VARIATION OF FOLDED POLYPEPTIDE SURFACE-AREA WITH PROBE SIZE

被引:11
作者
ISLAM, SA
WEAVER, DL
机构
[1] TUFTS UNIV,DEPT PHYS,ROBINSON HALL,COLL AVE,MEDFORD,MA 02155
[2] IMPERIAL CANC RES FUND,BIOMOLEC MODELLING LAB,LONDON WC2A 3PX,ENGLAND
来源
PROTEINS-STRUCTURE FUNCTION AND GENETICS | 1991年 / 10卷 / 04期
关键词
ACCESSIBLE AREA; CONTACT AREA; MOLECULAR SURFACE; FRACTAL DIMENSION; HELICES; GLOBINS; VARIABLE PROBE RADIUS; ANALYTICAL SURFACE MODELS;
D O I
10.1002/prot.340100404
中图分类号
Q5 [生物化学]; Q7 [分子生物学];
学科分类号
071010 ; 081704 ;
摘要
Three types of polypeptide surface area (contact, accessible, and molecular) have been studied as a function of the radius of a probe sphere used to map the surface. The surfaces are: (1) three alpha-helices, the H-helix of myoglobin, the E-helix of leghemoglobin, and an artificial polyalanine helix, each with 26 residues; (2) two globins, myoglobin and leghemoglobin, each with 153 residues; and (3) a two-center model system for which the three types of surface area have been calculated analytically. The two globin helices have almost identical surface areas as a function of probe size as do the two globins. The polyalanine helix surface area is smaller but similar in shape to the globin helix areas. All three helix contact areas tend to the same limit as the probe size increases, and the globin contact areas behave similarly. Fractal dimensions were calculated for the helix and globin contact and molecular surfaces. All fractal dimensions showed strong dependence on probe size. The contact fractal dimension peaks at larger values for both the helices and globins. Most residues do not make contrast with large probes (15-angstrom).
引用
收藏
页码:300 / 314
页数:15
相关论文
共 31 条
[1]   DIFFUSION OF MOLECULES ON BIOLOGICAL-MEMBRANES OF NONPLANAR FORM - A THEORETICAL-STUDY [J].
AIZENBUD, BM ;
GERSHON, ND .
BIOPHYSICAL JOURNAL, 1982, 38 (03) :287-293
[2]   SURFACE FRACTALITY AS A GUIDE FOR STUDYING PROTEIN - PROTEIN INTERACTIONS [J].
AQVIST, J ;
TAPIA, O .
JOURNAL OF MOLECULAR GRAPHICS, 1987, 5 (01) :30-&
[3]   REFINEMENT OF BOND ANGLES OF AN ALPHA-HELIX [J].
ARNOTT, S ;
DOVER, SD .
JOURNAL OF MOLECULAR BIOLOGY, 1967, 30 (01) :209-&
[4]  
ARUTYUNYAN EG, 1980, SOV PHYS-CRYSTALLOGR, V25, P43
[5]  
Barnsley MF., 2014, FRACTALS EVERYWHERE
[6]   INTRINSIC AND EXTRINSIC FACTORS IN PROTEIN ANTIGENIC STRUCTURE [J].
BERZOFSKY, JA .
SCIENCE, 1985, 229 (4717) :932-940
[7]   HARMONIC DYNAMICS OF PROTEINS - NORMAL-MODES AND FLUCTUATIONS IN BOVINE PANCREATIC TRYPSIN-INHIBITOR [J].
BROOKS, B ;
KARPLUS, M .
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA-BIOLOGICAL SCIENCES, 1983, 80 (21) :6571-6575
[8]   THE SURFACE-AREA OF MONOMERIC PROTEINS - SIGNIFICANCE OF POWER LAW BEHAVIOR [J].
BRYANT, SH ;
ISLAM, SA ;
WEAVER, DL .
PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS, 1989, 6 (04) :418-423
[9]  
CHOTHIA C, 1984, ANNU REV BIOCHEM, V53, P537
[10]   FRACTAL AND SPECTRAL DIMENSIONS OF BIO-POLYMER CHAINS - SOLVENT STUDIES OF ELECTRON-SPIN RELAXATION RATES IN MYOGLOBIN AZIDE [J].
COLVIN, JT ;
STAPLETON, HJ .
JOURNAL OF CHEMICAL PHYSICS, 1985, 82 (10) :4699-4706