List of works - Vikas Nanda

A knowledge-based potential highlights unique features of membrane α-helical and β-barrel protein insertion and folding

scientific article

A new method for determining the local environment and orientation of individual side chains of membrane-binding peptides

scientific article published in April 2004

A push-pull mechanism for regulating integrin function

scientific article

Anoxic photochemical oxidation of siderite generates molecular hydrogen and iron oxides

scientific article published on 03 June 2013

Are aromatic carbon donor hydrogen bonds linear in proteins?

scientific article

Aromatic interactions in homeodomains contribute to the low quantum yield of a conserved, buried tryptophan

scientific article published in July 2000

Aromatic interactions promote self-association of collagen triple-helical peptides to higher-order structures

scientific article published on August 2009

Association of a model transmembrane peptide containing gly in a heptad sequence motif

scientific article

Automated use of mutagenesis data in structure prediction

scientific article

Biophysical analysis of the structural evolution of substrate specificity in RuBisCO

scientific article published on 16 November 2020

Building bigger beta-barrels

Circular permutation directs orthogonal assembly in complex collagen peptide mixtures

scientific article published on 16 September 2013

Collagen mimetic peptide discs promote assembly of a broad range of natural protein fibers through hydrophobic interactions.

scientific article published on 5 July 2017

Comparative dynamics of tropomyosin in vertebrates and invertebrates

scientific article published on 28 August 2019

Compositional control of higher order assembly using synthetic collagen peptides

scientific article

Computational De Novo Design and Characterization of a Four-Helix Bundle Protein that Selectively Binds a Nonbiological Cofactor [J.Am. Chem. Soc.2005,127, 1346−1347]

article

Computational Design of Intermolecular Stability and Specificity in Protein Self-assembly

article by Vikas Nanda et al published 2011 in Methods in Enzymology

Computational Design of Thermostabilizing d -Amino Acid Substitutions

scientific article

Computational de novo design and characterization of a four-helix bundle protein that selectively binds a nonbiological cofactor

scientific article

Computational design of a collagen A:B:C-type heterotrimer

scientific article published on 14 September 2011

Computational design of heterochiral peptides against a helical target

scientific article

Computational design of metalloproteins

scientific article published on January 2014

Computational redesign of the lipid-facing surface of the outer membrane protein OmpA.

scientific article

De novo design of a non-natural fold for an iron-sulfur protein: alpha-helical coiled-coil with a four-iron four-sulfur cluster binding site in its central core

scientific article

De novo design of a redox-active minimal rubredoxin mimic

scientific article

De novo design of symmetric ferredoxins that shuttle electrons in vivo

scientific article published on 01 July 2019

De novo self-assembling collagen heterotrimers using explicit positive and negative design

scientific article

Design of a Fe4 S4 Cluster into the Core of a De Novo 4-Helix Bundle

scientific article published on 08 August 2020

Design of net-charged abc-type collagen heterotrimers

scientific article published on 18 April 2013

Design principles for chlorophyll-binding sites in helical proteins

scientific article published on 01 February 2011

Designing artificial enzymes by intuition and computation ⬇️

scientific article published on December 17, 2009

Designing phenylalanine-based hybrid biological materials: controlling morphology via molecular composition

scientific article published on 22 March 2018

Dimerization of the transmembrane domain of Integrin alphaIIb subunit in cell membranes

scientific article

Do-it-yourself enzymes

May 2008 scholarly article in Nature Chemical Biology

Empirical and computational design of iron-sulfur cluster proteins

scientific article published on 8 February 2012

Empirical lipid propensities of amino acid residues in multispan alpha helical membrane proteins

scientific article published in May 2005

Energetic selection of topology in ferredoxins

scientific article

Erratum: Structural basis for the function and inhibition of an influenza virus proton channel

scientific article published in Nature

Evaluating pH-induced gastrointestinal aggregation of Arachis hypogaea 1 fragments as potential components of peanut allergy

scientific article published on 23 August 2013

Ez, a Depth-dependent Potential for Assessing the Energies of Insertion of Amino Acid Side-chains into Membranes: Derivation and Applications to Determining the Orientation of Transmembrane and Interfacial Helices

article

Function-based assessment of structural similarity measurements using metal co-factor orientation

scientific article published on 22 November 2013

Hetero-assembly of a dual β-amyloid variant peptide system

scholarly article by Jason Candreva et al published 2018 in Chemical Communications

Hydrodynamic Radius Coincides with the Slip Plane Position in the Electrokinetic Behavior of Lysozyme.

scientific article published on 31 January 2018

Hydrophobic Clustering in Acid-Denatured IL-2 and Fluorescence of a Trp NH···π H-bond

scientific article published in 2000

In Vivo Biogenesis of a De Novo Designed Iron-Sulfur Protein

scientific article published on 13 November 2020

Lysosomal protein thermal stability does not correlate with cellular half-life: global observations and a case study of tripeptidyl-peptidase 1

scientific article published on 01 February 2020

Marginal protein stability drives subcellular proteome isoelectric point

article published in the Proceedings of the National Academy of Sciences of the United States of America

Melittin as model system for probing interactions between proteins and cyclodextrins

scientific article published in May 2004

Metal Stabilization of Collagen and de Novo Designed Mimetic Peptides

scientific article published on 30 July 2015

Metal-activated histidine carbon donor hydrogen bonds contribute to metalloprotein folding and function.

scientific article

Methacrylation induces rapid, temperature-dependent, reversible self-assembly of type-I collagen

scientific article

Minimal Heterochiral de Novo Designed 4Fe–4S Binding Peptide Capable of Robust Electron Transfer

scientific article published on 29 August 2018

Mirrors in the PDB: left-handed alpha-turns guide design with D-amino acids

scientific article

Morphological diversity and polymorphism of self-assembling collagen peptides controlled by length of hydrophobic domains

scientific article

Nanosecond Dynamics of InfluenzaA/M2TM and an Amantadine Resistant Mutant Probed by Time-Dependent Red Shifts of a Native Tryptophan

scientific article

Phyla-specific Correlated Dynamics in Tropomyosin

article

Polar Networks Control Oligomeric Assembly in Membranes

article

Potential pitfalls and solutions for use of fluorescent fusion proteins to study the lysosome

scientific article

Prediction and design of outer membrane protein-protein interactions

scientific article

Protein tolerance to random circular permutation correlates with thermostability and local energetics of residue-residue contacts

scientific article published on 06 July 2020

Rotational orientation of monomers within a designed homo-oligomer transmembrane helical bundle

scientific article

Searching for the Pareto frontier in multi-objective protein design

scientific article published on 10 August 2017

Self-assembly of left- and right-handed molecular screws

scientific article published on 3 December 2013

Sequence determinants of a transmembrane proton channel: an inverse relationship between stability and function

scientific article published on 21 January 2005

Sequence recombination improves target specificity in a redesigned collagen peptide abc-type heterotrimer

scientific article published on 5 November 2012

Simulated Evolution of Emergent Chiral Structures in Polyalanine

article

Small protein folds at the root of an ancient metabolic network

scientific article published on 18 March 2020

Structural and Dynamic Properties of Allergen and Non-Allergen Forms of Tropomyosin

scientific article published on 07 June 2018

Structural basis for the function and inhibition of an influenza virus proton channel

scientific article

Synergistic Interactions between Aqueous and Membrane Domains of a Designed Protein Determine its Fold and Stability

article

Temperature Dependent Reversible Self Assembly of Methacrylated Collagen Gels

The conformation of the pore region of the M2 proton channel depends on lipid bilayer environment

scientific article published on March 2005

The effects of protein crowding in bacterial photosynthetic membranes on the flow of quinone redox species between the photochemical reaction center and the ubiquinol-cytochrome c2 oxidoreductase

scientific article published on 20 June 2011

The orphan GPCR, Gpr161, regulates the retinoic acid and canonical Wnt pathways during neurulation

scientific article

The role of protein homochirality in shaping the energy landscape of folding

scientific article

Using D-Amino Acids to Delineate the Mechanism of Protein Folding: Application to Trp-cage

scientific article published on August 2013

Using alpha-helical coiled-coils to design nanostructured metalloporphyrin arrays

scientific article published on 19 August 2008

Zeta Potential Prediction from Protein Structure in General Aqueous Electrolyte Solutions

scientific article published on 13 November 2020

List of works by Vikas Nanda

A knowledge-based potential highlights unique features of membrane α-helical and β-barrel protein insertion and folding

A new method for determining the local environment and orientation of individual side chains of membrane-binding peptides

A push-pull mechanism for regulating integrin function

Anoxic photochemical oxidation of siderite generates molecular hydrogen and iron oxides

Are aromatic carbon donor hydrogen bonds linear in proteins?

Aromatic interactions in homeodomains contribute to the low quantum yield of a conserved, buried tryptophan

Aromatic interactions promote self-association of collagen triple-helical peptides to higher-order structures

Association of a model transmembrane peptide containing gly in a heptad sequence motif

Automated use of mutagenesis data in structure prediction

Biophysical analysis of the structural evolution of substrate specificity in RuBisCO

Building bigger beta-barrels

Circular permutation directs orthogonal assembly in complex collagen peptide mixtures

Collagen mimetic peptide discs promote assembly of a broad range of natural protein fibers through hydrophobic interactions.

Comparative dynamics of tropomyosin in vertebrates and invertebrates

Compositional control of higher order assembly using synthetic collagen peptides

Computational De Novo Design and Characterization of a Four-Helix Bundle Protein that Selectively Binds a Nonbiological Cofactor [J.Am. Chem. Soc.2005,127, 1346−1347]

Computational Design of Intermolecular Stability and Specificity in Protein Self-assembly

Computational Design of Thermostabilizing d -Amino Acid Substitutions

Computational de novo design and characterization of a four-helix bundle protein that selectively binds a nonbiological cofactor

Computational design of a collagen A:B:C-type heterotrimer

Computational design of heterochiral peptides against a helical target

Computational design of metalloproteins

Computational redesign of the lipid-facing surface of the outer membrane protein OmpA.

De novo design of a non-natural fold for an iron-sulfur protein: alpha-helical coiled-coil with a four-iron four-sulfur cluster binding site in its central core

De novo design of a redox-active minimal rubredoxin mimic

De novo design of symmetric ferredoxins that shuttle electrons in vivo

De novo self-assembling collagen heterotrimers using explicit positive and negative design

Design of a Fe4 S4 Cluster into the Core of a De Novo 4-Helix Bundle

Design of net-charged abc-type collagen heterotrimers

Design principles for chlorophyll-binding sites in helical proteins

Designing artificial enzymes by intuition and computation ⬇️

Designing phenylalanine-based hybrid biological materials: controlling morphology via molecular composition

Dimerization of the transmembrane domain of Integrin alphaIIb subunit in cell membranes

Do-it-yourself enzymes

Empirical and computational design of iron-sulfur cluster proteins

Empirical lipid propensities of amino acid residues in multispan alpha helical membrane proteins

Energetic selection of topology in ferredoxins

Erratum: Structural basis for the function and inhibition of an influenza virus proton channel

Evaluating pH-induced gastrointestinal aggregation of Arachis hypogaea 1 fragments as potential components of peanut allergy

Ez, a Depth-dependent Potential for Assessing the Energies of Insertion of Amino Acid Side-chains into Membranes: Derivation and Applications to Determining the Orientation of Transmembrane and Interfacial Helices

Function-based assessment of structural similarity measurements using metal co-factor orientation

Hetero-assembly of a dual β-amyloid variant peptide system

Hydrodynamic Radius Coincides with the Slip Plane Position in the Electrokinetic Behavior of Lysozyme.

Hydrophobic Clustering in Acid-Denatured IL-2 and Fluorescence of a Trp NH···π H-bond

In Vivo Biogenesis of a De Novo Designed Iron-Sulfur Protein

Lysosomal protein thermal stability does not correlate with cellular half-life: global observations and a case study of tripeptidyl-peptidase 1

Marginal protein stability drives subcellular proteome isoelectric point

Melittin as model system for probing interactions between proteins and cyclodextrins

Metal Stabilization of Collagen and de Novo Designed Mimetic Peptides

Metal-activated histidine carbon donor hydrogen bonds contribute to metalloprotein folding and function.

Methacrylation induces rapid, temperature-dependent, reversible self-assembly of type-I collagen

Minimal Heterochiral de Novo Designed 4Fe–4S Binding Peptide Capable of Robust Electron Transfer

Mirrors in the PDB: left-handed alpha-turns guide design with D-amino acids

Morphological diversity and polymorphism of self-assembling collagen peptides controlled by length of hydrophobic domains

Nanosecond Dynamics of InfluenzaA/M2TM and an Amantadine Resistant Mutant Probed by Time-Dependent Red Shifts of a Native Tryptophan

Phyla-specific Correlated Dynamics in Tropomyosin

Polar Networks Control Oligomeric Assembly in Membranes

Potential pitfalls and solutions for use of fluorescent fusion proteins to study the lysosome

Prediction and design of outer membrane protein-protein interactions

Protein tolerance to random circular permutation correlates with thermostability and local energetics of residue-residue contacts

Rotational orientation of monomers within a designed homo-oligomer transmembrane helical bundle

Searching for the Pareto frontier in multi-objective protein design

Self-assembly of left- and right-handed molecular screws

Sequence determinants of a transmembrane proton channel: an inverse relationship between stability and function

Sequence recombination improves target specificity in a redesigned collagen peptide abc-type heterotrimer

Simulated Evolution of Emergent Chiral Structures in Polyalanine

Small protein folds at the root of an ancient metabolic network

Structural and Dynamic Properties of Allergen and Non-Allergen Forms of Tropomyosin

Structural basis for the function and inhibition of an influenza virus proton channel

Synergistic Interactions between Aqueous and Membrane Domains of a Designed Protein Determine its Fold and Stability

Temperature Dependent Reversible Self Assembly of Methacrylated Collagen Gels

The conformation of the pore region of the M2 proton channel depends on lipid bilayer environment

The effects of protein crowding in bacterial photosynthetic membranes on the flow of quinone redox species between the photochemical reaction center and the ubiquinol-cytochrome c2 oxidoreductase

The orphan GPCR, Gpr161, regulates the retinoic acid and canonical Wnt pathways during neurulation

The role of protein homochirality in shaping the energy landscape of folding

Using D-Amino Acids to Delineate the Mechanism of Protein Folding: Application to Trp-cage

Using alpha-helical coiled-coils to design nanostructured metalloporphyrin arrays

Zeta Potential Prediction from Protein Structure in General Aqueous Electrolyte Solutions