Methods of translating NMR proton distances into their corresponding heavy atom distances for protein structure prediction with limited experimental data.

نویسندگان

  • Oscar Hur
  • Kevin Karplus
چکیده

This paper proposes a strategy to translate experimental 1H NMR proton distance restraints into their corresponding heavy atom distance restraints for the purpose of protein structure prediction. The relationships between interproton distances and the corresponding heavy atom distances are determined by studying well-resolved X-ray protein structures. The data from the interproton distances of amide protons, alpha-protons, beta-protons and side chain methyl protons are plotted against the corresponding heavy atoms in scatter plots and then fitted with linear equations for lower bounds, upper bounds and optimal fits. We also transform the scatter plots into two-dimensional heat maps and three-dimensional histograms, which identify the regions where data points concentrate. The common interproton distances between amide protons, alpha-protons, beta-protons in alpha-helices, anti-parallel beta-sheets and parallel beta-sheets are also tabulated. We have found several patterns emerging from the distance relationships between heavy atom pairs and their corresponding proton pairs. All our upper bound, lower bound and optimal fit results for translating the interproton distance into their corresponding heavy atom distances are tabulated.

برای دانلود رایگان متن کامل این مقاله و بیش از 32 میلیون مقاله دیگر ابتدا ثبت نام کنید

ثبت نام

اگر عضو سایت هستید لطفا وارد حساب کاربری خود شوید

منابع مشابه

NMR structure determination for larger proteins using backbone-only data.

Conventional protein structure determination from nuclear magnetic resonance data relies heavily on side-chain proton-to-proton distances. The necessary side-chain resonance assignment, however, is labor intensive and prone to error. Here we show that structures can be accurately determined without nuclear magnetic resonance (NMR) information on the side chains for proteins up to 25 kilodaltons...

متن کامل

A Geometric Build-Up Algorithm for Solving the Molecular Distance Geometry Problem with Sparse Distance Data

Nuclear magnetic resonance (NMR) structure modeling usually produces a sparse set of inter-atomic distances in protein. In order to calculate the three-dimensional structure of protein, current approaches need to estimate all other “missing” distances to build a full set of distances. However, the estimation step is costly and prone to introducing errors. In this report, we describe a geometric...

متن کامل

Discrete Approaches for Solving Molecular Distance Geometry Problems Using Nmr Data

The molecular distance geometry problem (MDGP) is the problem of finding the conformation of a molecule by exploiting known distances between some pairs of its atoms. Estimates of the distances between the atoms can be obtained through experiments of nuclear magnetic resonance (NMR) spectroscopy. The information on the distances, however, is usually limited, because only distances between hydro...

متن کامل

Discrete Approaches for Solving Molecular Distance Geometry Problems Using Nmr Dta

The molecular distance geometry problem (MDGP) is the problem of finding the conformation of a molecule by exploiting known distances between some pairs of its atoms. Estimates of the distances between the atoms can be obtained through experiments of nuclear magnetic resonance (NMR) spectroscopy. The information on the distances, however, is usually limited, because only distances between hydro...

متن کامل

All-atom structure prediction and folding simulations of a stable protein.

We present results from all-atom, fully unrestrained ab initio folding simulations for a stable protein with nontrivial secondary structure elements and a hydrophobic core. The construct, "trpcage", is a 20-residue sequence optimized by the Andersen group at University of Washington and is currently the smallest protein that displays two-state folding properties. Compared over the well-defined ...

متن کامل

ذخیره در منابع من


  با ذخیره ی این منبع در منابع من، دسترسی به آن را برای استفاده های بعدی آسان تر کنید

عنوان ژورنال:
  • Protein engineering, design & selection : PEDS

دوره 18 12  شماره 

صفحات  -

تاریخ انتشار 2005