Hom's Blog

MBI workshop 2:Multiple Faces of Biomolecular Electrostatics



2015-10-12, Monday

John Zhang (NYU)

Multi-level theory for protein structure and dynamics

Fragment QM, Polarized FF for protein, AIMD for bimolecules. cut residue A-B to A-c + c-c* + c*-B EE-GMFCC ACR, 2014, 2748-2757 Polarized proteiin-specific charge (PPC), derived from QM calculated ESP, fixed atomic charges for a given protein configuration. Improvement in MD simulation on H-bond. Nature Struc Mol Biol. 2009 684-690. Environment dependent hydrogen bond energy

OH..O 5kacal NH..O 2 kcal.

JCP 2011, 12230-12233

Dynamic polarized protein-specific charge. (动力学中一定间隔重新计算PPC)

动态PPC可以优化出H键驱动二级结构结构. JACS, 2010, 11159-1116

AIMD(ab initial MD).

Nathan baker (Pacific Northwest National Laboratory)

Quantifying the influence of conformational uncertainty in biomolecular solvation

构象不确定性. Gnp非极性 = Gcav + Gvdw,s - Gvdw,v (v是真空)

Dongping Zhong (OSU)

Watching water motions at biological interfaces

Water motion (bio physics), femosclae

Huan-Xiang Zhou(FSU)

Electrostatic Interactions in Protein Structure, Folding, Binding, and Assembly

ES interaction in protein structure,folding and so on. vdw surface better than molecular surface. TransComp Web Server 预测蛋白-蛋白结合常数 link

Julie Mitchell (UW-Madison)

What Data-Driven Models of Biophysics Tell Us About Protein Electrostatics

KFC methond link What Data-Driven Models of Biophysics Tell Us About Protein Electrostatics sensitivity, scpecificity,precision,accuracy,strength, mcc, toc

features; shape complementary.

Sharon Hammes-Schiffer (UIUC, web)

Probing Electrostatics and Conformational Motions in Enzyme Catalysis
Group focus on studying proton-coupled electron transfer reactions in enzyme(especially NADH enzyme LADH,NADPH enzyme DHFR). many great work on computational chemistry, focus on QM.


Teresa Head-Gordon (UC Berkeley, website)

Atomistic and coarse-grained models and methods for electrostatics

Polarized. AMOEBA.(极化原子力场) ForceBalance (->iAMOEBA, inexpensive AMOEBA). Mutal Polarization(可能pka相关).

Maria Sushko (Pacific Northwest National Lab.)

Ionic atmosphere around DNA: role of ion correlatios and solvation

ion atmosphrer to DNA.

Zhen-Gang Wang (CIT)

self energy of a ion interacted with itself.

Xueyu Song (Iowa State)

Beyond Poisson-Boltzmann approach in macromolecules electrostatics

pair atom, introduce maxwell equation to ion distribution and influence.

Weihua Geng (SMU)

A treecode-accelerated boundary integral Poisson-Botlzmann solver: modeling, algorithm and application.

singular triangel and complex multiange. MPI and GPU accelerate


Tyler Luchko (California State)

Partial Molar Volume Corrected Solvation Energies, Entropies and Free Energies from 3D-RISM


Alexey Onufriev (virginia tech)

condenseation of RNA/DNA by multi-valent counter-ions (由于反离子的中和,可以帮助DNA压缩)

monovalent ions: too little attraction, for same entropy need more ions
trivalent ions can condese short dsDNA in solution, but can’t work for dsRNA.

NAR, 2014 10823-10831 (MD, 500ns) ion bind to the groove of RNA but only around DNA to create a atmosphrer

elestristatic potential revel that RNA narrow groove have stronger negative charge inside. Furthermore, DNA have aternating charge pattern at outside, but RNA has nearly uniformly charged duplex(ion binding to groove and eliminate the alternating charge), no chance to lower energy further by bringing them closer.

When MD, Na+ distribution is sensitive to water model; but multi-valent ion is insensitive to water model.

condensation propensity of double stranded nucleic acid depends on the distribution of multivalent

G_aggregation= G_attr+G_el-rep-TS_conf

Stephen White (UC Irvine, website)

Electrostatics inside the SecY translocon protein that guides membrane protein assembly
Group focus on study of membrane protein

translocation is water driven in SecYEG complex to open channel (hydrophobic gate) and transfer the protein into membrane. ref

Yingkai Zhang (NYU, web)

Role of Water and Ions in Enzyme Catalysis: from Mechanistic Insights to Modulator Design


HDAC ENZYME, K+ 离子在结合口袋附近时影响了Zn+中心离子的电荷从而干扰了其活性和性质. JACS,2010,9471-9479; ACS Chem. Biol. 2015. 687-692

JCIM 20115, 1585.link Protein-protein fctm(fragment-centric topographical mapping)

Chia-en (Angelina) Chang (UC Riversite, web)

Modeling of enhanced catalysis in multienzyme nanostructures: effect of molecular scaffolds, spatial organization, and concentration

bioengineered spatial organization (将酶组织在板上空间一致)


John Herbert (OSU, web)

What can quantum-inspired electrostatics methods contribute to biomolecular applications?

PCM (polarizable continuum models). QM/PCM and QM/MM/PCM for MD. Molecular Fragmentation. Many-body expansion (MBE). XPol.

Irina Moreira (web)

Structural/energetic analysis of protein-based interactions: highlighting the electrostatics contribution

Hot spot, warm spot, null spot.

JCIM, 2015,1077

TPR=TP/TP+FN, FPR=FP/FP+TN, Specificity= TN/FP+TN, Precision=TP/TP+FP, F1=2TP/2TP+FP+FN

Marharyta Petukh

BION webserver: electrostatics based prediction of surface bound ions

TODO: check 电势线.

Lin Li

Electrostatic interactions play important roles in kinesin proceeding on microtubule.

Protein, 2015, pKa prediction for proteins RNAs, DNAs with the Gaussian Dielectric function using delphipka.


Patrice Koehl [UC Davis]

Biomolecular electrostatics beyond Poisson-Boltzmann

self-consistent mean-field sampling (J Mol Biol. 1994)

Using PB to calculate probabilistic of sidechain.

Donald Jacobs [University of North Carolina, Charlotte]

Free Energy Driven Geometrical Simulation of Protein Dynamics

Distance Constraint Model (DCM)

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Source 类别: Life  标签: Life