skip to main content
DOE PAGES title logo U.S. Department of Energy
Office of Scientific and Technical Information

Title: A spin-1 representation for dual-funnel energy landscapes

Abstract

The interconversion between the left- and right-handed helical folds of a polypeptide defines a dual-funneled free energy landscape. In this context, the funnel minima are connected through a continuum of unfolded conformations, evocative of the classical helix-coil transition. Physical intuition and recent conjectures suggest that this landscape can be mapped by assigning a left- or right-handed helical state to each residue. In this study, we explore this possibility using all-atom replica exchange molecular dynamics and an Ising-like model, demonstrating that the energy landscape architecture is at odds with a two-state picture. A three-state model—left, right, and unstructured—can account for most key intermediates during chiral interconversion. Additionally, competing folds and excited conformational states still impose limitations on the scope of this approach. However, the improvement is stark: Moving from a two-state to a three-state model decreases the fit error from 1.6 k BT to 0.3 k BT along the left-to-right interconversion pathway.

Authors:
 [1]; ORCiD logo [2]; ORCiD logo [3]
  1. National Inst. of Standards and Technology (NIST), Gaithersburg, MD (United States); Univ. of Maryland, College Park, MD (United States)
  2. Los Alamos National Lab. (LANL), Los Alamos, NM (United States)
  3. National Inst. of Standards and Technology (NIST), Gaithersburg, MD (United States)
Publication Date:
Research Org.:
Los Alamos National Lab. (LANL), Los Alamos, NM (United States)
Sponsoring Org.:
USDOE National Nuclear Security Administration (NNSA); USDOE Laboratory Directed Research and Development (LDRD) Program
OSTI Identifier:
1471315
Report Number(s):
LA-UR-18-28756
Journal ID: ISSN 0021-9606
Grant/Contract Number:  
AC52-06NA25396
Resource Type:
Accepted Manuscript
Journal Name:
Journal of Chemical Physics
Additional Journal Information:
Journal Volume: 149; Journal Issue: 3; Journal ID: ISSN 0021-9606
Publisher:
American Institute of Physics (AIP)
Country of Publication:
United States
Language:
English
Subject:
37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CHEMISTRY

Citation Formats

Elenewski, Justin E., Velizhanin, Kirill A., and Zwolak, Michael. A spin-1 representation for dual-funnel energy landscapes. United States: N. p., 2018. Web. doi:10.1063/1.5036677.
Elenewski, Justin E., Velizhanin, Kirill A., & Zwolak, Michael. A spin-1 representation for dual-funnel energy landscapes. United States. doi:10.1063/1.5036677.
Elenewski, Justin E., Velizhanin, Kirill A., and Zwolak, Michael. Fri . "A spin-1 representation for dual-funnel energy landscapes". United States. doi:10.1063/1.5036677. https://www.osti.gov/servlets/purl/1471315.
@article{osti_1471315,
title = {A spin-1 representation for dual-funnel energy landscapes},
author = {Elenewski, Justin E. and Velizhanin, Kirill A. and Zwolak, Michael},
abstractNote = {The interconversion between the left- and right-handed helical folds of a polypeptide defines a dual-funneled free energy landscape. In this context, the funnel minima are connected through a continuum of unfolded conformations, evocative of the classical helix-coil transition. Physical intuition and recent conjectures suggest that this landscape can be mapped by assigning a left- or right-handed helical state to each residue. In this study, we explore this possibility using all-atom replica exchange molecular dynamics and an Ising-like model, demonstrating that the energy landscape architecture is at odds with a two-state picture. A three-state model—left, right, and unstructured—can account for most key intermediates during chiral interconversion. Additionally, competing folds and excited conformational states still impose limitations on the scope of this approach. However, the improvement is stark: Moving from a two-state to a three-state model decreases the fit error from 1.6 kBT to 0.3 kBT along the left-to-right interconversion pathway.},
doi = {10.1063/1.5036677},
journal = {Journal of Chemical Physics},
number = 3,
volume = 149,
place = {United States},
year = {2018},
month = {7}
}

Journal Article:
Free Publicly Available Full Text
Publisher's Version of Record

Save / Share:

Works referenced in this record:

Principal component analysis on a torus: Theory and application to protein dynamics
journal, December 2017

  • Sittel, Florian; Filk, Thomas; Stock, Gerhard
  • The Journal of Chemical Physics, Vol. 147, Issue 24
  • DOI: 10.1063/1.4998259

The dynamics of structural transitions in sodium chloride clusters
journal, December 1999

  • Doye, Jonathan P. K.; Wales, David J.
  • The Journal of Chemical Physics, Vol. 111, Issue 24
  • DOI: 10.1063/1.480465

Phase changes in 38-atom Lennard-Jones clusters. II. A parallel tempering study of equilibrium and dynamic properties in the molecular dynamics and microcanonical ensembles
journal, June 2000

  • Calvo, F.; Neirotti, J. P.; Freeman, David L.
  • The Journal of Chemical Physics, Vol. 112, Issue 23
  • DOI: 10.1063/1.481672

Energy Transport in Peptide Helices: A Comparison between High- and Low-Energy Excitations
journal, July 2008

  • Backus, Ellen H. G.; Nguyen, Phuong H.; Botan, Virgiliu
  • The Journal of Physical Chemistry B, Vol. 112, Issue 30
  • DOI: 10.1021/jp711046e

Phase behavior of the 38-atom Lennard-Jones cluster
journal, March 2014

  • Sehgal, Ray M.; Maroudas, Dimitrios; Ford, David M.
  • The Journal of Chemical Physics, Vol. 140, Issue 10
  • DOI: 10.1063/1.4866810

The crystal structure of a 3 10 helical decapeptide containing α-aminoisobutyric acid
journal, May 1983


Phase changes in 38-atom Lennard-Jones clusters. I. A parallel tempering study in the canonical ensemble
journal, June 2000

  • Neirotti, J. P.; Calvo, F.; Freeman, David L.
  • The Journal of Chemical Physics, Vol. 112, Issue 23
  • DOI: 10.1063/1.481671

Conformation-specific spectroscopy of capped, gas-phase Aib oligomers: tests of the Aib residue as a 3 10 -helix former
journal, January 2016

  • Gord, Joseph R.; Hewett, Daniel M.; Hernandez-Castillo, Alicia O.
  • Physical Chemistry Chemical Physics, Vol. 18, Issue 36
  • DOI: 10.1039/c6cp04909e

Peptidic foldamers: ramping up diversity
journal, January 2012

  • Martinek, Tamás A.; Fülöp, Ferenc
  • Chem. Soc. Rev., Vol. 41, Issue 2
  • DOI: 10.1039/c1cs15097a

Nonequilibrium molecular dynamics simulation of the energy transport through a peptide helix
journal, January 2010

  • Nguyen, Phuong H.; Park, Sang-Min; Stock, Gerhard
  • The Journal of Chemical Physics, Vol. 132, Issue 2
  • DOI: 10.1063/1.3284742

Vibrational circular dichroism of polypeptides, V. A study of 310-helical-octapeptides
journal, January 1986

  • Yasui, Sritana C.; Keiderling, Timothy A.; Bonora, Gian Maria
  • Biopolymers, Vol. 25, Issue 1
  • DOI: 10.1002/bip.360250107

Conformational study of an Aib-rich peptide in DMSO by NMR
journal, February 2001


Evolved Minimal Frustration in Multifunctional Biomolecules
journal, May 2018

  • Röder, Konstantin; Wales, David J.
  • The Journal of Physical Chemistry B, Vol. 122, Issue 49
  • DOI: 10.1021/acs.jpcb.8b03632

Infrared signatures of the peptide dynamical transition: A molecular dynamics simulation study
journal, July 2010

  • Kobus, Maja; Nguyen, Phuong H.; Stock, Gerhard
  • The Journal of Chemical Physics, Vol. 133, Issue 3
  • DOI: 10.1063/1.3462961

Solvent effects on the energy landscapes and folding kinetics of polyalanine
journal, February 2001

  • Levy, Y.; Jortner, J.; Becker, O. M.
  • Proceedings of the National Academy of Sciences, Vol. 98, Issue 5
  • DOI: 10.1073/pnas.041611998

Hidden complexity of free energy surfaces for peptide (protein) folding
journal, October 2004

  • Krivov, S. V.; Karplus, M.
  • Proceedings of the National Academy of Sciences, Vol. 101, Issue 41
  • DOI: 10.1073/pnas.0406234101

Coordinate-dependent diffusion in protein folding
journal, December 2009

  • Best, R. B.; Hummer, G.
  • Proceedings of the National Academy of Sciences, Vol. 107, Issue 3
  • DOI: 10.1073/pnas.0910390107

Long polypeptide 310-helices at atomic resolution
journal, April 1986

  • Bavoso, A.; Benedetti, E.; Di Blasio, B.
  • Proceedings of the National Academy of Sciences, Vol. 83, Issue 7
  • DOI: 10.1073/pnas.83.7.1988

Coherent vibrational energy transfer along a peptide helix
journal, March 2011

  • Kobus, Maja; Nguyen, Phuong H.; Stock, Gerhard
  • The Journal of Chemical Physics, Vol. 134, Issue 12
  • DOI: 10.1063/1.3574395

Metal-Coordination-Assisted Folding and Guest Binding in Helical Aromatic Oligoamide Molecular Capsules
journal, May 2017

  • Horeau, Maxime; Lautrette, Guillaume; Wicher, Barbara
  • Angewandte Chemie International Edition, Vol. 56, Issue 24
  • DOI: 10.1002/anie.201701693

Transition states and folding dynamics of proteins and heteropolymers
journal, June 1994

  • Chan, Hue Sun; Dill, Ken A.
  • The Journal of Chemical Physics, Vol. 100, Issue 12
  • DOI: 10.1063/1.466677

Improved Treatment of the Protein Backbone in Empirical Force Fields
journal, January 2004

  • MacKerell, Alexander D.; Feig, Michael; Brooks, Charles L.
  • Journal of the American Chemical Society, Vol. 126, Issue 3
  • DOI: 10.1021/ja036959e

Folding Simulations of the A and B Domains of Protein G
journal, January 2012

  • Kouza, Maksim; Hansmann, Ulrich H. E.
  • The Journal of Physical Chemistry B, Vol. 116, Issue 23
  • DOI: 10.1021/jp210497h

Transition networks for modeling the kinetics of conformational change in macromolecules
journal, April 2008


Discrete path sampling
journal, October 2002


Force Field Bias in Protein Folding Simulations
journal, May 2009


Conformations and free energy landscapes of polyproline peptides
journal, November 2009

  • Moradi, M.; Babin, V.; Roland, C.
  • Proceedings of the National Academy of Sciences, Vol. 106, Issue 49
  • DOI: 10.1073/pnas.0906500106

Generalized-Ensemble Algorithms for the Isobaric–Isothermal Ensemble
journal, July 2010

  • Mori, Yoshiharu; Okamoto, Yuko
  • Journal of the Physical Society of Japan, Vol. 79, Issue 7
  • DOI: 10.1143/jpsj.79.074003

Onset of 3 10 -Helical Secondary Structure in Aib Oligopeptides Probed by Coherent 2D IR Spectroscopy
journal, May 2008

  • Maekawa, Hiroaki; Formaggio, Fernando; Toniolo, Claudio
  • Journal of the American Chemical Society, Vol. 130, Issue 20
  • DOI: 10.1021/ja8007165

Length-Dependent Formation of Transmembrane Pores by 3 10 -Helical α-Aminoisobutyric Acid Foldamers
journal, January 2016

  • Jones, Jennifer E.; Diemer, Vincent; Adam, Catherine
  • Journal of the American Chemical Society, Vol. 138, Issue 2
  • DOI: 10.1021/jacs.5b12057

Probing helical transitions in a DNA duplex
journal, January 2017

  • Chakraborty, Debayan; Wales, David J.
  • Physical Chemistry Chemical Physics, Vol. 19, Issue 1
  • DOI: 10.1039/c6cp06309h

Optimization of the Additive CHARMM All-Atom Protein Force Field Targeting Improved Sampling of the Backbone ϕ, ψ and Side-Chain χ 1 and χ 2 Dihedral Angles
journal, August 2012

  • Best, Robert B.; Zhu, Xiao; Shim, Jihyun
  • Journal of Chemical Theory and Computation, Vol. 8, Issue 9
  • DOI: 10.1021/ct300400x

Free-energy landscapes from adaptively biased methods: Application to quantum systems
journal, October 2010


Dynamic foldamer chemistry
journal, January 2016

  • Le Bailly, Bryden A. F.; Clayden, Jonathan
  • Chemical Communications, Vol. 52, Issue 27
  • DOI: 10.1039/c6cc00788k

On the Theory of Helix—Coil Transition in Polypeptides
journal, June 1961

  • Lifson, Shneior; Roig, A.
  • The Journal of Chemical Physics, Vol. 34, Issue 6
  • DOI: 10.1063/1.1731802

Intermediates and barrier crossing in a random energy model (with applications to protein folding)
journal, September 1989

  • Bryngelson, Joseph D.; Wolynes, Peter G.
  • The Journal of Physical Chemistry, Vol. 93, Issue 19
  • DOI: 10.1021/j100356a007

Folding study of an Aib-rich peptide in DMSO by molecular dynamics simulations
journal, February 2001


Polymorphic transitions in single crystals: A new molecular dynamics method
journal, December 1981

  • Parrinello, M.; Rahman, A.
  • Journal of Applied Physics, Vol. 52, Issue 12
  • DOI: 10.1063/1.328693

PACKMOL: A package for building initial configurations for molecular dynamics simulations
journal, October 2009

  • Martínez, L.; Andrade, R.; Birgin, E. G.
  • Journal of Computational Chemistry, Vol. 30, Issue 13
  • DOI: 10.1002/jcc.21224

Unraveling Solvent-Driven Equilibria between α- and 3 10 -Helices through an Integrated Spin Labeling and Computational Approach
journal, September 2007

  • Carlotto, Silvia; Cimino, Paola; Zerbetto, Mirco
  • Journal of the American Chemical Society, Vol. 129, Issue 36
  • DOI: 10.1021/ja073516s

Left-Handed Helical Preference in an Achiral Peptide Chain Is Induced by an l -Amino Acid in an N-Terminal Type II β-Turn
journal, January 2013

  • De Poli, Matteo; De Zotti, Marta; Raftery, James
  • The Journal of Organic Chemistry, Vol. 78, Issue 6
  • DOI: 10.1021/jo302705k

Chain length, temperature and solvent effects on the structural properties of α-aminoisobutyric acid homooligopeptides
journal, January 2016

  • Grubišić, Sonja; Chandramouli, Balasubramanian; Barone, Vincenzo
  • Physical Chemistry Chemical Physics, Vol. 18, Issue 30
  • DOI: 10.1039/c6cp01120a

Three complete turns of a 3 10 -helix at atomic resolution: the crystal structure of Z-(Aib) 11 -O t Bu : CRYSTAL STRUCTURE OF Z-(Aib)
journal, November 2003

  • Gessmann, Renate; Brückner, Hans; Petratos, Kyriacos
  • Journal of Peptide Science, Vol. 9, Issue 11-12
  • DOI: 10.1002/psc.490

Conformational photoswitching of a synthetic peptide foldamer bound within a phospholipid bilayer
journal, March 2016

  • De Poli, Matteo; Zawodny, Wojciech; Quinonero, Ophélie
  • Science, Vol. 352, Issue 6285
  • DOI: 10.1126/science.aad8352

Foldamers as versatile frameworks for the design and evolution of function
journal, April 2007

  • Goodman, Catherine M.; Choi, Sungwook; Shandler, Scott
  • Nature Chemical Biology, Vol. 3, Issue 5
  • DOI: 10.1038/nchembio876

Discriminating the Helical Forms of Peptides by NMR and Molecular Dynamics Simulation
journal, August 2004

  • Freedberg, Darón I.; Venable, Richard M.; Rossi, Angelo
  • Journal of the American Chemical Society, Vol. 126, Issue 33
  • DOI: 10.1021/ja0484146

Perspective: Insight into reaction coordinates and dynamics from the potential energy landscape
journal, April 2015

  • Wales, D. J.
  • The Journal of Chemical Physics, Vol. 142, Issue 13
  • DOI: 10.1063/1.4916307

Low-Temperature Structural Transitions: Circumventing the Broken-Ergodicity Problem
journal, March 2007


Conformational Switching of a Foldamer in a Multicomponent System by pH-Filtered Selection between Competing Noncovalent Interactions
journal, May 2015

  • Brioche, Julien; Pike, Sarah J.; Tshepelevitsh, Sofja
  • Journal of the American Chemical Society, Vol. 137, Issue 20
  • DOI: 10.1021/jacs.5b03284

A Foldamer-Based Chiroptical Molecular Switch That Displays Complete Inversion of the Helical Sense upon Anion Binding
journal, September 2011

  • Suk, Jae-min; Naidu, Veluru Ramesh; Liu, Xinfang
  • Journal of the American Chemical Society, Vol. 133, Issue 35
  • DOI: 10.1021/ja206546b

Archetypal energy landscapes
journal, August 1998

  • Wales, David J.; Miller, Mark A.; Walsh, Tiffany R.
  • Nature, Vol. 394, Issue 6695
  • DOI: 10.1038/29487

A Smoothed Backbone-Dependent Rotamer Library for Proteins Derived from Adaptive Kernel Density Estimates and Regressions
journal, June 2011


310 Helix Versus .alpha.-Helix: A Molecular Dynamics Study of Conformational Preferences of Aib and Alanine
journal, December 1994

  • Zhang, Li; Hermans, Jan
  • Journal of the American Chemical Society, Vol. 116, Issue 26
  • DOI: 10.1021/ja00105a034

Energy landscapes and the collapse dynamics of homopolymers
journal, August 1993

  • Chan, Hue Sun; Dill, Ken A.
  • The Journal of Chemical Physics, Vol. 99, Issue 3
  • DOI: 10.1063/1.465277

A Nonradial Coarse-Grained Potential for Proteins Produces Naturally Stable Secondary Structure Elements
journal, December 2009

  • Alemani, Davide; Collu, Francesca; Cascella, Michele
  • Journal of Chemical Theory and Computation, Vol. 6, Issue 1
  • DOI: 10.1021/ct900457z

A Field Guide to Foldamers
journal, December 2001

  • Hill, David J.; Mio, Matthew J.; Prince, Ryan B.
  • Chemical Reviews, Vol. 101, Issue 12
  • DOI: 10.1021/cr990120t

Conformational Free Energy Surfaces of Ala 10 and Aib 10 Peptide Helices in Solution
journal, March 2001

  • Mahadevan, Janaki; Lee, Kyung-Hoon; Kuczera, Krzysztof
  • The Journal of Physical Chemistry B, Vol. 105, Issue 9
  • DOI: 10.1021/jp002474q

Fast Parallel Algorithms for Short-Range Molecular Dynamics
journal, March 1995


Rapid estimation of elastic constants by molecular dynamics simulation under constant stress
journal, April 2004


Free energy landscape from path-sampling: application to the structural transition in LJ38
journal, September 2006


Spin glasses and the statistical mechanics of protein folding.
journal, November 1987

  • Bryngelson, J. D.; Wolynes, P. G.
  • Proceedings of the National Academy of Sciences, Vol. 84, Issue 21
  • DOI: 10.1073/pnas.84.21.7524

Symmetrisation schemes for global optimisation of atomic clusters
journal, January 2013

  • Oakley, Mark T.; Johnston, Roy L.; Wales, David J.
  • Physical Chemistry Chemical Physics, Vol. 15, Issue 11
  • DOI: 10.1039/c3cp44332a

Hierarchical Biomolecular Dynamics: Picosecond Hydrogen Bonding Regulates Microsecond Conformational Transitions
journal, February 2015

  • Buchenberg, Sebastian; Schaudinnus, Norbert
  • Journal of Chemical Theory and Computation, Vol. 11, Issue 3
  • DOI: 10.1021/ct501156t

Theory of the Phase Transition between Helix and Random Coil in Polypeptide Chains
journal, August 1959

  • Zimm, B. H.; Bragg, J. K.
  • The Journal of Chemical Physics, Vol. 31, Issue 2
  • DOI: 10.1063/1.1730390

Design of Folded Peptides
journal, October 2001

  • Venkatraman, Janani; Shankaramma, Sasalu C.; Balaram, Padmanabhan
  • Chemical Reviews, Vol. 101, Issue 10
  • DOI: 10.1021/cr000053z

Structural Transitions and Melting in LJ 74 - 78 Lennard-Jones Clusters from Adaptive Exchange Monte Carlo Simulations
journal, April 2006

  • Mandelshtam, Vladimir A.; Frantsuzov, Pavel A.; Calvo, Florent
  • The Journal of Physical Chemistry A, Vol. 110, Issue 16
  • DOI: 10.1021/jp055839l

Simulating structural transitions by direct transition current sampling: The example of LJ 38
journal, July 2011

  • Picciani, Massimiliano; Athènes, Manuel; Kurchan, Jorge
  • The Journal of Chemical Physics, Vol. 135, Issue 3
  • DOI: 10.1063/1.3609972

Ligand-modulated conformational switching in a fully synthetic membrane-bound receptor
journal, March 2017

  • Lister, Francis G. A.; Le Bailly, Bryden A. F.; Webb, Simon J.
  • Nature Chemistry, Vol. 9, Issue 5
  • DOI: 10.1038/nchem.2736

Thermoresponsive Helical Poly(phenylacetylene)s
journal, May 2014

  • Li, Shu; Liu, Kun; Kuang, Guichao
  • Macromolecules, Vol. 47, Issue 10
  • DOI: 10.1021/ma5003529

Energy Landscape and Pathways for Transitions between Watson–Crick and Hoogsteen Base Pairing in DNA
journal, December 2017


An improved AMBER force field for α,α-dialkylated peptides: intrinsic and solvent-induced conformational preferences of model systems
journal, January 2013

  • Grubišić, Sonja; Brancato, Giuseppe; Barone, Vincenzo
  • Physical Chemistry Chemical Physics, Vol. 15, Issue 40
  • DOI: 10.1039/c3cp52721b

Flows in Complex Networks: Theory, Algorithms, and Application to Lennard–Jones Cluster Rearrangement
journal, May 2014


Vibrational circular dichroism of polypeptides. 9. A study of chain length dependence for 310-helix formation in solution
journal, August 1986

  • Yasui, S. C.; Keiderling, T. A.; Formaggio, F.
  • Journal of the American Chemical Society, Vol. 108, Issue 16
  • DOI: 10.1021/ja00276a046

Energy transport in peptide helices
journal, July 2007

  • Botan, V.; Backus, E. H. G.; Pfister, R.
  • Proceedings of the National Academy of Sciences, Vol. 104, Issue 31
  • DOI: 10.1073/pnas.0701762104

One-Dimensional Free-Energy Profiles of Complex Systems:  Progress Variables that Preserve the Barriers
journal, June 2006

  • Krivov, Sergei V.; Karplus, Martin
  • The Journal of Physical Chemistry B, Vol. 110, Issue 25
  • DOI: 10.1021/jp060039b

α- and 3 10 -Helix Interconversion:  A Quantum-Chemical Study on Polyalanine Systems in the Gas Phase and in Aqueous Solvent
journal, June 2001

  • Topol, Igor A.; Burt, Stanley K.; Deretey, Eugen
  • Journal of the American Chemical Society, Vol. 123, Issue 25
  • DOI: 10.1021/ja0038934

Vibrational Energy Transport in Peptide Helices after Excitation of C−D Modes in Leu- d 10
journal, October 2009

  • Schade, Marco; Moretto, Alessandro; Crisma, Marco
  • The Journal of Physical Chemistry B, Vol. 113, Issue 40
  • DOI: 10.1021/jp906363a

Protein folding funnels: a kinetic approach to the sequence-structure relationship.
journal, September 1992

  • Leopold, P. E.; Montal, M.; Onuchic, J. N.
  • Proceedings of the National Academy of Sciences, Vol. 89, Issue 18
  • DOI: 10.1073/pnas.89.18.8721

Coupled linear and rotary motion in supramolecular helix handedness inversion
journal, January 2011

  • Chakrabarti, Dwaipayan; Wales, David J.
  • Soft Matter, Vol. 7, Issue 6
  • DOI: 10.1039/c0sm01507e

A Survey of Left-handed Helices in Protein Structures
journal, March 2005


Some further applications of discrete path sampling to cluster isomerization
journal, May 2004


Thermoresponsive On−Off Switching of Chiroptical Property Induced in Poly(4‘-ethynylbenzo-15-crown-5)/α-Amino Acid System
journal, June 2006

  • Sakai, Ryosuke; Otsuka, Issei; Satoh, Toshifumi
  • Macromolecules, Vol. 39, Issue 12
  • DOI: 10.1021/ma060376i

A left-handed building block self-assembles into right- and left-handed helices
journal, January 2013

  • Olesen, Scott W.; Fejer, Szilard N.; Chakrabarti, Dwaipayan
  • RSC Advances, Vol. 3, Issue 31
  • DOI: 10.1039/c3ra41813h

Three Force Fields' Views of the 310 Helix
journal, October 2011


Sensitivity of polypeptide conformation to geometry. Theoretical conformational analysis of oligomers of .alpha.-aminoisobutyric acid
journal, June 1981

  • Paterson, Yvonne; Rumsey, Shirley M.; Benedetti, Ettore
  • Journal of the American Chemical Society, Vol. 103, Issue 11
  • DOI: 10.1021/ja00401a007

Using collective variables to drive molecular dynamics simulations
journal, December 2013


Conformational Transitions between Enantiomeric 310-Helices
journal, November 1987

  • Hummel, Rolf-Peter; Toniolo, Claudio; Jung, Günther
  • Angewandte Chemie International Edition in English, Vol. 26, Issue 11
  • DOI: 10.1002/anie.198711501

Structural Flexibility of a Helical Peptide Regulates Vibrational Energy Transport Properties
journal, December 2008

  • Backus, Ellen H. G.; Nguyen, Phuong H.; Botan, Virgiliu
  • The Journal of Physical Chemistry B, Vol. 112, Issue 48
  • DOI: 10.1021/jp806403p

Dynamical Transition in a Small Helical Peptide and Its Implication for Vibrational Energy Transport
journal, October 2009

  • Backus, Ellen H. G.; Bloem, Robbert; Pfister, Rolf
  • The Journal of Physical Chemistry B, Vol. 113, Issue 40
  • DOI: 10.1021/jp904905d

Constant pressure molecular dynamics algorithms
journal, September 1994

  • Martyna, Glenn J.; Tobias, Douglas J.; Klein, Michael L.
  • The Journal of Chemical Physics, Vol. 101, Issue 5
  • DOI: 10.1063/1.467468

Potential Energy and Free Energy Landscapes
journal, October 2006

  • Wales, David J.; Bogdan, Tetyana V.
  • The Journal of Physical Chemistry B, Vol. 110, Issue 42
  • DOI: 10.1021/jp0680544

The double-funnel energy landscape of the 38-atom Lennard-Jones cluster
journal, April 1999

  • Doye, Jonathan P. K.; Miller, Mark A.; Wales, David J.
  • The Journal of Chemical Physics, Vol. 110, Issue 14
  • DOI: 10.1063/1.478595

Transforming the Energy Landscape of a Coiled-Coil Peptide via Point Mutations
journal, February 2017

  • Röder, Konstantin; Wales, David J.
  • Journal of Chemical Theory and Computation, Vol. 13, Issue 3
  • DOI: 10.1021/acs.jctc.7b00024