; Dixon, D A

Related Subjects

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CHEMISTRY

Title: A systematic study of minima in alanine dipeptide

Citation Formats

References (66)

Similar Records

Related Subjects